chore: bump version to 0.11.3

.gitattributes

@@ -1,7 +1,3 @@
 * text=auto eol=lf
 
-.github/workflows/*.lock.yml linguist-generated=true merge=ours -whitespace
-# The project constitution is the one dogfooding artifact carried forward.
-# Keep it exempt from git's whitespace checks (git diff --check / CI) since its
-# generated formatting is not hand-edited.
-.specify/memory/constitution.md -whitespace
+.github/workflows/*.lock.yml linguist-generated=true merge=ours -whitespace

.github/ISSUE_TEMPLATE/agent_request.yml

@@ -8,7 +8,7 @@ body:
       value: |
         Thanks for requesting a new agent! Before submitting, please check if the agent is already supported.
         
-        **Currently supported agents**: Amp, Antigravity, Auggie CLI, Claude Code, Cline, CodeBuddy, Codex CLI, Cursor, Devin for Terminal, Firebender, Forge, Gemini CLI, GitHub Copilot, Goose, Hermes Agent, IBM Bob, iFlow CLI, Junie, Kilo Code, Kimi Code, Kiro CLI, Lingma, Mistral Vibe, opencode, Pi Coding Agent, Qoder CLI, Qwen Code, Roo Code, RovoDev ACLI, SHAI, Tabnine CLI, Trae, Windsurf, ZCode, Zed
+        **Currently supported agents**: Claude Code, Gemini CLI, GitHub Copilot, Cursor, Qwen Code, opencode, Codex CLI, Windsurf, Kilo Code, Auggie CLI, Roo Code, CodeBuddy, Qoder CLI, Kiro CLI, Amp, SHAI, Tabnine CLI, Antigravity, IBM Bob, Mistral Vibe, Kimi Code, Trae, Pi Coding Agent, iFlow CLI, Devin for Terminal
 
   - type: input
     id: agent-name

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -62,41 +62,24 @@ body:
       label: AI Agent
       description: Which AI agent are you using?
       options:
-        - Amp
-        - Antigravity
-        - Auggie CLI
         - Claude Code
-        - Cline
-        - CodeBuddy
-        - Codex CLI
-        - Cursor
-        - Devin for Terminal
-        - Firebender
-        - Forge
         - Gemini CLI
         - GitHub Copilot
-        - Goose
-        - Hermes Agent
-        - IBM Bob
-        - iFlow CLI
-        - Junie
-        - Kilo Code
-        - Kimi Code
-        - Kiro CLI
-        - Lingma
-        - Mistral Vibe
-        - opencode
-        - Pi Coding Agent
-        - Qoder CLI
+        - Cursor
         - Qwen Code
-        - Roo Code
-        - RovoDev ACLI
-        - SHAI
-        - Tabnine CLI
-        - Trae
+        - opencode
+        - Codex CLI
         - Windsurf
-        - ZCode
-        - Zed
+        - Kilo Code
+        - Auggie CLI
+        - Roo Code
+        - CodeBuddy
+        - Qoder CLI
+        - Kiro CLI
+        - Amp
+        - SHAI
+        - IBM Bob
+        - Antigravity
         - Not applicable
     validations:
       required: true

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -56,41 +56,24 @@ body:
       description: Does this feature relate to a specific AI agent?
       options:
         - All agents
-        - Amp
-        - Antigravity
-        - Auggie CLI
         - Claude Code
-        - Cline
-        - CodeBuddy
-        - Codex CLI
-        - Cursor
-        - Devin for Terminal
-        - Firebender
-        - Forge
         - Gemini CLI
         - GitHub Copilot
-        - Goose
-        - Hermes Agent
-        - IBM Bob
-        - iFlow CLI
-        - Junie
-        - Kilo Code
-        - Kimi Code
-        - Kiro CLI
-        - Lingma
-        - Mistral Vibe
-        - opencode
-        - Pi Coding Agent
-        - Qoder CLI
+        - Cursor
         - Qwen Code
-        - Roo Code
-        - RovoDev ACLI
-        - SHAI
-        - Tabnine CLI
-        - Trae
+        - opencode
+        - Codex CLI
         - Windsurf
-        - ZCode
-        - Zed
+        - Kilo Code
+        - Auggie CLI
+        - Roo Code
+        - CodeBuddy
+        - Qoder CLI
+        - Kiro CLI
+        - Amp
+        - SHAI
+        - IBM Bob
+        - Antigravity
         - Not applicable
 
   - type: textarea

.github/workflows/publish-pypi.yml

@@ -1,80 +0,0 @@
-name: Publish to PyPI
-
-on:
-  workflow_dispatch:
-    inputs:
-      tag:
-        description: 'Release tag to publish (e.g., v0.10.1)'
-        required: true
-        type: string
-
-permissions:
-  contents: read
-
-jobs:
-  build:
-    runs-on: ubuntu-latest
-    permissions:
-      contents: read
-      actions: write
-    steps:
-      - name: Verify tag format
-        run: |
-          TAG="${{ inputs.tag }}"
-          if [[ ! "$TAG" =~ ^v[0-9]+\.[0-9]+\.[0-9]+$ ]]; then
-            echo "Error: '$TAG' is not a valid release tag (expected vX.Y.Z)"
-            exit 1
-          fi
-
-      - name: Checkout release tag
-        uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
-        with:
-          ref: refs/tags/${{ inputs.tag }}
-
-      - name: Install uv
-        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
-
-      - name: Set up Python
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
-        with:
-          python-version: "3.13"
-
-      - name: Verify tag matches package version
-        run: |
-          TAG_VERSION="${{ inputs.tag }}"
-          TAG_VERSION="${TAG_VERSION#v}"
-          PROJECT_VERSION="$(python -c 'import tomllib; print(tomllib.load(open("pyproject.toml","rb"))["project"]["version"])')"
-          if [[ "$TAG_VERSION" != "$PROJECT_VERSION" ]]; then
-            echo "Error: Tag version ($TAG_VERSION) does not match pyproject.toml version ($PROJECT_VERSION)"
-            exit 1
-          fi
-
-      - name: Build package
-        run: uv build
-
-      - name: Upload build artifacts
-        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
-        with:
-          name: dist
-          path: dist/
-          if-no-files-found: error
-
-  publish:
-    needs: build
-    runs-on: ubuntu-latest
-    environment: pypi
-    permissions:
-      id-token: write
-      actions: read
-    steps:
-      - name: Download build artifacts
-        uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1
-        with:
-          name: dist
-          path: dist/
-
-      - name: Install uv
-        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
-
-      - name: Publish to PyPI
-        run: uv publish

.gitignore

@@ -10,8 +10,8 @@ dist/
 downloads/
 eggs/
 .eggs/
-/lib/
-/lib64/
+lib/
+lib64/
 parts/
 sdist/
 var/

.specify/memory/constitution.md

@@ -1,214 +0,0 @@
-<!--
-SYNC IMPACT REPORT
-==================
-Version change: (template/unratified) → 1.0.0
-Bump rationale: Initial ratification of a concrete constitution for the brownfield
-  Spec Kit / specify-cli codebase, derived from an exhaustive multi-pass analysis of
-  the source tree, test suite, CI pipelines, and project conventions (AGENTS.md,
-  CONTRIBUTING.md, DEVELOPMENT.md). MAJOR baseline because it establishes binding
-  governance where none previously existed.
-
-Principles defined:
-  I.   Code Quality & Architectural Discipline
-  II.  Test-Backed Change (NON-NEGOTIABLE)
-  III. CLI & User-Experience Consistency
-  IV.  Offline-First Performance & Resource Discipline
-  V.   Minimal Dependencies & Safe, Idempotent File Operations
-
-Added sections:
-  - Security & Cross-Platform Constraints
-  - Development Workflow & Quality Gates
-  - Governance
-
-Templates reviewed for alignment:
-  ✅ .specify/templates/plan-template.md — generic "Constitution Check" gate (line 39)
-       remains valid; gates are now concretely populated by Principles I–V at plan time.
-  ✅ .specify/templates/spec-template.md — no constitution-specific tokens; no change needed.
-  ✅ .specify/templates/tasks-template.md — task categories (setup/foundational/story/polish)
-       already accommodate testing + performance + UX tasks mandated here; no change needed.
-  ✅ .github/agents/speckit.*.agent.md — command guidance is agent-agnostic; no change needed.
-
-Follow-up TODOs: none. RATIFICATION_DATE set to first adoption date below.
--->
-
-# Spec Kit Constitution
-
-Spec Kit (the `specify-cli` package and its bundled assets) is a local, offline-capable
-developer CLI that bootstraps and operates Spec-Driven Development workflows for AI coding
-agents. These principles are derived from the patterns the codebase already enforces. They
-are binding on all changes — including the `specify bundle` subcommand and any future
-command group, integration, extension, preset, or workflow.
-
-## Core Principles
-
-### I. Code Quality & Architectural Discipline
-
-The codebase follows a strict, registry-driven, layered architecture, and all changes MUST
-preserve it.
-
-- **Separate the CLI surface from importable logic.** User-facing commands live in Typer
-  sub-apps (e.g. `commands/`, `*/_commands.py`); business logic lives in plain, importable
-  modules with no `@app.command()` decorators. New features MUST keep orchestration logic
-  testable independently of Typer.
-- **Use the established extension pattern.** New agents/integrations MUST subclass one of the
-  standard base classes (`MarkdownIntegration`, `TomlIntegration`, `YamlIntegration`,
-  `SkillsIntegration`) and declare the required class attributes (`key`, `config`,
-  `registrar_config`, and `context_file` where applicable). Extending `IntegrationBase`
-  directly is permitted only when no base class fits, and the deviation MUST be justified.
-- **Honor the single source of truth.** Built-ins are wired through the relevant registry
-  (e.g. `INTEGRATION_REGISTRY` via `_register_builtins()`), with imports and registrations
-  kept in alphabetical order. Duplicate keys MUST fail loudly rather than silently override.
-- **Naming and typing are not optional.** Private modules/functions are `_`-prefixed and MUST
-  NOT be imported across package boundaries. Every new module begins with
-  `from __future__ import annotations` and uses modern type syntax (`dict[str, Any]`,
-  `str | None`); legacy `Dict`/`List`/`Optional` forms are rejected.
-- **Package directories use underscores; keys keep their canonical (often hyphenated) form**
-  (e.g. package `kiro_cli/`, `key = "kiro-cli"`). For CLI-backed integrations the `key` MUST
-  match the executable name so `shutil.which(key)` resolves.
-
-**Rationale:** A registry-plus-base-class architecture is what lets dozens of integrations,
-extensions, and workflows coexist with minimal coupling. Drift here multiplies maintenance
-cost and breaks the "add one subclass, register once, ship a test" contract.
-
-### II. Test-Backed Change (NON-NEGOTIABLE)
-
-Every behavioral change MUST be accompanied by automated tests, and the suite is a hard gate.
-
-- **Tests gate merges.** CI runs `pytest` across a matrix of ubuntu + windows × Python 3.11,
-  3.12, and 3.13. Changes MUST pass on every cell of that matrix.
-- **Parity invariants MUST hold.** Every integration MUST be present in the registry, have a
-  `CommandRegistrar` config entry where required, and ship a dedicated
-  `tests/integrations/test_integration_<key>.py` (hyphens in the key become underscores in the
-  filename). These are enforced by parametrized tests (e.g. `test_registry.py`) and MUST NOT
-  be weakened.
-- **Follow pytest conventions.** Test modules/classes/functions use the `test_*` / `Test*`
-  naming the project configures, run under `--strict-markers`, and isolate state with
-  `tmp_path`, `monkeypatch`, and the autouse auth-isolation fixture. Platform-specific tests
-  MUST be guarded (e.g. `@requires_bash`) rather than left to fail.
-- **Security and idempotency tests are mandatory categories.** Path-traversal rejection,
-  manifest hash integrity/symlink safety, and no-overwrite idempotency are covered by existing
-  suites; changes touching file writes, path handling, or setup scripts MUST extend (never
-  reduce) that coverage.
-- **Network is mocked.** No test may make a real outbound network call; HTTP MUST be stubbed
-  so the suite is deterministic and offline-runnable.
-
-**Rationale:** The breadth of supported agents and the offline/air-gapped guarantees can only
-be sustained by exhaustive, parametrized tests. The parity and security suites are what stop a
-single new integration from regressing the whole matrix.
-
-### III. CLI & User-Experience Consistency
-
-The CLI presents one coherent surface; every command group MUST feel like the others.
-
-- **Reuse the shared verb vocabulary.** Consumer-facing groups use the established verbs —
-  `list`, `add`/`install`, `remove`, `search`, `info`, `update`, plus `enable`/`disable` and
-  `set-priority` where relevant. New verbs MUST NOT be invented when an existing one fits, and
-  any genuinely new verb MUST be justified.
-- **Mirror the catalog-stack model.** Catalog-backed groups MUST expose
-  `<group> catalog list|add|remove`, back it with a priority-ordered source stack (lower number
-  = higher precedence) plus per-source install policy (`install-allowed` vs `discovery-only`),
-  and fall back to a built-in default stack when no project config is present.
-- **Register sub-apps the standard way.** Command groups are `typer.Typer(...)` instances
-  attached via `app.add_typer(child, name="...")`, preferably through a modular
-  `register(app)` function imported in `__init__.py`. Nesting MUST stay within ~2–3 levels.
-- **Output is consistent and machine-friendly.** Human output uses the shared Rich
-  conventions (e.g. `[green]✓[/green]` success, `[red]Error:[/red]` + non-zero exit on
-  failure, actionable remediation in messages). Where a `--json` flag is offered, valid JSON
-  goes to stdout and all other logging is redirected to stderr.
-- **Interactions are safe and idempotent.** Destructive actions show what will change before
-  confirming; "already installed / already present" outcomes succeed (exit 0) rather than
-  error. User-facing command groups MUST be documented under `docs/reference/`.
-
-**Rationale:** Predictability is the product. Users learn one set of verbs, one catalog model,
-and one output grammar, then apply them to every group — including `specify bundle`.
-
-### IV. Offline-First Performance & Resource Discipline
-
-Spec Kit is a local CLI; responsiveness, offline operability, and graceful degradation are the
-performance contract.
-
-- **`specify init` and core scaffolding MUST work fully offline** using bundled `core_pack`
-  assets. Asset resolution MUST prefer bundled assets, then a source checkout, before ever
-  reaching the network.
-- **Network use is lazy, bounded, and degradable.** Network calls happen only on explicit
-  user commands, MUST set timeouts, MUST cache catalog results (1-hour TTL) and fall back to
-  stale cache on failure, and MUST surface offline/rate-limit conditions as clear messages
-  without crashing.
-- **Keep startup cheap.** Avoid adding heavyweight work to import time. New optional
-  subsystems SHOULD prefer lazy loading over unconditional eager imports so that unrelated
-  commands (including `--help`) stay fast.
-- **Filesystem writes are minimal and idempotent.** Installs MUST track files (SHA-256
-  manifests), avoid clobbering user-modified content, only uninstall files whose hash still
-  matches, and never follow symlinks out of the project root.
-
-**Rationale:** Developers run this tool in air-gapped, enterprise, and flaky-network
-environments. Offline-first behavior and idempotent, hash-tracked file operations are what
-make it safe and fast to run repeatedly.
-
-### V. Minimal Dependencies & Safe, Idempotent File Operations
-
-The project guards its dependency surface and its on-disk footprint deliberately.
-
-- **Zero new runtime dependencies by default.** The runtime dependency set is intentionally
-  small and pinned to a minimum major version. Adding a dependency requires maintainer
-  agreement and a justification that existing deps (typer, click, rich, pyyaml, packaging,
-  platformdirs, pathspec, json5, readchar) cannot serve the need. New subsystems SHOULD reuse
-  existing primitive machinery in-process rather than re-implementing or re-shipping it.
-- **All paths are validated.** Any project-relative path derived from user/manifest/catalog
-  input MUST be confined to the project root (`Path.relative_to` checks) and reject traversal
-  payloads; symlink escapes MUST be refused.
-- **Errors are explicit and chained.** Validate inputs up front, raise with actionable context
-  (offending field/value plus a hint), and use `raise ... from exc` to preserve causes. I/O
-  that can legitimately fail MUST degrade gracefully rather than emit a raw traceback.
-- **Versioning follows SemVer.** User-visible and packaged behavior changes follow
-  MAJOR.MINOR.PATCH semantics; backward-incompatible changes MUST be called out and justified.
-
-**Rationale:** A lean, pinned dependency set and hardened, idempotent file handling are what
-keep the tool trustworthy in enterprise and air-gapped contexts and cheap to maintain.
-
-## Security & Cross-Platform Constraints
-
-- **Cross-platform parity is required.** Code MUST run on Linux, macOS, and Windows and on
-  Python 3.11–3.13. Windows specifics (UTF-8 stream reconfiguration, bash-dependent tests
-  auto-skipping) MUST be respected; do not introduce POSIX-only assumptions without a guarded
-  fallback.
-- **Security tooling is a gate.** CodeQL and the project's security test suites
-  (path-traversal, manifest/symlink hardening) MUST remain green. Network access MUST default
-  to off in tests and be opt-in, timeout-bounded, and credential-isolated at runtime.
-- **Formatting is enforced.** `.editorconfig` rules (LF endings, final newline, no trailing
-  whitespace, 4-space Python / 2-space YAML-JSON-Markdown), `ruff check src/`, and
-  `markdownlint-cli2` MUST pass.
-
-## Development Workflow & Quality Gates
-
-- **Branch naming** follows `<type>/<number>-<short-slug>` (or `<type>/<short-slug>` with no
-  issue), with `<type>` ∈ {feat, fix, docs, community, chore}.
-- **PRs are focused** and MUST: pass `ruff`, `pytest` (full matrix), markdown lint, and CodeQL;
-  add/extend tests for new behavior; update user-facing docs (`README.md`, `docs/`,
-  `spec-driven.md`) when behavior changes; and disclose any AI assistance used.
-- **Slash-command-affecting changes** MUST be manually exercised through a coding agent and the
-  results reported in the PR, per CONTRIBUTING.md.
-- **Large or cross-cutting changes** (new templates, arguments, command groups) MUST be agreed
-  with maintainers before implementation.
-
-## Governance
-
-This constitution supersedes ad-hoc convention where they conflict; the existing codebase
-patterns it codifies remain authoritative references.
-
-- **Authority.** Principles I–V are binding gates. The `## Constitution Check` section of the
-  plan template MUST be evaluated against these principles, and `/speckit.analyze` treats
-  conflicts with a MUST as CRITICAL. Violations are resolved by changing the spec, plan, or
-  tasks — not by diluting a principle.
-- **Amendments.** Changes to this document require a PR with rationale, maintainer approval,
-  and a version bump per the policy below. Any amendment MUST propagate to dependent templates
-  and command guidance in the same change, recorded in the Sync Impact Report at the top of
-  this file.
-- **Versioning policy (SemVer for governance).** MAJOR = backward-incompatible governance or
-  principle removal/redefinition; MINOR = a new principle/section or materially expanded
-  guidance; PATCH = clarifications and non-semantic refinements.
-- **Compliance review.** Every PR and review MUST verify compliance with these principles.
-  Added complexity or any deviation MUST be justified in-PR (and, for plans, in the plan's
-  Complexity Tracking section). Unjustified violations block merge.
-
-**Version**: 1.0.0 | **Ratified**: 2026-06-19 | **Last Amended**: 2026-06-19

AGENTS.md

@@ -14,7 +14,7 @@ The toolkit supports multiple AI coding assistants, allowing teams to use their
 
 Each AI agent is a self-contained **integration subpackage** under `src/specify_cli/integrations/<key>/`. The subpackage exposes a single class that declares all metadata and inherits setup/teardown logic from a base class. Built-in integrations are then instantiated and added to the global `INTEGRATION_REGISTRY` by `src/specify_cli/integrations/__init__.py` via `_register_builtins()`.
 
-```text
+```
 src/specify_cli/integrations/
 ├── __init__.py            # INTEGRATION_REGISTRY + _register_builtins()
 ├── base.py                # IntegrationBase, MarkdownIntegration, TomlIntegration, YamlIntegration, SkillsIntegration
@@ -340,21 +340,18 @@ Some agents require custom processing beyond the standard template transformatio
 ### Copilot Integration
 
 GitHub Copilot has unique requirements:
-
 - Commands use `.agent.md` extension (not `.md`)
 - Each command gets a companion `.prompt.md` file in `.github/prompts/`
 - Installs `.vscode/settings.json` with prompt file recommendations
 - Context file lives at `.github/copilot-instructions.md`
 
 Implementation: Extends `IntegrationBase` with custom `setup()` method that:
-
 1. Processes templates with `process_template()`
 2. Generates companion `.prompt.md` files
 3. Merges VS Code settings
 
 **Skills mode (`--skills`):** Copilot also supports an alternative skills-based layout
 via `--integration-options="--skills"`. When enabled:
-
 - Commands are scaffolded as `speckit-<name>/SKILL.md` under `.github/skills/`
 - No companion `.prompt.md` files are generated
 - No `.vscode/settings.json` merge
@@ -374,13 +371,11 @@ specify init my-project --integration copilot --integration-options="--skills"
 ### Forge Integration
 
 Forge has special frontmatter and argument requirements:
-
 - Uses `{{parameters}}` instead of `$ARGUMENTS`
 - Strips `handoffs` frontmatter key (Forge-specific collaboration feature)
 - Injects `name` field into frontmatter when missing
 
 Implementation: Extends `MarkdownIntegration` with custom `setup()` method that:
-
 1. Inherits standard template processing from `MarkdownIntegration`
 2. Adds extra `$ARGUMENTS` → `{{parameters}}` replacement after template processing
 3. Applies Forge-specific transformations via `_apply_forge_transformations()`
@@ -390,13 +385,11 @@ Implementation: Extends `MarkdownIntegration` with custom `setup()` method that:
 ### Goose Integration
 
 Goose is a YAML-format agent using Block's recipe system:
-
 - Uses `.goose/recipes/` directory for YAML recipe files
 - Uses `{{args}}` argument placeholder
 - Produces YAML with `prompt: |` block scalar for command content
 
 Implementation: Extends `YamlIntegration` (parallel to `TomlIntegration`):
-
 1. Processes templates through the standard placeholder pipeline
 2. Extracts title and description from frontmatter
 3. Renders output as Goose recipe YAML (version, title, description, author, extensions, activities, prompt)
@@ -407,7 +400,7 @@ Implementation: Extends `YamlIntegration` (parallel to `TomlIntegration`):
 
 Branches follow one of two patterns depending on whether an issue exists:
 
-```text
+```
 <type>/<number>-<short-slug>   # when an issue is created first
 <type>/<short-slug>            # when no issue exists (PR-only changes)
 ```
@@ -470,7 +463,6 @@ Disclosure is **continuous**, not a one-time event. A single AI-disclosure parag
 3. **Incorrect `requires_cli` value**: Set to `True` only for agents that have a CLI tool; set to `False` for IDE-based agents.
 4. **Wrong argument format**: Use `$ARGUMENTS` for Markdown agents, `{{args}}` for TOML agents.
 5. **Skipping registration**: The import and `_register()` call in `_register_builtins()` must both be added.
-6. **Running tests against the wrong environment**: Always run the suite inside this working tree's own virtualenv (`uv sync --extra test` then `.venv/bin/python -m pytest`, or activate the venv first). A bare `uv run pytest` can resolve to an ambient/global interpreter whose editable `.pth` points at a *different* worktree. The failure is sneaky: test collection still imports `specify_cli` successfully, but newly-added subpackages (e.g. a fresh `specify_cli/bundler/`) resolve as a stale namespace package and raise `ModuleNotFoundError`. If a brand-new subpackage imports under `python -c` but not under pytest, suspect environment contamination, not your code.
 
 ---
 

CHANGELOG.md

@@ -2,51 +2,6 @@
 
 <!-- insert new changelog below this comment -->
 
-## [0.11.6] - 2026-06-23
-
-### Changed
-
-- [extension] Update Spec Kit Preview extension to v1.1.0 and sync Firebender agent lists (#3116)
-- Add Spec Kit Discovery Extension to community catalog (#3119)
-- Update Architecture Workflow extension to v1.2.1 (#3118)
-- docs: clarify project-defined constitution articles (#2994)
-- Add Intake extension to community catalog (#3117)
-- feat: add Firebender integration (Android Studio / IntelliJ) (#3077)
-- Update DocGuard — CDD Enforcement extension to v0.28.0 (#3115)
-- chore: sync issue template agent lists (#3052)
-- fix(shared-infra): remove stale managed scripts the core no longer ships (#3076) (#3098)
-- chore: release 0.11.5, begin 0.11.6.dev0 development (#3105)
-
-## [0.11.5] - 2026-06-22
-
-### Changed
-
-- fix: register enabled extensions for agent on integration use/upgrade (#2949)
-- Add SicarioSpec Core preset to community catalog (#3102)
-- Update Game Narrative Writing preset to v1.1.0 (#3099)
-- feat: add PyPI publishing workflow and readme metadata (#2915)
-- refactor: move extension command handlers to extensions/_commands.py (PR-7/8) (#3014)
-- feat: add ZCode (Z.AI) integration (#3063)
-- fix(agent-context): support multiple context files safely (#2969)
-- Update DocGuard — CDD Enforcement extension to v0.27.0 (#3094)
-- fix(presets): use _repo_root() for bundled-core source-checkout fallback (#3086) (#3091)
-- chore: release 0.11.4, begin 0.11.5.dev0 development (#3092)
-
-## [0.11.4] - 2026-06-22
-
-### Changed
-
-- [extension] Add Tasks to GitHub Project extension to community catalog (#3090)
-- Update Linear Integration extension to v0.7.0 (#3089)
-- fix: fail loudly on an unknown workflow expression filter (#3074)
-- fix: anchor lib/ and lib64/ patterns to repo root in .gitignore (#3083)
-- fix(build): include specify_cli.bundler.lib in built distribution (#3085)
-- Harden command registration path handling (#3088)
-- fix(presets): preserve argument-hint in preset SKILL.md generation (#2978)
-- feat: surface gate detail in the workflow run/resume --json payload (#2965)
-- feat: add `specify bundle` command (#3070)
-- chore: release 0.11.3, begin 0.11.4.dev0 development (#3072)
-
 ## [0.11.3] - 2026-06-19
 
 ### Changed
@@ -62,6 +17,8 @@
 - Add Token Economy extension to community catalog (#3049)
 - chore: release 0.11.2, begin 0.11.3.dev0 development (#3059)
 
+- feat(scripts): add SPECIFY_INIT_DIR to target a member project from the repo root (#2892)
+
 ## [0.11.2] - 2026-06-18
 
 ### Changed

CONTRIBUTING.md

@@ -95,24 +95,6 @@ uv run python -m pytest tests/test_agent_config_consistency.py -q
 
 Run this when you change agent metadata, context update scripts, or integration wiring.
 
-#### Running the full test suite
-
-Install the test dependencies into the project's own virtual environment and run
-`pytest` through that interpreter:
-
-```bash
-uv pip install -e ".[test]"
-.venv/bin/python -m pytest tests -q   # Windows: .venv\Scripts\python -m pytest tests -q
-```
-
-> **Note:** prefer `.venv/bin/python -m pytest` over a bare `uv run pytest`.
-> If another Spec Kit checkout has an editable (`-e`) install registered in a
-> shared/global environment, `uv run pytest` can resolve `specify_cli` to that
-> *other* worktree, turning it into a partial namespace package that fails to
-> import newly added subpackages. Running through the project `.venv` resolves
-> `specify_cli` to this checkout's `src/`. This matches the gotcha documented in
-> `AGENTS.md` (Common Pitfalls).
-
 ### Manual testing
 
 #### Testing setup
@@ -167,7 +149,7 @@ the command templates in templates/commands/ to understand what each command
 invokes. Use these mapping rules:
 
 - templates/commands/X.md → the command it defines
-- scripts/bash/Y.sh or scripts/powershell/Y.ps1 → every command that invokes that script (grep templates/commands/ for the script name). Also check transitive dependencies: if the changed script is sourced by other scripts (e.g., common.sh is sourced by create-new-feature.sh, check-prerequisites.sh, setup-plan.sh), then every command invoking those downstream scripts is also affected
+- scripts/bash/Y.sh or scripts/powershell/Y.ps1 → every command that invokes that script (grep templates/commands/ for the script name). Also check transitive dependencies: if the changed script is sourced by other scripts (e.g., common.sh is sourced by create-new-feature.sh, check-prerequisites.sh, setup-plan.sh, update-agent-context.sh), then every command invoking those downstream scripts is also affected
 - templates/Z-template.md → every command that consumes that template during execution
 - src/specify_cli/*.py → CLI commands (`specify init`, `specify check`, `specify extension *`, `specify preset *`); test the affected CLI command and, for init/scaffolding changes, at minimum test /speckit.specify
 - extensions/X/commands/* → the extension command it defines

README.md

@@ -26,7 +26,6 @@
 - [🤖 Supported AI Coding Agent Integrations](#-supported-ai-coding-agent-integrations)
 - [🔧 Specify CLI Reference](#-specify-cli-reference)
 - [🧩 Making Spec Kit Your Own: Extensions & Presets](#-making-spec-kit-your-own-extensions--presets)
-- [📦 Bundles: Role-Based Setups](#-bundles-role-based-setups)
 - [📚 Core Philosophy](#-core-philosophy)
 - [🌟 Development Phases](#-development-phases)
 - [🎯 Experimental Goals](#-experimental-goals)
@@ -229,56 +228,6 @@ For example, presets could restructure spec templates to require regulatory trac
 
 See the [Presets reference](https://github.github.io/spec-kit/reference/presets.html) for the full command guide, including resolution order and priority stacking.
 
-## 📦 Bundles: Role-Based Setups
-
-Extensions and presets are individual building blocks. A **bundle** packages a
-curated set of them — extensions, presets, steps, and workflows — into a single,
-versioned, role-oriented setup so a whole team persona (product manager, business
-analyst, security researcher, developer, …) can be provisioned with one command.
-
-A bundle is described by a hand-written `bundle.yml` manifest. It pins each
-component to a version and, optionally, targets a specific integration; a bundle
-with no `integration` is **agnostic** and inherits whatever integration the
-project already uses.
-
-```bash
-# Discover bundles in the active catalog stack
-specify bundle search [<query>]
-
-# Inspect the exact component set a bundle will add (equals what install does)
-specify bundle info <bundle-id>
-
-# Install a bundle's full component set in one operation
-specify bundle install <bundle-id>
-
-# See what's installed, then update or remove non-destructively
-specify bundle list
-specify bundle update <bundle-id>     # or --all
-specify bundle remove <bundle-id>     # removes only this bundle's components
-```
-
-Bundles resolve from a **priority-ordered catalog stack** (project > user >
-built-in). Each source carries an install policy: `install-allowed` sources can
-be installed from, while `discovery-only` sources are visible in `search`/`info`
-but refuse installation. Manage the stack with `specify bundle catalog list|add|remove`.
-
-Authors validate and package bundles locally — there is no first-class publish;
-distribution is hosting the built artifact and adding a catalog entry:
-
-```bash
-specify bundle validate --path ./my-bundle      # structural + reference checks
-specify bundle build --path ./my-bundle         # produce a versioned .zip artifact
-```
-
-Four ready-to-read example manifests live under
-[`examples/bundles/`](examples/bundles/) (product manager, business analyst,
-security researcher, developer).
-
-Key guarantees: `info` shows exactly what `install` adds (transparency);
-installs are idempotent and confined to the project root; `remove` never touches
-components another installed bundle still needs; and all consume/author commands
-work **offline** against local or pinned sources.
-
 ### When to Use Which
 
 | Goal | Use |
@@ -288,7 +237,6 @@ work **offline** against local or pinned sources.
 | Integrate an external tool or service | Extension |
 | Enforce organizational or regulatory standards | Preset |
 | Ship reusable domain-specific templates | Either — presets for template overrides, extensions for templates bundled with new commands |
-| Provision a complete role-based setup in one command | Bundle |
 
 ## 📚 Core Philosophy
 
@@ -403,7 +351,7 @@ specify init . --force --integration copilot
 specify init --here --force --integration copilot
 ```
 
-The CLI will check if you have Claude Code, Gemini CLI, Cursor CLI, Qwen CLI, opencode, Codex CLI, Qoder CLI, Tabnine CLI, Kiro CLI, Pi, Forge, Goose, Mistral Vibe, or ZCode installed. If you do not, or you prefer to get the templates without checking for the right tools, use `--ignore-agent-tools` with your command:
+The CLI will check if you have Claude Code, Gemini CLI, Cursor CLI, Qwen CLI, opencode, Codex CLI, Qoder CLI, Tabnine CLI, Kiro CLI, Pi, Forge, Goose, or Mistral Vibe installed. If you do not, or you prefer to get the templates without checking for the right tools, use `--ignore-agent-tools` with your command:
 
 ```bash
 specify init <project_name> --integration copilot --ignore-agent-tools

docs/community/extensions.md

@@ -31,7 +31,7 @@ The following community-contributed extensions are available in [`catalog.commun
 | API Evolve | Managed API contract evolution — breaking-change detection, semver enforcement, deprecation orchestration, and lifecycle gates across REST, GraphQL, and gRPC | `process` | Read+Write | [spec-kit-api-evolve](https://github.com/Quratulain-bilal/spec-kit-api-evolve) |
 | Architect Impact Previewer | Predicts architectural impact, complexity, and risks of proposed changes before implementation. | `visibility` | Read-only | [spec-kit-architect-preview](https://github.com/UmmeHabiba1312/spec-kit-architect-preview) |
 | Architecture Guard | Framework-agnostic architecture review extension for validating implementation against governance and architecture constitutions, detecting architectural drift, and generating non-blocking refactor tasks | `process` | Read+Write | [spec-kit-architecture-guard](https://github.com/DyanGalih/spec-kit-architecture-guard) |
-| Architecture Workflow | Generate or reverse project-level 4+1 architecture views as separate commands | `docs` | Read+Write | [spec-kit-arch](https://github.com/bigsmartben/spec-kit-arch) |
+| Architecture Workflow | Generate or reverse project-level 4+1 architecture view artifacts and synthesis | `docs` | Read+Write | [spec-kit-arch](https://github.com/bigsmartben/spec-kit-arch) |
 | Archive Extension | Archive merged features into main project memory. | `docs` | Read+Write | [spec-kit-archive](https://github.com/stn1slv/spec-kit-archive) |
 | Azure DevOps Integration | Sync user stories and tasks to Azure DevOps work items using OAuth authentication | `integration` | Read+Write | [spec-kit-azure-devops](https://github.com/pragya247/spec-kit-azure-devops) |
 | Blueprint | Stay code-literate in AI-driven development: review a complete code blueprint for every task from spec artifacts before /speckit.implement runs | `docs` | Read+Write | [spec-kit-blueprint](https://github.com/chordpli/spec-kit-blueprint) |
@@ -57,7 +57,7 @@ The following community-contributed extensions are available in [`catalog.commun
 | GitHub Issues Integration 1 | Generate spec artifacts from GitHub Issues - import issues, sync updates, and maintain bidirectional traceability | `integration` | Read+Write | [spec-kit-github-issues](https://github.com/Fatima367/spec-kit-github-issues) |
 | GitHub Issues Integration 2 | Creates and syncs local specs from an existing GitHub issue | `integration` | Read+Write | [spec-kit-issue](https://github.com/aaronrsun/spec-kit-issue) |
 | Improve Extension | Audits any codebase as a senior advisor and writes prioritized, self-contained spec prompts under specs/ that the spec-kit lifecycle can process | `process` | Read+Write | [spec-kit-improve](https://github.com/d0whc3r/spec-kit-improve) |
-| Intake | Normalize PRD, design, and test-case evidence into SDD-ready intake artifacts | `docs` | Read+Write | [spec-kit-intake](https://github.com/bigsmartben/spec-kit-intake) |
+| Interactive HTML Preview | Generate self-contained interactive HTML prototypes from Spec Kit artifacts | `docs` | Read+Write | [spec-kit-preview](https://github.com/bigsmartben/spec-kit-preview) |
 | Intelligent Agent Orchestrator | Cross-catalog agent discovery and intelligent prompt-to-command routing | `process` | Read+Write | [spec-kit-orchestrator](https://github.com/pragya247/spec-kit-orchestrator) |
 | Iterate | Iterate on spec documents with a two-phase define-and-apply workflow — refine specs mid-implementation and go straight back to building | `docs` | Read+Write | [spec-kit-iterate](https://github.com/imviancagrace/spec-kit-iterate) |
 | Jira Integration | Create Jira Epics, Stories, and Issues from spec-kit specifications and task breakdowns with configurable hierarchy and custom field support | `integration` | Read+Write | [spec-kit-jira](https://github.com/mbachorik/spec-kit-jira) |
@@ -110,8 +110,6 @@ The following community-contributed extensions are available in [`catalog.commun
 | Spec Changelog | Auto-generate changelogs and release notes from spec git history and requirement diffs | `docs` | Read-only | [spec-kit-changelog](https://github.com/Quratulain-bilal/spec-kit-changelog) |
 | Spec Critique Extension | Dual-lens critical review of spec and plan from product strategy and engineering risk perspectives | `docs` | Read-only | [spec-kit-critique](https://github.com/arunt14/spec-kit-critique) |
 | Spec Diagram | Auto-generate Mermaid diagrams of SDD workflow state, feature progress, and task dependencies | `visibility` | Read-only | [spec-kit-diagram-](https://github.com/Quratulain-bilal/spec-kit-diagram-) |
-| Spec Kit Discovery Extension | Run technical discovery commands for feasibility, technology selection, scenario-specific technical decisions, legacy codebase assessment, implementation understanding, and proof-of-concept validation | `process` | Read+Write | [spec-kit-discovery](https://github.com/bigsmartben/spec-kit-discovery) |
-| Spec Kit Preview | Generate evidence-backed low, mid, or high fidelity previews from Spec Kit artifacts as Markdown or self-contained HTML | `docs` | Read+Write | [spec-kit-preview](https://github.com/bigsmartben/spec-kit-preview) |
 | Spec Kit Schedule | Optimal multi-agent task scheduling via CP-SAT — DAG precedence, hallucination-aware caps, file-conflict avoidance, stochastic durations, replanning, and interactive HTML output | `process` | Read+Write | [spec-kit-schedule](https://github.com/jfranc38/spec-kit-schedule) |
 | Spec Kit TLDR | Render a feature's spec.md / plan.md into a review-oriented TLDR (self-contained HTML dashboard + PR-native Markdown) that surfaces risks for faster PR review. | `visibility` | Read+Write | [speckit-tldr](https://github.com/qurore/speckit-tldr) |
 | Spec Orchestrator | Cross-feature orchestration — track state, select tasks, and detect conflicts across parallel specs | `process` | Read-only | [spec-kit-orchestrator](https://github.com/Quratulain-bilal/spec-kit-orchestrator) |
@@ -130,7 +128,6 @@ The following community-contributed extensions are available in [`catalog.commun
 | Superpowers Bridge | Bridges selected Superpowers disciplines into Spec Kit as evidence-first trust gates for agent workflows. | `process` | Read+Write | [superpowers-bridge](https://github.com/RbBtSn0w/spec-kit-extensions/tree/main/superpowers-bridge) |
 | Superpowers Implementation Bridge | Thin orchestrator between Spec Kit (design) and Superpowers (implementation). Cross-agent. | `process` | Read+Write | [speckit-superpowers-bridge](https://github.com/lihan3238/speckit-superpowers-bridge) |
 | Superspec | Bridges spec-kit with obra/superpowers (brainstorming, TDD, subagent, code-review) into a unified, resumable workflow with graceful degradation and session progress tracking | `process` | Read+Write | [superspec](https://github.com/WangX0111/superspec) |
-| Tasks to GitHub Project | Publish and synchronize Spec Kit tasks as cards on a GitHub Project (v2) kanban board, with priority and status sync between spec.md/tasks.md and the board. | `integration` | Read+Write | [spec-kit-tasks-to-project](https://github.com/mancioshell/spec-kit-tasks-to-project) |
 | Team Assign | Assign tasks.md items to human engineers, split into subtasks, and generate a per-engineer workboard | `process` | Read+Write | [spec-kit-team-assign](https://github.com/tarunkumarbhati/spec-kit-team-assign) |
 | Time Machine | Retroactively apply the full SDD workflow to existing codebases — analyse, spec, and ship feature-by-feature | `process` | Read+Write | [spec-kit-time-machine](https://github.com/teeyo/spec-kit-time-machine) |
 | TinySpec | Lightweight single-file workflow for small tasks — skip the heavy multi-step SDD process | `process` | Read+Write | [spec-kit-tinyspec](https://github.com/Quratulain-bilal/spec-kit-tinyspec) |

docs/community/presets.md

@@ -17,7 +17,7 @@ The following community-contributed presets customize how Spec Kit behaves — o
 | Cross-Platform Governance | Adds Bash + PowerShell parity, Unix man-pages, bilingual comment-based help, Verb-Noun Cmdlet discipline, and audit-ready Spec Kit run evidence for scripting projects managed with Spec Kit | 8 templates, 3 commands | — | [spec-kit-preset-cross-platform-governance](https://github.com/hindermath/spec-kit-preset-cross-platform-governance) |
 | Explicit Task Dependencies | Adds explicit `(depends on T###)` dependency declarations and an Execution Wave DAG to tasks.md for parallel scheduling | 1 template, 1 command | — | [spec-kit-preset-explicit-task-dependencies](https://github.com/Quratulain-bilal/spec-kit-preset-explicit-task-dependencies) |
 | Fiction Book Writing | It adapts the Spec-Driven Development workflow for storytelling to create books or audiobooks (with annotations) in 12 languages: features become story elements, specs become story briefs, plans become story structures, and tasks become scene-by-scene writing tasks. Supports single and multi-POV, all major plot structure frameworks, and two style modes: an author voice sample or humanized AI prose principles. Supports interactive elements like brainstorming, interview, roleplay, and extras like statistics, cover builder, illustration builder, and bio command. Export with templates for KDP, D2D, etc. | 26 templates, 34 commands, 2 scripts | — | [speckit-preset-fiction-book-writing](https://github.com/adaumann/speckit-preset-fiction-book-writing) |
-| Game Narrative Writing | Preset for game narrative design and interactive storytelling. It adapts the Spec-Driven Development workflow for game narratives: features become story mechanics, specs become narrative briefs, plans become story maps, and tasks become dialogue and scene-writing tasks. Supports branching narratives, player agency systems, state machines, and interactive dialogue trees. | 37 templates, 34 commands, 5 scripts | — | [speckit-preset-game-narrative-writing](https://github.com/adaumann/speckit-preset-game-narrative-writing) |
+| Game Narrative Writing | Spec-Driven Development for interactive game narrative pre-production for video games. Authors write in a portable generic format, Twine/Sugarcube (.twee) or Ink (.ink). Covers choice-IF, visual novels, and branching dialogue. Supports Tier 1 mechanic hooks (flag, counter, inventory, timer, trust, currency, npc_state, ending_condition), multi-ending design, series carry-over variable registry, and NPC-focused character architecture. | 22 templates, 36 commands, 2 scripts | — | [speckit-preset-game-narrative-writing](https://github.com/adaumann/speckit-preset-game-narrative-writing) |
 | iSAQB Architecture Governance | Adds general iSAQB/CPSA-F and arc42 software-architecture governance, including audit-ready Spec Kit run evidence for architecture goals, views, quality scenarios, ADRs, risks, and technical debt. | 13 templates, 3 commands | — | [spec-kit-preset-isaqb-architecture-governance](https://github.com/hindermath/spec-kit-preset-isaqb-architecture-governance) |
 | Jira Issue Tracking | Overrides `speckit.taskstoissues` to create Jira epics, stories, and tasks instead of GitHub Issues via Atlassian MCP tools | 1 command | — | [spec-kit-preset-jira](https://github.com/luno/spec-kit-preset-jira) |
 | Model Driven Engineering | Focuses on streamlined commands, app repository support, cross-spec support, and capability-aware project memory for model-driven engineering workflows | 6 templates, 11 commands | MDE extension | [spec-kit-preset-mde](https://github.com/AI-MDE/spec-kit-preset-mde) |
@@ -25,7 +25,6 @@ The following community-contributed presets customize how Spec Kit behaves — o
 | Pirate Speak (Full) | Transforms all Spec Kit output into pirate speak — specs become "Voyage Manifests", plans become "Battle Plans", tasks become "Crew Assignments" | 6 templates, 9 commands | — | [spec-kit-presets](https://github.com/mnriem/spec-kit-presets) |
 | Screenwriting | Spec-Driven Development for screenwriting/scriptwriting/tutorials: feature films, television (pilot, episode, limited series), and stage plays. Adapts the Spec Kit workflow to screenplay craft — slug lines, action lines, act breaks, beat sheets, and industry-standard pitch documents. Supports three-act, Save the Cat, TV pilot, network episode, cable/streaming episode, and stage-play structural frameworks. Export to Fountain, FTX, PDF | 26 templates, 32 commands, 1 script | — | [speckit-preset-screenwriting](https://github.com/adaumann/speckit-preset-screenwriting) |
 | Security Governance | Adds memory-safe-language preference, language-specific secure coding profiles, audit-ready Spec-Kit run evidence, ASVS verification, SBOM/AI-SBOM supply-chain transparency, CRA awareness, and regulatory applicability screening for NIS2, CRA, EU AI Act, and DORA | 14 templates, 3 commands | — | [spec-kit-preset-security-governance](https://github.com/hindermath/spec-kit-preset-security-governance) |
-| SicarioSpec Core | Evidence-first security operations governance that maps feature risk to controls, gates, evidence, owners, approval, and accepted-risk decisions. | 5 templates | — | [sicario-spec](https://github.com/dfirs1car1o/sicario-spec) |
 | Spec2Cloud | Spec-driven workflow tuned for shipping to Azure: spec → plan → tasks → implement → deploy | 5 templates, 8 commands | — | [spec2cloud](https://github.com/Azure-Samples/Spec2Cloud) |
 | Table of Contents Navigation | Adds a navigable Table of Contents to generated spec.md, plan.md, and tasks.md documents | 3 templates, 3 commands | — | [spec-kit-preset-toc-navigation](https://github.com/Quratulain-bilal/spec-kit-preset-toc-navigation) |
 | VS Code Ask Questions | Enhances the clarify command to use `vscode/askQuestions` for batched interactive questioning. | 1 command | — | [spec-kit-presets](https://github.com/fdcastel/spec-kit-presets) |

docs/reference/bundles.md

@@ -1,156 +0,0 @@
-# Bundles
-
-Bundles compose existing Spec Kit components — extensions, presets, workflows, and steps — into a single, versioned, installable unit. Where extensions and presets are primitives, a bundle is a curated stack that declares everything a team or role needs and installs it in one step through each component's own machinery. Bundles add no new runtime behavior of their own: they are a distribution and composition layer over the primitives you already use.
-
-A bundle is described by a `bundle.yml` manifest and is discovered through the same catalog stack as other components. Installing a bundle resolves its declared components against pinned versions, checks for the single cross-bundle conflict point (the active integration), and applies each component idempotently with full provenance tracking so it can be cleanly removed or refreshed later.
-
-## Search Available Bundles
-
-```bash
-specify bundle search [query]
-```
-
-| Option      | Description                  |
-| ----------- | ---------------------------- |
-| `--offline` | Do not access the network    |
-| `--json`    | Emit machine-readable JSON   |
-
-Searches all active catalogs for bundles matching the query. Without a query, lists every available bundle with its version, role, source, and a trust indicator (`verified` for org-curated catalog entries, `community` otherwise) so you can judge trust before installing.
-
-## Bundle Info
-
-```bash
-specify bundle info <bundle_id>
-```
-
-| Option       | Description                       |
-| ------------ | --------------------------------- |
-| `--offline`  | Do not access the network         |
-| `--json`     | Emit machine-readable JSON        |
-
-Shows full metadata for a bundle along with the **fully expanded component set** it installs — every extension, preset, step, and workflow with its pinned version, plus preset priority and strategy. The output also includes a trust indicator (`verified` vs `community`) so you can judge trust before installing. This preview is the same plan `install` applies, so you can see exactly what will be added before committing. Foreseeable overlaps with components already provided by installed bundles are surfaced here as well.
-
-## Install a Bundle
-
-```bash
-specify bundle install <bundle_id | path>
-```
-
-| Option           | Description                                                         |
-| ---------------- | ------------------------------------------------------------------ |
-| `--integration`  | Override the integration used when initializing/installing         |
-| `--offline`      | Do not access the network                                          |
-
-Installs a bundle's full component set through each primitive's machinery. The argument may be a catalog bundle id, or a local path to a built `.zip` artifact, a bundle directory, or a `bundle.yml` file; local sources install directly without consulting the catalog stack.
-
-If the current directory is not yet a Spec Kit project, `install` initializes one first so a fresh checkout reaches a working state in a single command. `--integration` selects the integration when initializing a new project, and confirms the target when a bundle pins a specific integration but the project's active integration can't be determined (missing or unreadable `.specify/integration.json`). It does **not** override an already-initialized project's active integration: if a bundle targets a different integration than the project's, install aborts with no changes. Integration-agnostic bundles inherit the project's active integration. Installation is idempotent — components already present are skipped. On failure, no provenance record is written (a failed install records nothing), and the components installed during that run are removed on a best-effort basis — removal errors are swallowed, so partial on-disk state may remain.
-
-## Update Bundles
-
-```bash
-specify bundle update [<bundle_id>]
-```
-
-| Option       | Description                          |
-| ------------ | ------------------------------------ |
-| `--all`      | Update every installed bundle        |
-| `--offline`  | Do not access the network            |
-
-Re-resolves a bundle and **refreshes** its components through each primitive's update path, bringing already-installed components up to the bundle's newly pinned versions while preserving primitive-level overrides (such as preset priority). Provide a bundle id, or use `--all` to update everything installed.
-
-> **Pin enforcement is install-time only.** Idempotency checks are id-based, not version-aware: a component that is already present is skipped during `install` without comparing its on-disk version to the manifest pin. Version pins are therefore guaranteed to be applied only when the bundler actually installs a component for the first time or refreshes it. Run `specify bundle update` to re-apply every owned component at its pinned version.
-
-## Remove a Bundle
-
-```bash
-specify bundle remove <bundle_id>
-```
-
-Uninstalls only the components this bundle contributed, leaving any component that another installed bundle still needs in place (no collateral removals).
-
-## List Installed Bundles
-
-```bash
-specify bundle list
-```
-
-| Option   | Description                  |
-| -------- | ---------------------------- |
-| `--json` | Emit machine-readable JSON   |
-
-Lists the bundles installed in the project with their versions, component counts, and install timestamps.
-
-## Initialize a Project with a Bundle
-
-```bash
-specify bundle init [<bundle_id>]
-```
-
-| Option           | Description                              |
-| ---------------- | ---------------------------------------- |
-| `--integration`  | Integration override                     |
-| `--offline`      | Do not access the network                |
-
-Ensures the current directory is a Spec Kit project (initializing it idempotently if needed), then optionally installs the given bundle. Useful as an explicit one-step bootstrap for a new checkout.
-
-## Validate a Bundle
-
-```bash
-specify bundle validate
-```
-
-| Option       | Description                                                          |
-| ------------ | ------------------------------------------------------------------- |
-| `--path`     | Bundle directory or `bundle.yml` (default: current directory)       |
-| `--offline`  | Verify references against bundled/installed components only          |
-
-Reports whether a `bundle.yml` is well-formed and whether every declared component reference resolves. References are checked against bundled components, the project's installed components, and — when online — the active catalogs. Validation fails only when a reference is definitively absent everywhere it could be checked: that is, when an active catalog is reachable and confirms the component is missing. References that cannot be verified — because validation is offline, or because a catalog is unreachable — are downgraded to warnings so authoring can continue, rather than failing the run.
-
-## Build a Bundle Artifact
-
-```bash
-specify bundle build
-```
-
-| Option      | Description                                              |
-| ----------- | ------------------------------------------------------- |
-| `--path`    | Bundle directory (default: current directory)           |
-| `--output`  | Output directory for the artifact                       |
-
-Produces a single versioned, distributable `.zip` artifact from a bundle directory. The artifact embeds the manifest and can be installed directly with `specify bundle install <artifact.zip>`.
-
-## Manage Catalog Sources
-
-Bundles are discovered through a priority-ordered stack of catalog sources (project, user, and built-in scopes).
-
-### List the Catalog Stack
-
-```bash
-specify bundle catalog list
-```
-
-Prints the active, priority-ordered catalog stack with each source's scope and install policy.
-
-### Add a Catalog Source
-
-```bash
-specify bundle catalog add <url>
-```
-
-| Option        | Description                                              |
-| ------------- | ------------------------------------------------------- |
-| `--policy`    | `install-allowed` or `discovery-only`                   |
-| `--priority`  | Source priority (lower = higher precedence; default 10) |
-| `--id`        | Explicit source id                                      |
-
-Registers a project-scoped catalog source and persists it.
-
-### Remove a Catalog Source
-
-```bash
-specify bundle catalog remove <id_or_url>
-```
-
-Removes a project-scoped catalog source. Built-in default sources cannot be deleted.
-
-> **Note:** `search` and `info` work anywhere — with no project they fall back to the built-in/user catalog stack. The remaining state-changing commands (`list`, `update`, `remove`, `catalog`) require a project already initialized with `specify init`. `install` and `init` will initialize a project on demand when run in an uninitialized directory.

docs/reference/integrations.md

@@ -15,7 +15,6 @@ The Specify CLI supports a wide range of AI coding agents. When you run `specify
 | [Codex CLI](https://github.com/openai/codex)                                         | `codex`          | Skills-based integration; installs skills into `.agents/skills` and invokes them as `$speckit-<command>` |
 | [Cursor](https://cursor.sh/)                                                         | `cursor-agent`   |                                                                                                                                           |
 | [Devin for Terminal](https://cli.devin.ai/docs)                                      | `devin`          | Skills-based integration; installs skills into `.devin/skills/` and invokes them as `/speckit-<command>` |
-| [Firebender](https://firebender.com/)                                                | `firebender`     | IDE-based agent for Android Studio / IntelliJ                                                                                             |
 | [Forge](https://forgecode.dev/)                                                      | `forge`          |                                                                                                                                           |
 | [Gemini CLI](https://github.com/google-gemini/gemini-cli)                            | `gemini`         |                                                                                                                                           |
 | [GitHub Copilot](https://code.visualstudio.com/)                                     | `copilot`        |                                                                                                                                           |
@@ -39,7 +38,6 @@ The Specify CLI supports a wide range of AI coding agents. When you run `specify
 | [Tabnine CLI](https://docs.tabnine.com/main/getting-started/tabnine-cli)             | `tabnine`        |                                                                                                                                           |
 | [Trae](https://www.trae.ai/)                                                         | `trae`           | Skills-based integration; skills are installed automatically                                                                               |
 | [Windsurf](https://windsurf.com/)                                                    | `windsurf`       |                                                                                                                                           |
-| [ZCode](https://zcode.z.ai/)                                                         | `zcode`          | Skills-based integration; installs skills into `.zcode/skills/` and invokes them as `$speckit-<command>`                                  |
 | [Zed](https://zed.dev/)                                                              | `zed`            | Skills-based integration; installs skills into `.agents/skills` and invokes them as `/speckit-<command>`                                  |
 | Generic                                                                              | `generic`        | Bring your own agent — use `--integration generic --integration-options="--commands-dir <path>"` for AI coding agents not listed above     |
 
@@ -186,7 +184,6 @@ The currently declared multi-install safe integrations are:
 | `codebuddy` | `.codebuddy/commands`, `CODEBUDDY.md` |
 | `codex` | `.agents/skills`, `AGENTS.md` |
 | `cursor-agent` | `.cursor/skills`, `.cursor/rules/specify-rules.mdc` |
-| `firebender` | `.firebender/commands`, `.firebender/rules/specify-rules.mdc` |
 | `gemini` | `.gemini/commands`, `GEMINI.md` |
 | `iflow` | `.iflow/commands`, `IFLOW.md` |
 | `junie` | `.junie/commands`, `.junie/AGENTS.md` |

docs/reference/overview.md

@@ -31,9 +31,3 @@ Presets customize how Spec Kit works — overriding command files, template file
 Workflows automate multi-step Spec-Driven Development processes into repeatable sequences. They chain commands, prompts, shell steps, and human checkpoints together, with support for conditional logic, loops, fan-out/fan-in, and the ability to pause and resume from the exact point of interruption.
 
 [Workflows reference →](workflows.md)
-
-## Bundles
-
-Bundles compose existing extensions, presets, workflows, and steps into a single, versioned, installable unit. Rather than adding new behavior, a bundle curates a stack of primitives — everything a team or role needs — and installs it in one step through each component's own machinery, with version pinning, conflict checks, and provenance tracking for clean updates and removal.
-
-[Bundles reference →](bundles.md)

examples/bundles/business-analyst/README.md

@@ -1,22 +0,0 @@
-# Business Analyst bundle
-
-A role bundle for business analysts working in a Spec-Driven Development flow:
-requirements elicitation, traceability, and acceptance criteria.
-
-## What it installs
-
-- **Extension** `agent-context` — keeps the agent context file in sync.
-- **Preset** `requirements-elicitation` (priority 10, append) — elicitation and
-  analysis command set.
-- **Steps** `capture-requirements`, `trace-acceptance-criteria`.
-- **Workflow** `requirements-to-spec` — turns captured requirements into a spec.
-
-This bundle is **integration-agnostic**: it inherits the project's active
-integration.
-
-## Usage
-
-```bash
-specify bundle validate --path examples/bundles/business-analyst
-specify bundle build --path examples/bundles/business-analyst --output dist/
-```

examples/bundles/business-analyst/bundle.yml

@@ -1,33 +0,0 @@
-schema_version: "1.0"
-
-bundle:
-  id: "business-analyst"
-  name: "Business Analyst"
-  version: "1.0.0"
-  role: "business-analyst"
-  description: "Spec-Driven Development setup for business analysts: requirements elicitation, traceability, and acceptance criteria."
-  author: "spec-kit-examples"
-  license: "MIT"
-
-requires:
-  speckit_version: ">=0.9.0"
-  tools: []
-  mcp: []
-
-provides:
-  extensions:
-    - id: "agent-context"
-      version: "1.0.0"
-  presets:
-    - id: "requirements-elicitation"
-      version: "1.0.0"
-      priority: 10
-      strategy: "append"
-  steps:
-    - id: "capture-requirements"
-    - id: "trace-acceptance-criteria"
-  workflows:
-    - id: "requirements-to-spec"
-      version: "1.0.0"
-
-tags: ["requirements", "traceability", "analysis"]

examples/bundles/developer/README.md

@@ -1,22 +0,0 @@
-# Developer bundle
-
-A role bundle for developers practicing Spec-Driven Development: implementation
-planning, task breakdown, and code review.
-
-## What it installs
-
-- **Extension** `agent-context` — keeps the agent context file in sync.
-- **Preset** `implementation-planning` (priority 10, append) — implementation
-  planning command set.
-- **Steps** `plan-implementation`, `break-down-tasks`.
-- **Workflow** `spec-to-implementation` — drives a spec through to code.
-
-This bundle is **integration-agnostic**: it inherits the project's active
-integration.
-
-## Usage
-
-```bash
-specify bundle validate --path examples/bundles/developer
-specify bundle build --path examples/bundles/developer --output dist/
-```

examples/bundles/developer/bundle.yml

@@ -1,33 +0,0 @@
-schema_version: "1.0"
-
-bundle:
-  id: "developer"
-  name: "Developer"
-  version: "1.0.0"
-  role: "developer"
-  description: "Spec-Driven Development setup for developers: implementation planning, task breakdown, and code review."
-  author: "spec-kit-examples"
-  license: "MIT"
-
-requires:
-  speckit_version: ">=0.9.0"
-  tools: []
-  mcp: []
-
-provides:
-  extensions:
-    - id: "agent-context"
-      version: "1.0.0"
-  presets:
-    - id: "implementation-planning"
-      version: "1.0.0"
-      priority: 10
-      strategy: "append"
-  steps:
-    - id: "plan-implementation"
-    - id: "break-down-tasks"
-  workflows:
-    - id: "spec-to-implementation"
-      version: "1.0.0"
-
-tags: ["development", "implementation", "code-review"]

examples/bundles/product-manager/README.md

@@ -1,22 +0,0 @@
-# Product Manager bundle
-
-A role bundle that prepares a Spec Kit project for product managers driving
-Spec-Driven Development: discovery, specification, and roadmap planning.
-
-## What it installs
-
-- **Extension** `agent-context` — keeps the agent context file in sync.
-- **Preset** `product-discovery` (priority 10, append) — discovery-oriented
-  command set.
-- **Steps** `draft-spec`, `review-spec` — specification authoring steps.
-- **Workflow** `spec-to-roadmap` — turns an approved spec into a roadmap.
-
-This bundle is **integration-agnostic**: it inherits whatever integration the
-project already uses (e.g. `copilot`, `claude`).
-
-## Usage
-
-```bash
-specify bundle validate --path examples/bundles/product-manager
-specify bundle build --path examples/bundles/product-manager --output dist/
-```

examples/bundles/product-manager/bundle.yml

@@ -1,35 +0,0 @@
-schema_version: "1.0"
-
-bundle:
-  id: "product-manager"
-  name: "Product Manager"
-  version: "1.0.0"
-  role: "product-manager"
-  description: "Spec-Driven Development setup for product managers: discovery, specification, and roadmap workflows."
-  author: "spec-kit-examples"
-  license: "MIT"
-
-requires:
-  speckit_version: ">=0.9.0"
-  tools: []
-  mcp: []
-
-# Agnostic bundle: inherits the project's active integration.
-
-provides:
-  extensions:
-    - id: "agent-context"
-      version: "1.0.0"
-  presets:
-    - id: "product-discovery"
-      version: "1.0.0"
-      priority: 10
-      strategy: "append"
-  steps:
-    - id: "draft-spec"
-    - id: "review-spec"
-  workflows:
-    - id: "spec-to-roadmap"
-      version: "1.0.0"
-
-tags: ["product", "discovery", "roadmap"]

examples/bundles/security-researcher/README.md

@@ -1,23 +0,0 @@
-# Security Researcher bundle
-
-A role bundle for security researchers practicing Spec-Driven Development:
-threat modeling, security review, and compliance.
-
-## What it installs
-
-- **Extension** `agent-context` — keeps the agent context file in sync.
-- **Preset** `security-compliance` (priority 5, append) — security and
-  compliance command set; presets apply in ascending priority order, so this
-  low number (5) places it ahead of higher-numbered presets in the stack.
-- **Steps** `threat-model`, `security-review`.
-- **Workflow** `secure-sdd` — a security-first SDD workflow.
-
-This bundle is **integration-agnostic**: it inherits the project's active
-integration.
-
-## Usage
-
-```bash
-specify bundle validate --path examples/bundles/security-researcher
-specify bundle build --path examples/bundles/security-researcher --output dist/
-```

examples/bundles/security-researcher/bundle.yml

@@ -1,33 +0,0 @@
-schema_version: "1.0"
-
-bundle:
-  id: "security-researcher"
-  name: "Security Researcher"
-  version: "1.0.0"
-  role: "security-researcher"
-  description: "Spec-Driven Development setup for security researchers: threat modeling, security review, and compliance checks."
-  author: "spec-kit-examples"
-  license: "MIT"
-
-requires:
-  speckit_version: ">=0.9.0"
-  tools: []
-  mcp: []
-
-provides:
-  extensions:
-    - id: "agent-context"
-      version: "1.0.0"
-  presets:
-    - id: "security-compliance"
-      version: "1.0.0"
-      priority: 5
-      strategy: "append"
-  steps:
-    - id: "threat-model"
-    - id: "security-review"
-  workflows:
-    - id: "secure-sdd"
-      version: "1.0.0"
-
-tags: ["security", "compliance", "threat-modeling"]

extensions/agent-context/README.md

@@ -10,7 +10,6 @@ Not every Spec Kit user wants Spec Kit to write into the coding agent's context
 
 - **Opt out** entirely with `specify extension disable agent-context` — Spec Kit will then never create or modify the agent context file.
 - **Customize the markers** by editing `.specify/extensions/agent-context/agent-context-config.yml` — both the Python layer and the bundled scripts honor the same `context_markers` value.
-- **Synchronize multiple agent anchors** by setting `context_files` when a project intentionally uses more than one coding agent context file, such as `AGENTS.md` and `CLAUDE.md`.
 - **Refresh on demand** with `/speckit.agent-context.update`, or automatically through the hooks declared in `extension.yml` (`after_specify`, `after_plan`).
 
 ## Commands
@@ -28,12 +27,6 @@ All configuration flows through the extension's own config file at
 # Path to the coding agent context file managed by this extension
 context_file: CLAUDE.md
 
-# Optional list of coding agent context files to manage together.
-# When non-empty, this takes precedence over context_file.
-context_files:
-  - AGENTS.md
-  - CLAUDE.md
-
 # Delimiters for the managed Spec Kit section
 context_markers:
   start: "<!-- SPECKIT START -->"
@@ -41,7 +34,6 @@ context_markers:
 ```
 
 - `context_file` — the project-relative path to the coding agent context file, written by `specify init` and `specify integration install`.
-- `context_files` — optional project-relative paths to multiple coding agent context files. When non-empty, the list takes precedence over `context_file`. Absolute paths, backslash separators, and `..` path segments are rejected.
 - `context_markers.start` / `.end` — the delimiters around the managed section. Edit these to use custom markers.
 
 ## Requirements
@@ -63,4 +55,3 @@ specify extension disable agent-context
 ```
 
 When disabled, Spec Kit skips context file creation, updates, and removal (the gates are inside `upsert_context_section()` and `remove_context_section()`).
-Disabled projects also ignore stale `context_files` values during command rendering so disabling the extension remains a complete opt-out.

extensions/agent-context/agent-context-config.yml

@@ -2,17 +2,12 @@
 # These values are populated automatically by `specify init` and
 # `specify integration use` / `specify integration install`.
 
-# Path (relative to the project root) to the default coding agent context file
+# Path (relative to the project root) to the coding agent context file
 # managed by this extension (e.g. CLAUDE.md, AGENTS.md,
 # .github/copilot-instructions.md). Set automatically from the active
 # integration and regenerated during `specify init` or integration switches.
 context_file: ""
 
-# Optional list of project-relative coding agent context files managed by this
-# extension. When non-empty, this list takes precedence over `context_file`.
-# Use this for projects that intentionally keep multiple agent anchors in sync.
-context_files: []
-
 # Delimiters for the managed Spec Kit section.
 # Edit these to use custom markers.
 context_markers:

extensions/agent-context/commands/speckit.agent-context.update.md

@@ -1,5 +1,5 @@
 ---
-description: "Refresh the managed Spec Kit section in coding agent context file(s)"
+description: "Refresh the managed Spec Kit section in the coding agent context file"
 ---
 
 # Update Coding Agent Context
@@ -12,12 +12,11 @@ The script reads the agent-context extension config at
 `.specify/extensions/agent-context/agent-context-config.yml` to discover:
 
 - `context_file` — the path of the coding agent context file to manage.
-- `context_files` — optional project-relative paths for multiple coding agent context files. When non-empty, the script updates each listed file and the list takes precedence over `context_file`.
 - `context_markers.start` / `.end` — the delimiters surrounding the managed section. Defaults to `<!-- SPECKIT START -->` and `<!-- SPECKIT END -->` when the field is missing.
 
 It then creates, replaces, or appends the managed block so that the section points at the most recent plan path when one can be discovered (`specs/<feature>/plan.md`).
 
-If `context_files` and `context_file` are empty, the command reports nothing to do and exits successfully. Context file paths must stay project-relative; absolute paths, Windows drive paths, backslash separators, and `..` path segments are rejected.
+If `context_file` is empty or the file cannot be located, the command reports nothing to do and exits successfully.
 
 ## Execution
 

extensions/agent-context/scripts/bash/update-agent-context.sh

@@ -1,10 +1,10 @@
 #!/usr/bin/env bash
 # update-agent-context.sh
 #
-# Refresh the managed Spec Kit section in the coding agent's context file(s)
+# Refresh the managed Spec Kit section in the coding agent's context file
 # (e.g. CLAUDE.md, .github/copilot-instructions.md, AGENTS.md).
 #
-# Reads `context_files` or `context_file`, plus `context_markers.{start,end}`, from the
+# Reads `context_file` and `context_markers.{start,end}` from the
 # agent-context extension config:
 #   .specify/extensions/agent-context/agent-context-config.yml
 #
@@ -26,41 +26,22 @@ if [[ ! -f "$EXT_CONFIG" ]]; then
   exit 0
 fi
 
-# Locate a Python 3 interpreter with PyYAML available.
+# Locate a suitable Python interpreter (python3, then python).
 _python=""
-_python_candidates=()
-[[ -n "${SPECKIT_PYTHON:-}" ]] && _python_candidates+=("$SPECKIT_PYTHON")
-_python_candidates+=("python3" "python")
-for _candidate in "${_python_candidates[@]}"; do
-  if command -v "$_candidate" >/dev/null 2>&1 \
-    && "$_candidate" - <<'PY' >/dev/null 2>&1
-import sys
-try:
-    import yaml  # noqa: F401
-except ImportError:
-    sys.exit(1)
-sys.exit(0 if sys.version_info[0] == 3 else 1)
-PY
-  then
-    _python="$_candidate"
-    break
-  fi
-done
-unset _candidate _python_candidates
+if command -v python3 >/dev/null 2>&1; then
+  _python="python3"
+elif command -v python >/dev/null 2>&1 && python --version 2>&1 | grep -q "^Python 3"; then
+  _python="python"
+fi
 
 if [[ -z "$_python" ]]; then
-  echo "agent-context: Python 3 with PyYAML not found on PATH; skipping update." >&2
-  echo "  To resolve: pip install pyyaml (or install it into the environment used by python3)." >&2
+  echo "agent-context: Python 3 not found on PATH; skipping update." >&2
   exit 0
 fi
-_case_insensitive_context_files=0
-case "$(uname -s 2>/dev/null || true)" in
-  MINGW*|MSYS*|CYGWIN*) _case_insensitive_context_files=1 ;;
-esac
 
-# Parse extension config once; emit context files as JSON, followed by marker strings.
-if ! _raw_opts="$("$_python" - "$EXT_CONFIG" "$_case_insensitive_context_files" <<'PY'
-import json
+# Parse extension config once; emit three newline-separated fields:
+# context_file, context_markers.start, context_markers.end
+if ! _raw_opts="$("$_python" - "$EXT_CONFIG" <<'PY'
 import sys
 try:
     import yaml
@@ -92,28 +73,7 @@ def get_str(obj, *keys):
         else:
             return ""
     return node if isinstance(node, str) else ""
-context_files = []
-seen_context_files = set()
-case_insensitive = sys.argv[2] == "1" or sys.platform.startswith(("win32", "cygwin"))
-raw_files = data.get("context_files")
-if isinstance(raw_files, list):
-    for value in raw_files:
-        if not isinstance(value, str):
-            continue
-        candidate = value.strip()
-        if not candidate:
-            continue
-        key = candidate.casefold() if case_insensitive else candidate
-        if key in seen_context_files:
-            continue
-        context_files.append(candidate)
-        seen_context_files.add(key)
-if not context_files:
-    raw_file = get_str(data, "context_file")
-    candidate = raw_file.strip()
-    if candidate:
-        context_files.append(candidate)
-print(json.dumps(context_files))
+print(get_str(data, "context_file"))
 print(get_str(data, "context_markers", "start"))
 print(get_str(data, "context_markers", "end"))
 PY
@@ -127,71 +87,31 @@ while IFS= read -r _line || [[ -n "$_line" ]]; do
   _opts_lines+=("$_line")
 done < <(printf '%s\n' "$_raw_opts")
 if (( ${#_opts_lines[@]} < 3 )); then
-  echo "agent-context: malformed config parser output; expected 3 lines (context_files, marker_start, marker_end), got ${#_opts_lines[@]}; skipping update." >&2
+  echo "agent-context: malformed config parser output; expected 3 lines (context_file, marker_start, marker_end), got ${#_opts_lines[@]}; skipping update." >&2
   exit 0
 fi
-CONTEXT_FILES_JSON="${_opts_lines[0]}"
+CONTEXT_FILE="${_opts_lines[0]}"
 MARKER_START="${_opts_lines[1]}"
 MARKER_END="${_opts_lines[2]}"
 
-if ! _context_files_raw="$("$_python" - "$CONTEXT_FILES_JSON" <<'PY'
-import json
-import sys
-try:
-    data = json.loads(sys.argv[1])
-except Exception:
-    data = []
-if not isinstance(data, list):
-    data = []
-for value in data:
-    if isinstance(value, str) and value:
-        print(value)
-PY
-)"; then
-  echo "agent-context: malformed context_files parser output; skipping update." >&2
+if [[ -z "$CONTEXT_FILE" ]]; then
+  echo "agent-context: context_file not set in extension config; nothing to do." >&2
   exit 0
 fi
 
-CONTEXT_FILES=()
-while IFS= read -r _line || [[ -n "$_line" ]]; do
-  [[ -n "$_line" ]] && CONTEXT_FILES+=("$_line")
-done < <(printf '%s\n' "$_context_files_raw")
-
-if (( ${#CONTEXT_FILES[@]} == 0 )); then
-  echo "agent-context: context_files/context_file not set in extension config; nothing to do." >&2
-  exit 0
+# Reject absolute paths, backslash separators, and '..' path segments in context_file
+if [[ "$CONTEXT_FILE" == /* ]] || [[ "$CONTEXT_FILE" =~ ^[A-Za-z]: ]]; then
+  echo "agent-context: context_file must be a project-relative path; got '$CONTEXT_FILE'." >&2
+  exit 1
 fi
-
-for CONTEXT_FILE in "${CONTEXT_FILES[@]}"; do
-  # Reject absolute paths, backslash separators, and '..' path segments in context files
-  if [[ "$CONTEXT_FILE" == /* ]] || [[ "$CONTEXT_FILE" =~ ^[A-Za-z]: ]]; then
-    echo "agent-context: context files must be project-relative paths; got '$CONTEXT_FILE'." >&2
-    exit 1
-  fi
-  if [[ "$CONTEXT_FILE" == *\\* ]]; then
-    echo "agent-context: context files must not contain backslash separators; got '$CONTEXT_FILE'." >&2
-    exit 1
-  fi
-  IFS='/' read -ra _cf_parts <<< "$CONTEXT_FILE"
-  for _seg in "${_cf_parts[@]}"; do
-    if [[ "$_seg" == ".." ]]; then
-      echo "agent-context: context files must not contain '..' path segments; got '$CONTEXT_FILE'." >&2
-      exit 1
-    fi
-  done
-  if ! "$_python" - "$PROJECT_ROOT" "$CONTEXT_FILE" <<'PY'
-import sys
-from pathlib import Path
-
-root = Path(sys.argv[1]).resolve()
-target = (root / sys.argv[2]).resolve(strict=False)
-try:
-    target.relative_to(root)
-except ValueError:
-    sys.exit(1)
-PY
-  then
-    echo "agent-context: context file path resolves outside the project root; got '$CONTEXT_FILE'." >&2
+if [[ "$CONTEXT_FILE" == *\\* ]]; then
+  echo "agent-context: context_file must not contain backslash separators; got '$CONTEXT_FILE'." >&2
+  exit 1
+fi
+IFS='/' read -ra _cf_parts <<< "$CONTEXT_FILE"
+for _seg in "${_cf_parts[@]}"; do
+  if [[ "$_seg" == ".." ]]; then
+    echo "agent-context: context_file must not contain '..' path segments; got '$CONTEXT_FILE'." >&2
     exit 1
   fi
 done
@@ -222,6 +142,9 @@ PY
   fi
 fi
 
+CTX_PATH="$PROJECT_ROOT/$CONTEXT_FILE"
+mkdir -p "$(dirname "$CTX_PATH")"
+
 # Build the managed section
 TMP_SECTION="$(mktemp)"
 trap 'rm -f "$TMP_SECTION"' EXIT
@@ -235,11 +158,7 @@ trap 'rm -f "$TMP_SECTION"' EXIT
   echo "$MARKER_END"
 } > "$TMP_SECTION"
 
-for CONTEXT_FILE in "${CONTEXT_FILES[@]}"; do
-  CTX_PATH="$PROJECT_ROOT/$CONTEXT_FILE"
-  mkdir -p "$(dirname "$CTX_PATH")"
-
-  "$_python" - "$CTX_PATH" "$MARKER_START" "$MARKER_END" "$TMP_SECTION" <<'PY'
+"$_python" - "$CTX_PATH" "$MARKER_START" "$MARKER_END" "$TMP_SECTION" <<'PY'
 import sys, os
 ctx_path, start, end, section_path = sys.argv[1:5]
 with open(section_path, "r", encoding="utf-8") as fh:
@@ -278,5 +197,4 @@ with open(ctx_path, "wb") as fh:
     fh.write(new_content.encode("utf-8"))
 PY
 
-  echo "agent-context: updated $CONTEXT_FILE"
-done
+echo "agent-context: updated $CONTEXT_FILE"

extensions/agent-context/scripts/powershell/update-agent-context.ps1

@@ -1,10 +1,10 @@
 #!/usr/bin/env pwsh
 # update-agent-context.ps1
 #
-# Refresh the managed Spec Kit section in the coding agent's context file(s)
+# Refresh the managed Spec Kit section in the coding agent's context file
 # (e.g. CLAUDE.md, .github/copilot-instructions.md, AGENTS.md).
 #
-# Reads `context_files` or `context_file`, plus `context_markers.{start,end}`, from the
+# Reads `context_file` and `context_markers.{start,end}` from the
 # agent-context extension config:
 #   .specify/extensions/agent-context/agent-context-config.yml
 #
@@ -52,66 +52,6 @@ function Test-ConfigObject {
     return $false
 }
 
-function Resolve-ContextPath {
-    param(
-        [Parameter(Mandatory = $true)][string]$Root,
-        [Parameter(Mandatory = $true)][string]$RelativePath
-    )
-
-    $rootFull = [System.IO.Path]::GetFullPath($Root)
-    $segments = $RelativePath -split '/'
-    $resolved = $rootFull
-
-    foreach ($segment in $segments) {
-        if ([string]::IsNullOrWhiteSpace($segment) -or $segment -eq '.') {
-            continue
-        }
-
-        $candidate = [System.IO.Path]::GetFullPath((Join-Path $resolved $segment))
-        if (Test-Path -LiteralPath $candidate) {
-            $item = Get-Item -LiteralPath $candidate -Force
-            if ($item.Attributes -band [System.IO.FileAttributes]::ReparsePoint) {
-                $target = $item.Target
-                if ($target -is [System.Array]) {
-                    $target = $target[0]
-                }
-                if ($target) {
-                    if ([System.IO.Path]::IsPathRooted($target)) {
-                        $candidate = [System.IO.Path]::GetFullPath($target)
-                    } else {
-                        $candidate = [System.IO.Path]::GetFullPath(
-                            (Join-Path (Split-Path -Parent $candidate) $target)
-                        )
-                    }
-                }
-            }
-        }
-        $resolved = $candidate
-    }
-
-    return $resolved
-}
-
-function Test-IsSubPath {
-    param(
-        [Parameter(Mandatory = $true)][string]$Root,
-        [Parameter(Mandatory = $true)][string]$Path
-    )
-
-    $comparison = if ([System.Environment]::OSVersion.Platform -eq [System.PlatformID]::Win32NT) {
-        [System.StringComparison]::OrdinalIgnoreCase
-    } else {
-        [System.StringComparison]::Ordinal
-    }
-    $rootFull = [System.IO.Path]::GetFullPath($Root).TrimEnd(
-        [System.IO.Path]::DirectorySeparatorChar,
-        [System.IO.Path]::AltDirectorySeparatorChar
-    )
-    $pathFull = [System.IO.Path]::GetFullPath($Path)
-    return $pathFull.Equals($rootFull, $comparison) -or
-        $pathFull.StartsWith($rootFull + [System.IO.Path]::DirectorySeparatorChar, $comparison)
-}
-
 $ErrorActionPreference = 'Stop'
 $DefaultStart = '<!-- SPECKIT START -->'
 $DefaultEnd   = '<!-- SPECKIT END -->'
@@ -135,16 +75,11 @@ if (Get-Command ConvertFrom-Yaml -ErrorAction SilentlyContinue) {
 if ($null -eq $Options) {
     # ConvertFrom-Yaml unavailable or failed; fall back to Python+PyYAML.
     $pythonCmd = $null
-    $pythonCandidates = @()
-    if ($env:SPECKIT_PYTHON) {
-        $pythonCandidates += $env:SPECKIT_PYTHON
-    }
-    $pythonCandidates += @('python3', 'python')
-    foreach ($candidate in $pythonCandidates) {
+    foreach ($candidate in @('python3', 'python')) {
         if (Get-Command $candidate -ErrorAction SilentlyContinue) {
-            # Verify it is Python 3 with PyYAML available.
-            $null = & $candidate -c "import sys; import yaml; sys.exit(0 if sys.version_info[0] == 3 else 1)" 2>$null
-            if ($LASTEXITCODE -eq 0) {
+            # Verify it is Python 3
+            $verOut = & $candidate --version 2>&1
+            if ($verOut -match 'Python 3') {
                 $pythonCmd = $candidate
                 break
             }
@@ -152,10 +87,8 @@ if ($null -eq $Options) {
     }
 
     if ($pythonCmd) {
-        $pyScript = $null
         try {
-            $pyScript = [System.IO.Path]::GetTempFileName()
-            Set-Content -LiteralPath $pyScript -Encoding UTF8 -Value @'
+            $jsonOut = & $pythonCmd -c @'
 import json
 import sys
 try:
@@ -181,17 +114,12 @@ if not isinstance(data, dict):
     data = {}
 
 print(json.dumps(data))
-'@
-            $jsonOut = & $pythonCmd $pyScript $ExtConfig
+'@ $ExtConfig
             if ($LASTEXITCODE -eq 0 -and $jsonOut) {
                 $Options = $jsonOut | ConvertFrom-Json -ErrorAction Stop
             }
         } catch {
             $Options = $null
-        } finally {
-            if ($pyScript -and (Test-Path -LiteralPath $pyScript)) {
-                Remove-Item -LiteralPath $pyScript -Force -ErrorAction SilentlyContinue
-            }
         }
     }
 
@@ -206,63 +134,21 @@ if (-not (Test-ConfigObject -Object $Options)) {
     exit 0
 }
 
-$ConfiguredContextFiles = Get-ConfigValue -Object $Options -Key 'context_files'
-$ContextFiles = @()
-if ($null -ne $ConfiguredContextFiles) {
-    foreach ($item in @($ConfiguredContextFiles)) {
-        if ($item -is [string] -and -not [string]::IsNullOrWhiteSpace($item)) {
-            $ContextFiles += $item.Trim()
-        }
-    }
-}
-if ($ContextFiles.Count -eq 0) {
-    $ContextFile = Get-ConfigValue -Object $Options -Key 'context_file'
-    if ($ContextFile -is [string] -and -not [string]::IsNullOrWhiteSpace($ContextFile)) {
-        $ContextFiles += $ContextFile.Trim()
-    }
-}
-$pathComparison = if ([System.Environment]::OSVersion.Platform -eq [System.PlatformID]::Win32NT) {
-    [System.StringComparer]::OrdinalIgnoreCase
-} else {
-    [System.StringComparer]::Ordinal
-}
-$seenContextFiles = [System.Collections.Generic.HashSet[string]]::new($pathComparison)
-$dedupedContextFiles = @()
-foreach ($ContextFile in $ContextFiles) {
-    if ($seenContextFiles.Add($ContextFile)) {
-        $dedupedContextFiles += $ContextFile
-    }
-}
-$ContextFiles = $dedupedContextFiles
-if ($ContextFiles.Count -eq 0) {
-    Write-Warning 'agent-context: context_files/context_file not set in extension config; nothing to do.'
+$ContextFile = Get-ConfigValue -Object $Options -Key 'context_file'
+if (-not $ContextFile) {
+    Write-Warning 'agent-context: context_file not set in extension config; nothing to do.'
     exit 0
 }
 
-foreach ($ContextFile in $ContextFiles) {
-    # Reject absolute paths, drive-qualified paths, backslash separators, and '..' path segments in context files
-    if ($ContextFile -match '^[A-Za-z]:') {
-        Write-Warning "agent-context: context files must be project-relative paths; got '$ContextFile'."
-        exit 1
-    }
-    if ([System.IO.Path]::IsPathRooted($ContextFile)) {
-        Write-Warning "agent-context: context files must be project-relative paths; got '$ContextFile'."
-        exit 1
-    }
-    if ($ContextFile.Contains('\')) {
-        Write-Warning "agent-context: context files must not contain backslash separators; got '$ContextFile'."
-        exit 1
-    }
-    $cfSegments = $ContextFile -split '[/\\]'
-    if ($cfSegments -contains '..') {
-        Write-Warning "agent-context: context files must not contain '..' path segments; got '$ContextFile'."
-        exit 1
-    }
-    $resolvedTarget = Resolve-ContextPath -Root $ProjectRoot -RelativePath $ContextFile
-    if (-not (Test-IsSubPath -Root $ProjectRoot -Path $resolvedTarget)) {
-        Write-Warning "agent-context: context file path resolves outside the project root; got '$ContextFile'."
-        exit 1
-    }
+# Reject absolute paths and '..' path segments in context_file
+if ([System.IO.Path]::IsPathRooted($ContextFile)) {
+    Write-Warning "agent-context: context_file must be a project-relative path; got '$ContextFile'."
+    exit 1
+}
+$cfSegments = $ContextFile -split '[/\\]'
+if ($cfSegments -contains '..') {
+    Write-Warning "agent-context: context_file must not contain '..' path segments; got '$ContextFile'."
+    exit 1
 }
 
 $MarkerStart = $DefaultStart
@@ -298,6 +184,12 @@ if (-not $PlanPath) {
     }
 }
 
+$CtxPath = Join-Path $ProjectRoot $ContextFile
+$CtxDir  = Split-Path -Parent $CtxPath
+if ($CtxDir -and -not (Test-Path -LiteralPath $CtxDir)) {
+    New-Item -ItemType Directory -Path $CtxDir -Force | Out-Null
+}
+
 $lines = @($MarkerStart,
            'For additional context about technologies to be used, project structure,',
            'shell commands, and other important information, read the current plan')
@@ -307,47 +199,39 @@ if ($PlanPath) {
 $lines += $MarkerEnd
 $Section = ($lines -join "`n") + "`n"
 
-foreach ($ContextFile in $ContextFiles) {
-    $CtxPath = Join-Path $ProjectRoot $ContextFile
-    $CtxDir  = Split-Path -Parent $CtxPath
-    if ($CtxDir -and -not (Test-Path -LiteralPath $CtxDir)) {
-        New-Item -ItemType Directory -Path $CtxDir -Force | Out-Null
-    }
-
-    if (Test-Path -LiteralPath $CtxPath) {
-        $rawBytes = [System.IO.File]::ReadAllBytes($CtxPath)
-        # Strip UTF-8 BOM if present
-        if ($rawBytes.Length -ge 3 -and $rawBytes[0] -eq 0xEF -and $rawBytes[1] -eq 0xBB -and $rawBytes[2] -eq 0xBF) {
-            $content = [System.Text.Encoding]::UTF8.GetString($rawBytes, 3, $rawBytes.Length - 3)
-        } else {
-            $content = [System.Text.Encoding]::UTF8.GetString($rawBytes)
-        }
-
-        $s = $content.IndexOf($MarkerStart)
-        $e = if ($s -ge 0) { $content.IndexOf($MarkerEnd, $s) } else { $content.IndexOf($MarkerEnd) }
-
-        if ($s -ge 0 -and $e -ge 0 -and $e -gt $s) {
-            $endOfMarker = $e + $MarkerEnd.Length
-            if ($endOfMarker -lt $content.Length -and $content[$endOfMarker] -eq "`r") { $endOfMarker++ }
-            if ($endOfMarker -lt $content.Length -and $content[$endOfMarker] -eq "`n") { $endOfMarker++ }
-            $newContent = $content.Substring(0, $s) + $Section + $content.Substring($endOfMarker)
-        } elseif ($s -ge 0) {
-            $newContent = $content.Substring(0, $s) + $Section
-        } elseif ($e -ge 0) {
-            $endOfMarker = $e + $MarkerEnd.Length
-            if ($endOfMarker -lt $content.Length -and $content[$endOfMarker] -eq "`r") { $endOfMarker++ }
-            if ($endOfMarker -lt $content.Length -and $content[$endOfMarker] -eq "`n") { $endOfMarker++ }
-            $newContent = $Section + $content.Substring($endOfMarker)
-        } else {
-            if ($content -and -not $content.EndsWith("`n")) { $content += "`n" }
-            if ($content) { $newContent = $content + "`n" + $Section } else { $newContent = $Section }
-        }
+if (Test-Path -LiteralPath $CtxPath) {
+    $rawBytes = [System.IO.File]::ReadAllBytes($CtxPath)
+    # Strip UTF-8 BOM if present
+    if ($rawBytes.Length -ge 3 -and $rawBytes[0] -eq 0xEF -and $rawBytes[1] -eq 0xBB -and $rawBytes[2] -eq 0xBF) {
+        $content = [System.Text.Encoding]::UTF8.GetString($rawBytes, 3, $rawBytes.Length - 3)
     } else {
-        $newContent = $Section
+        $content = [System.Text.Encoding]::UTF8.GetString($rawBytes)
     }
 
-    $newContent = $newContent.Replace("`r`n", "`n").Replace("`r", "`n")
-    [System.IO.File]::WriteAllText($CtxPath, $newContent, (New-Object System.Text.UTF8Encoding($false)))
+    $s = $content.IndexOf($MarkerStart)
+    $e = if ($s -ge 0) { $content.IndexOf($MarkerEnd, $s) } else { $content.IndexOf($MarkerEnd) }
 
-    Write-Host "agent-context: updated $ContextFile"
+    if ($s -ge 0 -and $e -ge 0 -and $e -gt $s) {
+        $endOfMarker = $e + $MarkerEnd.Length
+        if ($endOfMarker -lt $content.Length -and $content[$endOfMarker] -eq "`r") { $endOfMarker++ }
+        if ($endOfMarker -lt $content.Length -and $content[$endOfMarker] -eq "`n") { $endOfMarker++ }
+        $newContent = $content.Substring(0, $s) + $Section + $content.Substring($endOfMarker)
+    } elseif ($s -ge 0) {
+        $newContent = $content.Substring(0, $s) + $Section
+    } elseif ($e -ge 0) {
+        $endOfMarker = $e + $MarkerEnd.Length
+        if ($endOfMarker -lt $content.Length -and $content[$endOfMarker] -eq "`r") { $endOfMarker++ }
+        if ($endOfMarker -lt $content.Length -and $content[$endOfMarker] -eq "`n") { $endOfMarker++ }
+        $newContent = $Section + $content.Substring($endOfMarker)
+    } else {
+        if ($content -and -not $content.EndsWith("`n")) { $content += "`n" }
+        if ($content) { $newContent = $content + "`n" + $Section } else { $newContent = $Section }
+    }
+} else {
+    $newContent = $Section
 }
+
+$newContent = $newContent.Replace("`r`n", "`n").Replace("`r", "`n")
+[System.IO.File]::WriteAllText($CtxPath, $newContent, (New-Object System.Text.UTF8Encoding($false)))
+
+Write-Host "agent-context: updated $ContextFile"

extensions/catalog.community.json

@@ -1,6 +1,6 @@
 {
   "schema_version": "1.0",
-  "updated_at": "2026-06-23T00:00:00Z",
+  "updated_at": "2026-06-18T00:00:00Z",
   "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/extensions/catalog.community.json",
   "extensions": {
     "aide": {
@@ -187,10 +187,10 @@
     "arch": {
       "name": "Architecture Workflow",
       "id": "arch",
-      "description": "Generate or reverse project-level 4+1 architecture views as separate commands",
+      "description": "Generate or reverse project-level 4+1 architecture view artifacts and synthesis",
       "author": "bigsmartben",
-      "version": "1.2.1",
-      "download_url": "https://github.com/bigsmartben/spec-kit-arch/archive/refs/tags/v1.2.1.zip",
+      "version": "1.1.0",
+      "download_url": "https://github.com/bigsmartben/spec-kit-arch/archive/refs/tags/v1.1.0.zip",
       "repository": "https://github.com/bigsmartben/spec-kit-arch",
       "homepage": "https://github.com/bigsmartben/spec-kit-arch",
       "documentation": "https://github.com/bigsmartben/spec-kit-arch/blob/main/README.md",
@@ -202,7 +202,7 @@
         "speckit_version": ">=0.8.10.dev0"
       },
       "provides": {
-        "commands": 10,
+        "commands": 2,
         "hooks": 0
       },
       "tags": [
@@ -215,7 +215,7 @@
       "downloads": 0,
       "stars": 0,
       "created_at": "2026-05-14T00:00:00Z",
-      "updated_at": "2026-06-23T00:00:00Z"
+      "updated_at": "2026-05-15T00:00:00Z"
     },
     "architect-preview": {
       "name": "Architect Impact Previewer",
@@ -1001,47 +1001,13 @@
       "created_at": "2026-04-08T00:00:00Z",
       "updated_at": "2026-04-08T00:00:00Z"
     },
-    "discovery": {
-      "name": "Spec Kit Discovery Extension",
-      "id": "discovery",
-      "description": "Run technical discovery commands for feasibility, technology selection, scenario-specific technical decisions, legacy codebase assessment, implementation understanding, and proof-of-concept validation.",
-      "author": "bigsmartben",
-      "version": "0.2.0",
-      "download_url": "https://github.com/bigsmartben/spec-kit-discovery/archive/refs/tags/v0.2.0.zip",
-      "repository": "https://github.com/bigsmartben/spec-kit-discovery",
-      "homepage": "https://github.com/bigsmartben/spec-kit-discovery",
-      "documentation": "https://github.com/bigsmartben/spec-kit-discovery/blob/main/docs/usage.md",
-      "changelog": "https://github.com/bigsmartben/spec-kit-discovery/blob/main/CHANGELOG.md",
-      "license": "MIT",
-      "category": "process",
-      "effect": "read-write",
-      "requires": {
-        "speckit_version": ">=0.1.0"
-      },
-      "provides": {
-        "commands": 6,
-        "hooks": 0
-      },
-      "tags": [
-        "discovery",
-        "workflow",
-        "validation",
-        "feasibility",
-        "decision"
-      ],
-      "verified": false,
-      "downloads": 0,
-      "stars": 0,
-      "created_at": "2026-06-23T00:00:00Z",
-      "updated_at": "2026-06-23T00:00:00Z"
-    },
     "docguard": {
       "name": "DocGuard — CDD Enforcement",
       "id": "docguard",
       "description": "Canonical-Driven Development enforcement. Validates, scores, and traces project documentation with automated checks, AI-driven workflows, and spec-kit hooks. One pinned runtime dependency; pure Node.js otherwise.",
       "author": "raccioly",
-      "version": "0.28.0",
-      "download_url": "https://github.com/raccioly/docguard/releases/download/v0.28.0/spec-kit-docguard-v0.28.0.zip",
+      "version": "0.26.0",
+      "download_url": "https://github.com/raccioly/docguard/releases/download/v0.26.0/spec-kit-docguard-v0.26.0.zip",
       "repository": "https://github.com/raccioly/docguard",
       "homepage": "https://www.npmjs.com/package/docguard-cli",
       "documentation": "https://github.com/raccioly/docguard/blob/main/extensions/spec-kit-docguard/README.md",
@@ -1077,7 +1043,7 @@
       "downloads": 0,
       "stars": 0,
       "created_at": "2026-03-13T00:00:00Z",
-      "updated_at": "2026-06-23T00:00:00Z"
+      "updated_at": "2026-06-11T00:00:00Z"
     },
     "doctor": {
       "name": "Project Health Check",
@@ -1404,46 +1370,6 @@
       "created_at": "2026-06-16T00:00:00Z",
       "updated_at": "2026-06-16T00:00:00Z"
     },
-    "intake": {
-      "name": "Intake",
-      "id": "intake",
-      "description": "Normalize PRD, design, and test-case evidence into SDD-ready intake artifacts.",
-      "author": "bigsmartben",
-      "version": "0.1.2",
-      "download_url": "https://github.com/bigsmartben/spec-kit-intake/archive/refs/tags/v0.1.2.zip",
-      "repository": "https://github.com/bigsmartben/spec-kit-intake",
-      "homepage": "https://github.com/bigsmartben/spec-kit-intake",
-      "documentation": "https://github.com/bigsmartben/spec-kit-intake/blob/main/README.md",
-      "changelog": "https://github.com/bigsmartben/spec-kit-intake/blob/main/CHANGELOG.md",
-      "license": "MIT",
-      "category": "docs",
-      "effect": "read-write",
-      "requires": {
-        "speckit_version": ">=0.8.10.dev0",
-        "tools": [
-          {
-            "name": "figma-mcp",
-            "required": false
-          }
-        ]
-      },
-      "provides": {
-        "commands": 3,
-        "hooks": 1
-      },
-      "tags": [
-        "intake",
-        "sdd",
-        "requirements",
-        "validation",
-        "figma"
-      ],
-      "verified": false,
-      "downloads": 0,
-      "stars": 0,
-      "created_at": "2026-06-23T00:00:00Z",
-      "updated_at": "2026-06-23T00:00:00Z"
-    },
     "issue": {
       "name": "GitHub Issues Integration 2",
       "id": "issue",
@@ -1614,8 +1540,8 @@
       "id": "linear",
       "description": "Mirror spec-kit feature directories into Linear (filesystem → Linear, reconcile-based, unidirectional).",
       "author": "Ash Brener",
-      "version": "0.7.0",
-      "download_url": "https://github.com/ashbrener/spec-kit-linear-sync/archive/refs/tags/v0.7.0.zip",
+      "version": "0.6.0",
+      "download_url": "https://github.com/ashbrener/spec-kit-linear-sync/archive/refs/tags/v0.6.0.zip",
       "repository": "https://github.com/ashbrener/spec-kit-linear-sync",
       "homepage": "https://github.com/ashbrener/spec-kit-linear-sync",
       "documentation": "https://github.com/ashbrener/spec-kit-linear-sync/blob/main/README.md",
@@ -1642,7 +1568,7 @@
       "downloads": 0,
       "stars": 0,
       "created_at": "2026-06-01T00:00:00Z",
-      "updated_at": "2026-06-22T00:00:00Z"
+      "updated_at": "2026-06-17T00:00:00Z"
     },
     "loop": {
       "name": "Loop Engineering",
@@ -2421,12 +2347,12 @@
       "updated_at": "2026-03-18T00:00:00Z"
     },
     "preview": {
-      "name": "Spec Kit Preview",
+      "name": "Interactive HTML Preview",
       "id": "preview",
-      "description": "Generate evidence-backed low, mid, or high fidelity previews from Spec Kit artifacts as Markdown or self-contained HTML",
+      "description": "Generate self-contained interactive HTML prototypes from Spec Kit artifacts",
       "author": "bigsmartben",
-      "version": "1.1.0",
-      "download_url": "https://github.com/bigsmartben/spec-kit-preview/archive/refs/tags/v1.1.0.zip",
+      "version": "1.0.0",
+      "download_url": "https://github.com/bigsmartben/spec-kit-preview/archive/refs/tags/v1.0.0.zip",
       "repository": "https://github.com/bigsmartben/spec-kit-preview",
       "homepage": "https://github.com/bigsmartben/spec-kit-preview",
       "documentation": "https://github.com/bigsmartben/spec-kit-preview/blob/main/README.md",
@@ -2438,21 +2364,20 @@
         "speckit_version": ">=0.8.10.dev0"
       },
       "provides": {
-        "commands": 6,
+        "commands": 1,
         "hooks": 0
       },
       "tags": [
         "preview",
         "prototype",
         "html",
-        "markdown",
         "ux"
       ],
       "verified": false,
       "downloads": 0,
       "stars": 0,
       "created_at": "2026-05-15T00:00:00Z",
-      "updated_at": "2026-06-23T00:00:00Z"
+      "updated_at": "2026-05-15T00:00:00Z"
     },
     "product": {
       "name": "Product Spec Extension",
@@ -3616,44 +3541,6 @@
       "created_at": "2026-03-02T00:00:00Z",
       "updated_at": "2026-03-02T00:00:00Z"
     },
-    "tasks-to-project": {
-      "name": "Tasks to GitHub Project",
-      "id": "tasks-to-project",
-      "description": "Publish and synchronize Spec Kit tasks as cards on a GitHub Project (v2) kanban board, with priority and status sync between spec.md/tasks.md and the board.",
-      "author": "Alessandro Mancini",
-      "version": "0.2.0",
-      "download_url": "https://github.com/mancioshell/spec-kit-tasks-to-project/archive/refs/tags/v0.2.0.zip",
-      "repository": "https://github.com/mancioshell/spec-kit-tasks-to-project",
-      "homepage": "https://github.com/mancioshell/spec-kit-tasks-to-project",
-      "documentation": "https://github.com/mancioshell/spec-kit-tasks-to-project/blob/main/README.md",
-      "changelog": "https://github.com/mancioshell/spec-kit-tasks-to-project/blob/main/CHANGELOG.md",
-      "license": "MIT",
-      "category": "integration",
-      "effect": "read-write",
-      "requires": {
-        "speckit_version": ">=0.2.0",
-        "tools": [
-          { "name": "gh", "required": true },
-          { "name": "python3", "required": true }
-        ]
-      },
-      "provides": {
-        "commands": 2,
-        "hooks": 2
-      },
-      "tags": [
-        "github",
-        "project",
-        "kanban",
-        "automation",
-        "tasks"
-      ],
-      "verified": false,
-      "downloads": 0,
-      "stars": 0,
-      "created_at": "2026-06-22T00:00:00Z",
-      "updated_at": "2026-06-22T00:00:00Z"
-    },
     "team-assign": {
       "name": "Team Assign",
       "id": "team-assign",

integrations/catalog.json

@@ -1,6 +1,6 @@
 {
   "schema_version": "1.0",
-  "updated_at": "2026-06-22T00:00:00Z",
+  "updated_at": "2026-06-02T00:00:00Z",
   "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/integrations/catalog.json",
   "integrations": {
     "claude": {
@@ -102,15 +102,6 @@
       "repository": "https://github.com/github/spec-kit",
       "tags": ["cli"]
     },
-    "firebender": {
-      "id": "firebender",
-      "name": "Firebender",
-      "version": "1.0.0",
-      "description": "Firebender IDE integration for Android Studio / IntelliJ",
-      "author": "spec-kit-core",
-      "repository": "https://github.com/github/spec-kit",
-      "tags": ["ide"]
-    },
     "forge": {
       "id": "forge",
       "name": "Forge",
@@ -308,15 +299,6 @@
       "author": "spec-kit-core",
       "repository": "https://github.com/github/spec-kit",
       "tags": ["cli", "skills"]
-    },
-    "zcode": {
-      "id": "zcode",
-      "name": "ZCode",
-      "version": "1.0.0",
-      "description": "Z.AI ZCode CLI skills-based integration",
-      "author": "spec-kit-core",
-      "repository": "https://github.com/github/spec-kit",
-      "tags": ["cli", "skills", "z-ai"]
     }
   }
 }

presets/catalog.community.json

@@ -1,6 +1,6 @@
 {
   "schema_version": "1.0",
-  "updated_at": "2026-06-22T00:00:00Z",
+  "updated_at": "2026-06-16T00:00:00Z",
   "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/presets/catalog.community.json",
   "presets": {
     "a11y-governance": {
@@ -308,11 +308,11 @@
     "game-narrative-writing": {
       "name": "Game Narrative Writing",
       "id": "game-narrative-writing",
-      "version": "1.1.0",
-      "description": "Preset for game narrative design and interactive storytelling. It adapts the Spec-Driven Development workflow for game narratives: features become story mechanics, specs become narrative briefs, plans become story maps, and tasks become dialogue and scene-writing tasks. Supports branching narratives, player agency systems, state machines, and interactive dialogue trees.",
+      "version": "1.0.0",
+      "description": "Spec-Driven Development for interactive game-narrative pre-production in video games. Authors write in a portable generic format, Twine/Sugarcube (.twee) or Ink (.ink). Covers choice-IF, visual novels, and branching dialogue. Supports Tier 1 mechanic hooks (flag, counter, inventory, timer, trust, currency, npc_state, ending_condition), multi-ending design, series carry-over variable registry, and NPC-focused character architecture.",
       "author": "Andreas Daumann",
       "repository": "https://github.com/adaumann/speckit-preset-game-narrative-writing",
-      "download_url": "https://github.com/adaumann/speckit-preset-game-narrative-writing/releases/download/v1.1.0/v1.1.0-import.zip",
+      "download_url": "https://github.com/adaumann/speckit-preset-game-narrative-writing/archive/refs/tags/v1.0.0.zip",
       "homepage": "https://github.com/adaumann/speckit-preset-game-narrative-writing",
       "documentation": "https://github.com/adaumann/speckit-preset-game-narrative-writing/blob/main/game-narrative-writing/README.md",
       "license": "MIT",
@@ -320,19 +320,27 @@
         "speckit_version": ">=0.5.0"
       },
       "provides": {
-        "templates": 37,
-        "commands": 34,
-        "scripts": 5
+        "templates": 22,
+        "commands": 36,
+        "scripts": 2
       },
       "tags": [
+        "game-writing",
         "interactive-fiction",
-        "game-narrative",
-        "branching",
         "twine",
-        "ink"
+        "ink",
+        "renpy",
+        "point-and-click",
+        "branching-narrative",
+        "choice-if",
+        "visual-novel",
+        "mechanic-hooks",
+        "game-narrative",
+        "export",
+        "series"
       ],
       "created_at": "2026-05-05T08:00:00Z",
-      "updated_at": "2026-06-22T00:00:00Z"
+      "updated_at": "2026-05-05T08:00:00Z"
     },
     "isaqb-architecture-governance": {
       "name": "iSAQB Architecture Governance",
@@ -564,34 +572,6 @@
       "created_at": "2026-04-27T00:00:00Z",
       "updated_at": "2026-06-14T00:00:00Z"
     },
-    "sicario-core": {
-      "name": "SicarioSpec Core",
-      "id": "sicario-core",
-      "version": "0.4.0",
-      "description": "Evidence-first security operations governance that maps feature risk to controls, gates, evidence, owners, approval, and accepted-risk decisions.",
-      "author": "SicarioSpec Contributors",
-      "repository": "https://github.com/dfirs1car1o/sicario-spec",
-      "download_url": "https://github.com/dfirs1car1o/sicario-spec/releases/download/v0.4.0/sicario-core-0.4.0.zip",
-      "homepage": "https://github.com/dfirs1car1o/sicario-spec",
-      "documentation": "https://github.com/dfirs1car1o/sicario-spec/blob/main/README.md",
-      "license": "MIT",
-      "requires": {
-        "speckit_version": ">=0.9.0"
-      },
-      "provides": {
-        "templates": 5,
-        "commands": 0
-      },
-      "tags": [
-        "security",
-        "governance",
-        "security-ops",
-        "secure-by-default",
-        "evidence"
-      ],
-      "created_at": "2026-06-22T00:00:00Z",
-      "updated_at": "2026-06-22T00:00:00Z"
-    },
     "spec2cloud": {
       "name": "Spec2Cloud",
       "id": "spec2cloud",

pyproject.toml

@@ -1,8 +1,7 @@
 [project]
 name = "specify-cli"
-version = "0.11.6"
+version = "0.11.3"
 description = "Specify CLI, part of GitHub Spec Kit. A tool to bootstrap your projects for Spec-Driven Development (SDD)."
-readme = "README.md"
 requires-python = ">=3.11"
 dependencies = [
     "typer>=0.24.0",

spec-driven.md

@@ -318,12 +318,6 @@ No implementation code shall be written before:
 
 This completely inverts traditional AI code generation. Instead of generating code and hoping it works, the LLM must first generate comprehensive tests that define behavior, get them approved, and only then generate implementation.
 
-#### Articles IV, V & VI: Project-Defined Governance
-
-Articles IV, V, and VI are intentionally defined by each project's constitution rather than prescribed by Spec Kit. The constitution template provides placeholder slots and example concerns such as integration testing, observability, versioning, and breaking changes, but teams replace those placeholders with the principles that match their system and organization.
-
-This keeps the nine-article structure stable while allowing each project to encode its own non-negotiable standards. For one project, Article IV might govern security and access boundaries; for another, it might define integration test requirements. The `/speckit.analyze` command evaluates the concrete constitution in the project, so these project-defined articles participate in compliance checks just like the built-in examples.
-
 #### Articles VII & VIII: Simplicity and Anti-Abstraction
 
 These paired articles combat over-engineering:

src/specify_cli/_invocation_style.py

@@ -8,9 +8,6 @@ and ``specify init``'s next-steps output stay consistent.
 
 from __future__ import annotations
 
-# Agents that render $speckit-<name> (chat invocation) when in skills mode.
-DOLLAR_SKILLS_AGENTS: frozenset[str] = frozenset({"codex", "zcode"})
-
 # Agents that always render /speckit-<name>, regardless of ai_skills.
 ALWAYS_SLASH_AGENTS: frozenset[str] = frozenset({"devin", "trae", "zed"})
 
@@ -29,17 +26,6 @@ CONDITIONAL_SLASH_AGENTS: frozenset[str] = frozenset(
 )
 
 
-def is_dollar_skills_agent(selected_ai: str | None, ai_skills_enabled: bool) -> bool:
-    """Return ``True`` if *selected_ai* uses ``$speckit-<name>`` invocations.
-
-    Agents in `DOLLAR_SKILLS_AGENTS` (e.g. ``codex``, ``zcode``) render
-    ``$speckit-<name>`` chat invocations when installed in skills mode.
-    """
-    if not isinstance(selected_ai, str):
-        return False
-    return selected_ai in DOLLAR_SKILLS_AGENTS and ai_skills_enabled
-
-
 def is_slash_skills_agent(selected_ai: str | None, ai_skills_enabled: bool) -> bool:
     """Return ``True`` if *selected_ai* uses ``/speckit-<name>`` invocations.
 

src/specify_cli/_utils.py

@@ -9,7 +9,7 @@ import stat
 import subprocess
 import tempfile
 import yaml
-from pathlib import Path, PurePosixPath, PureWindowsPath
+from pathlib import Path
 from typing import Any
 from ._console import console
 
@@ -17,44 +17,6 @@ CLAUDE_LOCAL_PATH = Path.home() / ".claude" / "local" / "claude"
 CLAUDE_NPM_LOCAL_PATH = Path.home() / ".claude" / "local" / "node_modules" / ".bin" / "claude"
 
 
-def relative_extension_path_violation(value: Any) -> str | None:
-    """Return why ``value`` is unsafe as an extension-relative ``file`` path.
-
-    Single source of truth for the path-safety policy shared by
-    ``ExtensionManifest._validate()`` (manifest-load validation) and
-    ``CommandRegistrar.register_commands()`` (runtime guard), so the two cannot
-    drift. Returns a human-readable reason string when ``value`` is unsafe, or
-    ``None`` when it is an acceptable relative path within the extension
-    directory.
-
-    Policy: the value must be a non-empty string with no leading/trailing
-    whitespace, no absolute/anchored form, and no ``..`` traversal. The value is
-    evaluated under both POSIX and Windows path semantics because a native
-    ``Path`` is OS-dependent (a ``PurePosixPath`` on POSIX does not interpret
-    Windows drive/UNC forms, and ``C:foo`` is anchored but not ``is_absolute()``
-    yet resolves against the CWD on its drive). Rejecting any non-empty anchor
-    covers POSIX-absolute (``/abs``), Windows drive-relative (``C:foo``), Windows
-    absolute (``C:\\foo``), and UNC/rooted forms.
-    """
-    if not isinstance(value, str) or not value:
-        return "must be a non-empty string"
-    if value.strip() != value:
-        return "must not have leading or trailing whitespace"
-    posix_path = PurePosixPath(value)
-    win_path = PureWindowsPath(value)
-    if (
-        posix_path.anchor
-        or win_path.anchor
-        or ".." in posix_path.parts
-        or ".." in win_path.parts
-    ):
-        return (
-            "must be a relative path within the extension directory "
-            "(no absolute paths, drive letters, or '..' segments)"
-        )
-    return None
-
-
 def dump_frontmatter(data: dict[str, Any]) -> str:
     """Serialize skill/command frontmatter to a YAML string.
 

src/specify_cli/agents.py

@@ -16,7 +16,6 @@ from typing import Any, Dict, List, Optional
 import yaml
 
 from ._init_options import is_ai_skills_enabled, load_init_options
-from ._utils import relative_extension_path_violation
 
 
 def _build_agent_configs() -> dict[str, Any]:
@@ -357,33 +356,6 @@ class CommandRegistrar:
         }
         return skill_frontmatter
 
-    @staticmethod
-    def apply_argument_hint(
-        source_frontmatter: Dict[str, Any],
-        skill_frontmatter: Dict[str, Any],
-        integration: Optional[object] = None,
-    ) -> None:
-        """Carry a command's ``argument-hint`` into its generated skill frontmatter.
-
-        Copies ``argument-hint`` from the parsed source command frontmatter into
-        *skill_frontmatter* (mutated in place) before serialization, so that a
-        folded multi-line ``description`` cannot be split into invalid YAML. Only
-        integrations that support the field — those exposing
-        ``inject_argument_hint`` (currently Claude) — receive the key, leaving
-        :meth:`build_skill_frontmatter`'s shared shape unchanged for every other
-        agent. Built-in templates carry no ``argument-hint``, so this is a no-op
-        for the core path.
-        """
-        if not isinstance(source_frontmatter, dict) or not isinstance(skill_frontmatter, dict):
-            return
-        argument_hint = source_frontmatter.get("argument-hint")
-        if (
-            argument_hint
-            and integration is not None
-            and hasattr(integration, "inject_argument_hint")
-        ):
-            skill_frontmatter["argument-hint"] = str(argument_hint)
-
     @staticmethod
     def resolve_skill_placeholders(
         agent_name: str, frontmatter: dict, body: str, project_root: Path
@@ -427,34 +399,14 @@ class CommandRegistrar:
         body = body.replace("{ARGS}", "$ARGUMENTS").replace("__AGENT__", agent_name)
 
         # Resolve __CONTEXT_FILE__ from the agent-context extension config.
-        # When disabled, ignore stale context_files but keep the singular
-        # context_file value so generated commands still point at the agent
-        # context file managed before the extension was disabled.
-        from .integrations.base import IntegrationBase
-
+        # Fall back to init-options.json for projects that haven't migrated.
         # Local import: _load_agent_context_config lives in __init__.py which
         # imports agents.py, so a top-level import would be circular.
         from . import _load_agent_context_config
-
         ac_cfg = _load_agent_context_config(project_root)
-        extension_enabled = IntegrationBase._agent_context_extension_enabled(
-            project_root
-        )
-        if extension_enabled:
-            context_files = IntegrationBase._resolve_context_file_values(
-                project_root,
-                ac_cfg,
-                legacy_context_file=init_opts.get("context_file"),
-            )
-        else:
-            context_files = IntegrationBase._resolve_context_file_values(
-                project_root,
-                ac_cfg,
-                legacy_context_file=init_opts.get("context_file"),
-                include_context_files=False,
-                validate=False,
-            )
-        context_file = IntegrationBase._format_context_file_values(context_files)
+        context_file = ac_cfg.get("context_file") or ""
+        if not context_file:
+            context_file = init_opts.get("context_file") or ""
         body = body.replace("__CONTEXT_FILE__", context_file)
 
         return CommandRegistrar.rewrite_project_relative_paths(body)
@@ -588,42 +540,17 @@ class CommandRegistrar:
 
         registered = []
         is_cline_ext = agent_name == "cline" and source_id != "core"
-        source_root = source_dir.resolve()
 
         for cmd_info in commands:
             cmd_name = cmd_info["name"]
             aliases = cmd_info.get("aliases", [])
             cmd_file = cmd_info["file"]
 
-            # Guard against path traversal using the single shared policy in
-            # relative_extension_path_violation(), so the runtime guard stays
-            # aligned with ExtensionManifest._validate() and the skill/preset
-            # readers. Skip a malformed/unsafe ``file`` (non-string, empty,
-            # whitespace, absolute/anchored, or ``..`` traversal); the
-            # resolve()/relative_to() check below is the final containment
-            # backstop.
-            if relative_extension_path_violation(cmd_file):
-                continue
-            try:
-                source_file = (source_root / cmd_file).resolve()
-                source_file.relative_to(source_root)  # raises ValueError if outside
-            except (OSError, ValueError):
+            source_file = source_dir / cmd_file
+            if not source_file.exists():
                 continue
 
-            if not source_file.is_file():
-                continue
-
-            try:
-                content = source_file.read_text(encoding="utf-8")
-            except (OSError, UnicodeDecodeError) as exc:
-                import warnings
-
-                warnings.warn(
-                    f"Skipping command '{cmd_name}': could not read source file "
-                    f"'{cmd_file}' ({exc.__class__.__name__}: {exc}).",
-                    stacklevel=2,
-                )
-                continue
+            content = source_file.read_text(encoding="utf-8")
             frontmatter, body = self.parse_frontmatter(content)
 
             if frontmatter.get("strategy") == "wrap":

src/specify_cli/bundler/__init__.py

@@ -1,19 +0,0 @@
-"""Spec Kit bundler — importable, Typer-free logic for the ``specify bundle`` group.
-
-This package holds the models, services, and helpers behind the ``specify bundle``
-subcommand. It is intentionally free of any Typer/CLI imports so the orchestration
-logic can be unit-tested independently of the command surface (Constitution
-Principle I). The CLI wiring lives in ``specify_cli.commands.bundle``.
-"""
-from __future__ import annotations
-
-__all__ = ["BundlerError"]
-
-
-class BundlerError(Exception):
-    """Base class for all actionable bundler errors.
-
-    Carrying a clean message lets the CLI layer print a single, user-facing line
-    on stderr and exit non-zero without leaking a traceback (Constitution
-    Principle V — explicit, actionable errors).
-    """

src/specify_cli/bundler/commands_impl/__init__.py

@@ -1,2 +0,0 @@
-"""Bundler command-implementation helpers (kept thin; logic lives in services)."""
-from __future__ import annotations

src/specify_cli/bundler/commands_impl/catalog_config.py

@@ -1,191 +0,0 @@
-"""Persistence for the project-scoped catalog config (``.specify/bundle-catalogs.yml``).
-
-Only project scope is writable; built-in defaults are never deleted (they can be
-overridden by adding a same-id source). The on-disk shape mirrors
-``bundle-catalog.schema.md``: ``{schema_version, catalogs: [{id,url,priority,install_policy}]}``.
-"""
-from __future__ import annotations
-
-from pathlib import Path
-from urllib.parse import urlparse
-import re
-
-from .. import BundlerError
-from ..lib.yamlio import dump_yaml, ensure_within, load_yaml
-from ..models.catalog import (
-    CONFIG_FILENAME,
-    BUILTIN_DEFAULT_STACK,
-    CatalogSource,
-    InstallPolicy,
-    Scope,
-)
-
-CONFIG_SCHEMA_VERSION = "1.0"
-
-_BUILTIN_IDS = {raw["id"] for raw in BUILTIN_DEFAULT_STACK}
-
-# Windows absolute paths like ``C:\catalog.json`` parse with a single-letter
-# ``scheme`` under urlparse; treat them as local files rather than URLs.
-_WINDOWS_DRIVE_RE = re.compile(r"^[A-Za-z]:[\\/]")
-
-
-def _config_path(project_root: Path) -> Path:
-    return Path(project_root) / ".specify" / CONFIG_FILENAME
-
-
-def _read(project_root: Path) -> list[dict]:
-    # Confine the read (parity with the write path's within= guard): refuse to
-    # follow a symlinked or traversal-escaping .specify that resolves outside
-    # project_root.
-    path = ensure_within(project_root, _config_path(project_root))
-    if not path.exists():
-        return []
-    data = load_yaml(path)
-    if data is None:
-        return []
-    if not isinstance(data, dict):
-        raise BundlerError(
-            f"Malformed catalog config at {path}: expected a mapping at the top "
-            f"level, got {type(data).__name__}."
-        )
-    schema_version = data.get("schema_version")
-    if schema_version is not None and (
-        str(schema_version).strip().split(".")[0]
-        != CONFIG_SCHEMA_VERSION.split(".")[0]
-    ):
-        raise BundlerError(
-            f"Unsupported catalog config schema version "
-            f"'{str(schema_version).strip()}' at {path}; this Spec Kit "
-            f"understands version {CONFIG_SCHEMA_VERSION}. The file may have been "
-            "written by a newer version or is corrupt."
-        )
-    catalogs = data.get("catalogs")
-    if catalogs is None:
-        return []
-    if not isinstance(catalogs, list):
-        raise BundlerError(
-            f"Malformed catalog config at {path}: 'catalogs' must be a list, "
-            f"got {type(catalogs).__name__}."
-        )
-    for entry in catalogs:
-        if not isinstance(entry, dict):
-            raise BundlerError(
-                f"Malformed catalog config at {path}: each catalog entry must be "
-                f"a mapping, got {type(entry).__name__}."
-            )
-    return list(catalogs)
-
-
-def _write(project_root: Path, catalogs: list[dict]) -> None:
-    payload = {"schema_version": CONFIG_SCHEMA_VERSION, "catalogs": catalogs}
-    dump_yaml(_config_path(project_root), payload, within=project_root)
-
-
-def _slug(value: str) -> str:
-    # Lowercase so derived ids are deterministic and case-insensitive across
-    # platforms (e.g. 'Team-A.json' and 'team-a.json' yield the same id),
-    # keeping the case-sensitive duplicate check from admitting logical dupes.
-    return "".join(ch if ch.isalnum() else "-" for ch in value.lower()).strip("-")
-
-
-_REMOTE_SCHEMES = {"http", "https", "file", "builtin"}
-
-
-def _is_local_path(url: str) -> bool:
-    """True when *url* denotes a local filesystem path rather than a URL."""
-    if _WINDOWS_DRIVE_RE.match(url):
-        return True
-    scheme = urlparse(url).scheme.lower()
-    return scheme not in _REMOTE_SCHEMES
-
-
-def _canonicalize_url(url: str) -> str:
-    """Make local file paths absolute so config is independent of the caller's cwd.
-
-    Remote URLs (``http(s)://``, ``file://``, ``builtin://``) are returned
-    unchanged; only bare/relative local paths are resolved to an absolute path.
-    """
-    if _is_local_path(url):
-        return str(Path(url).expanduser().resolve())
-    return url
-
-
-def _derive_id(url: str) -> str:
-    parsed = urlparse(url)
-    if parsed.netloc:
-        # Use .hostname (not netloc.split(':')) so credentials, ports, and IPv6
-        # literals (e.g. https://[2001:db8::1]/x) are handled correctly. Use the
-        # full host (TLD included) so different domains sharing a second-level
-        # label (example.com vs example.net) don't collide. _slug() lowercases
-        # and turns separators into dashes, so 'Example.com' -> 'example-com'.
-        host = parsed.hostname or ""
-        path_stem = Path(parsed.path).stem if parsed.path else ""
-        parts = [p for p in (_slug(host), _slug(path_stem)) if p]
-        return "-".join(parts) or "catalog"
-    stem = Path(parsed.path or url).stem
-    return _slug(stem) or "catalog"
-
-
-def add_source(
-    project_root: Path,
-    url: str,
-    *,
-    policy: str,
-    priority: int,
-    source_id: str | None = None,
-) -> CatalogSource:
-    url = url.strip()
-    if not url:
-        raise BundlerError("A catalog url is required.")
-    parsed = urlparse(url)
-    if not (parsed.scheme or parsed.path):
-        raise BundlerError(f"Invalid catalog url: '{url}'.")
-    # Reject unsupported URL schemes (e.g. ssh://, ftp://) up front so they are
-    # never silently canonicalized as local filesystem paths. Local paths that
-    # merely contain a ':' but no '://' (e.g. Windows drives) are still allowed.
-    if "://" in url and parsed.scheme.lower() not in _REMOTE_SCHEMES:
-        raise BundlerError(
-            f"Unsupported catalog url scheme '{parsed.scheme}://' in '{url}'. "
-            "Use http(s)://, file://, builtin://, or a local path."
-        )
-
-    url = _canonicalize_url(url)
-    install_policy = InstallPolicy.parse(policy)
-    resolved_id = (source_id or _derive_id(url)).strip()
-
-    catalogs = _read(project_root)
-    for existing in catalogs:
-        if existing.get("id") == resolved_id or existing.get("url") == url:
-            raise BundlerError(
-                f"Catalog source '{resolved_id}' (or url) already exists in this project."
-            )
-
-    entry = {
-        "id": resolved_id,
-        "url": url,
-        "priority": int(priority),
-        "install_policy": install_policy.value,
-    }
-    catalogs.append(entry)
-    _write(project_root, catalogs)
-    return CatalogSource.from_dict(entry, Scope.PROJECT)
-
-
-def remove_source(project_root: Path, id_or_url: str) -> str:
-    target = id_or_url.strip()
-    if target in _BUILTIN_IDS:
-        raise BundlerError(
-            f"'{target}' is a built-in default source and cannot be deleted "
-            "(add a same-id source to override it instead)."
-        )
-
-    catalogs = _read(project_root)
-    remaining = [
-        c for c in catalogs if c.get("id") != target and c.get("url") != target
-    ]
-    if len(remaining) == len(catalogs):
-        raise BundlerError(
-            f"No project-scoped catalog source matching '{target}' was found."
-        )
-    _write(project_root, remaining)
-    return target

src/specify_cli/bundler/lib/__init__.py

@@ -1,2 +0,0 @@
-"""Shared, dependency-light helpers for the bundler (YAML/JSON IO, versioning, project detection)."""
-from __future__ import annotations

src/specify_cli/bundler/lib/project.py

@@ -1,62 +0,0 @@
-"""Spec Kit project detection and active-integration resolution."""
-from __future__ import annotations
-
-from pathlib import Path
-
-from .. import BundlerError
-from .yamlio import ensure_within, load_json
-
-DEFAULT_INTEGRATION = "copilot"
-
-
-def find_project_root(start: Path | None = None) -> Path | None:
-    """Return the nearest ancestor (incl. *start*) containing a ``.specify/`` dir, or None.
-
-    A symlinked ``.specify`` is not accepted as a project root: following it
-    could read/write outside the intended tree, and other CLI surfaces refuse
-    it for the same reason.
-    """
-    current = Path(start or Path.cwd()).resolve()
-    for candidate in (current, *current.parents):
-        marker = candidate / ".specify"
-        if marker.is_dir() and not marker.is_symlink():
-            return candidate
-    return None
-
-
-def require_project_root(start: Path | None = None) -> Path:
-    """Return the Spec Kit project root or raise an actionable error."""
-    root = find_project_root(start)
-    if root is None:
-        raise BundlerError(
-            "Not a Spec Kit project (no .specify/ directory). "
-            "Run 'specify bundle init' or 'specify init' first."
-        )
-    return root
-
-
-def active_integration(project_root: Path) -> str | None:
-    """Return the project's active integration id, if recorded.
-
-    Spec Kit records the chosen integration in ``.specify/integration.json``
-    during init. Returns None when it cannot be determined (e.g. agnostic).
-    """
-    marker = Path(project_root) / ".specify" / "integration.json"
-    # Confine the read (mirrors records/catalog IO): refuse to follow a
-    # symlinked or traversal-escaping .specify that resolves outside
-    # project_root. An escape is treated as "not determinable".
-    try:
-        marker = ensure_within(project_root, marker)
-    except BundlerError:
-        return None
-    if not marker.exists():
-        return None
-    try:
-        data = load_json(marker)
-    except BundlerError:
-        return None
-    if isinstance(data, dict):
-        value = data.get("integration") or data.get("id") or data.get("active")
-        if isinstance(value, str) and value:
-            return value
-    return None

src/specify_cli/bundler/lib/versioning.py

@@ -1,99 +0,0 @@
-"""SemVer parsing and constraint evaluation, built on ``packaging`` (already a dependency)."""
-from __future__ import annotations
-
-import re
-
-from packaging.specifiers import InvalidSpecifier, SpecifierSet
-from packaging.version import InvalidVersion, Version
-
-from .. import BundlerError
-
-# Common SemVer prerelease spellings (``1.2.3-rc1``, ``1.2.3-alpha.1``) that
-# PEP 440 / ``packaging`` rejects verbatim. Normalized to PEP 440 before
-# parsing so prerelease versions validate consistently (mirrors
-# ``specify_cli._version._normalize_tag``).
-_PRERELEASE_PATTERN = re.compile(
-    r"^([0-9]+\.[0-9]+\.[0-9]+)[-.]?(alpha|beta|a|b|rc)[-.]?([0-9]+)(.*)$",
-    flags=re.IGNORECASE,
-)
-
-
-def _normalize_semver(value: str) -> str:
-    """Normalize common SemVer prerelease spellings into PEP 440 text."""
-    text = str(value)
-    normalized = text[1:] if text[:1] in ("v", "V") else text
-    match = _PRERELEASE_PATTERN.match(normalized)
-    if match is None:
-        return normalized
-    base, label, number, rest = match.groups()
-    pep440_label = {"alpha": "a", "beta": "b"}.get(label.lower(), label.lower())
-    return f"{base}{pep440_label}{number}{rest}"
-
-
-def parse_version(value: str) -> Version:
-    """Parse a version string into a comparable :class:`Version`."""
-    try:
-        return Version(_normalize_semver(value))
-    except InvalidVersion as exc:
-        raise BundlerError(f"Invalid version '{value}': {exc}") from exc
-
-
-_SPECIFIER_CLAUSE = re.compile(r"^\s*(===|==|~=|!=|<=|>=|<|>)?\s*(.*?)\s*$")
-
-
-def _normalize_constraint(value: str) -> str:
-    """Normalize the version portion of each clause in a constraint string.
-
-    ``packaging.SpecifierSet`` rejects SemVer prerelease spellings like
-    ``>=1.2.3-rc1`` verbatim, even though :func:`parse_version` accepts the same
-    spelling for installed versions. Normalize each comma-separated clause's
-    version so prerelease handling is consistent across versions and constraints.
-    """
-    clauses = []
-    for raw in str(value).split(","):
-        if not raw.strip():
-            continue
-        match = _SPECIFIER_CLAUSE.match(raw)
-        operator, version = match.groups()
-        clauses.append(f"{operator or ''}{_normalize_semver(version)}")
-    return ",".join(clauses)
-
-
-def parse_constraint(value: str) -> SpecifierSet:
-    """Parse a version constraint such as ``>=0.9.0`` into a :class:`SpecifierSet`."""
-    try:
-        return SpecifierSet(_normalize_constraint(value))
-    except InvalidSpecifier as exc:
-        raise BundlerError(
-            f"Invalid version constraint '{value}': {exc}"
-        ) from exc
-
-
-def satisfies(installed: str, constraint: str) -> bool:
-    """Return True if *installed* satisfies *constraint* (e.g. ``">=0.9.0"``).
-
-    Pre-releases are allowed so a dev/pre build of Spec Kit still counts.
-    """
-    spec = parse_constraint(constraint)
-    version = parse_version(installed)
-    return spec.contains(version, prereleases=True)
-
-
-_SEMVER_RE = re.compile(
-    r"^(?:0|[1-9]\d*)\.(?:0|[1-9]\d*)\.(?:0|[1-9]\d*)"
-    r"(?:-(?:(?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*)"
-    r"(?:\.(?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?"
-    r"(?:\+(?:[0-9a-zA-Z-]+(?:\.[0-9a-zA-Z-]+)*))?$"
-)
-
-
-def is_semver(value: str) -> bool:
-    """Return True only for a full ``MAJOR.MINOR.PATCH`` SemVer string.
-
-    Stricter than ``packaging.version.Version``, which also accepts partial
-    versions like ``"1"`` or ``"1.0"``. An optional leading ``v`` or ``V`` is
-    tolerated (mirrors ``_normalize_semver``).
-    """
-    text = str(value)
-    core = text[1:] if text[:1] in ("v", "V") else text
-    return bool(_SEMVER_RE.match(core))

src/specify_cli/bundler/lib/yamlio.py

@@ -1,119 +0,0 @@
-"""YAML/JSON read-write helpers with path confinement (Constitution Principles IV & V).
-
-All reads/writes go through these functions so that:
-- IO failures degrade into actionable :class:`~specify_cli.bundler.BundlerError`s
-  rather than raw tracebacks, and
-- every path can be confined to an allowed root via :func:`ensure_within`.
-"""
-from __future__ import annotations
-
-import json
-import os
-import re
-from pathlib import Path, PurePosixPath
-from typing import Any
-
-import yaml
-
-from .. import BundlerError
-
-
-def ensure_within(root: Path, candidate: Path) -> Path:
-    """Resolve *candidate* and guarantee it stays within *root*.
-
-    Refuses path-traversal payloads and symlink escapes. Returns the resolved,
-    confined path. Raises :class:`BundlerError` if the path escapes *root*.
-    """
-    root_resolved = Path(root).resolve()
-    # Resolve symlinks so a symlinked component cannot point outside the root.
-    candidate_resolved = Path(candidate).resolve()
-    try:
-        candidate_resolved.relative_to(root_resolved)
-    except ValueError as exc:
-        raise BundlerError(
-            f"Refusing path '{candidate}' — it escapes the allowed root '{root}'."
-        ) from exc
-    return candidate_resolved
-
-
-def load_yaml(path: Path) -> Any:
-    """Parse a YAML file, returning ``{}`` for an empty document."""
-    path = Path(path)
-    if not path.exists():
-        raise BundlerError(f"File not found: {path}")
-    try:
-        with path.open("r", encoding="utf-8") as handle:
-            return yaml.safe_load(handle) or {}
-    except yaml.YAMLError as exc:
-        raise BundlerError(f"Invalid YAML in {path}: {exc}") from exc
-    except OSError as exc:
-        raise BundlerError(f"Could not read {path}: {exc}") from exc
-
-
-def dump_yaml(path: Path, data: Any, *, within: Path | None = None) -> Path:
-    """Write *data* as YAML to *path* (optionally confined to *within*)."""
-    path = Path(path)
-    if within is not None:
-        path = ensure_within(within, path)
-    try:
-        path.parent.mkdir(parents=True, exist_ok=True)
-        with path.open("w", encoding="utf-8") as handle:
-            yaml.safe_dump(data, handle, sort_keys=False, default_flow_style=False)
-    except OSError as exc:
-        raise BundlerError(f"Could not write {path}: {exc}") from exc
-    return path
-
-
-def load_json(path: Path) -> Any:
-    """Parse a JSON file."""
-    path = Path(path)
-    if not path.exists():
-        raise BundlerError(f"File not found: {path}")
-    try:
-        with path.open("r", encoding="utf-8") as handle:
-            return json.load(handle)
-    except json.JSONDecodeError as exc:
-        raise BundlerError(f"Invalid JSON in {path}: {exc}") from exc
-    except OSError as exc:
-        raise BundlerError(f"Could not read {path}: {exc}") from exc
-
-
-def loads_json(text: str, *, origin: str = "<string>") -> Any:
-    """Parse JSON from a string (used for catalog payloads fetched as text)."""
-    try:
-        return json.loads(text)
-    except json.JSONDecodeError as exc:
-        raise BundlerError(f"Invalid JSON from {origin}: {exc}") from exc
-
-
-def dump_json(path: Path, data: Any, *, within: Path | None = None) -> Path:
-    """Write *data* as pretty JSON to *path* (optionally confined to *within*)."""
-    path = Path(path)
-    if within is not None:
-        path = ensure_within(within, path)
-    try:
-        path.parent.mkdir(parents=True, exist_ok=True)
-        with path.open("w", encoding="utf-8") as handle:
-            json.dump(data, handle, indent=2, sort_keys=False)
-            handle.write("\n")
-    except OSError as exc:
-        raise BundlerError(f"Could not write {path}: {exc}") from exc
-    return path
-
-
-def is_safe_relpath(rel: str) -> bool:
-    """Return True if *rel* is a project-relative path with no traversal/absolute parts.
-
-    Platform-independent: a POSIX-absolute path (``/abs``) or a Windows
-    drive-absolute path (``C:\\x``) is rejected on every OS, since these strings
-    can appear in untrusted catalog/manifest data regardless of the host.
-    """
-    if not rel:
-        return False
-    normalized = rel.replace("\\", "/")
-    if os.path.isabs(rel) or normalized.startswith("/"):
-        return False
-    if re.match(r"^[A-Za-z]:", normalized):  # Windows drive-absolute (C:/...)
-        return False
-    parts = PurePosixPath(normalized).parts
-    return ".." not in parts

src/specify_cli/bundler/models/__init__.py

@@ -1,2 +0,0 @@
-"""Bundler data models (manifest, catalog, records)."""
-from __future__ import annotations

src/specify_cli/bundler/models/catalog.py

@@ -1,258 +0,0 @@
-"""Catalog models: source stack (priority + install policy) and catalog entries.
-
-Mirrors ``contracts/bundle-catalog.schema.md``. The stack precedence is
-project > user > built-in; install is permitted only from ``install-allowed``
-sources.
-"""
-from __future__ import annotations
-
-from dataclasses import dataclass, field
-from enum import Enum
-from pathlib import Path
-from typing import Any
-
-from .. import BundlerError
-from ..lib.yamlio import ensure_within, load_yaml
-
-CONFIG_FILENAME = "bundle-catalogs.yml"
-
-
-class InstallPolicy(str, Enum):
-    INSTALL_ALLOWED = "install-allowed"
-    DISCOVERY_ONLY = "discovery-only"
-
-    @classmethod
-    def parse(cls, value: Any) -> "InstallPolicy":
-        text = str(value or "").strip()
-        for policy in cls:
-            if policy.value == text:
-                return policy
-        raise BundlerError(
-            f"Invalid install_policy '{value}' "
-            f"(must be one of {[p.value for p in cls]})."
-        )
-
-
-class Scope(str, Enum):
-    PROJECT = "project"
-    USER = "user"
-    BUILTIN = "built-in"
-
-
-# Built-in default stack (used when no project/user config overrides it).
-BUILTIN_DEFAULT_STACK: tuple[dict[str, Any], ...] = (
-    {"id": "default", "url": "builtin://default", "priority": 1,
-     "install_policy": InstallPolicy.INSTALL_ALLOWED.value},
-    {"id": "community", "url": "builtin://community", "priority": 2,
-     "install_policy": InstallPolicy.DISCOVERY_ONLY.value},
-)
-
-
-@dataclass(frozen=True)
-class CatalogSource:
-    id: str
-    url: str
-    priority: int
-    install_policy: InstallPolicy
-    scope: Scope = Scope.PROJECT
-
-    @property
-    def install_allowed(self) -> bool:
-        return self.install_policy is InstallPolicy.INSTALL_ALLOWED
-
-    @classmethod
-    def from_dict(cls, data: Any, scope: Scope) -> "CatalogSource":
-        if not isinstance(data, dict):
-            raise BundlerError("Each catalog source must be a mapping.")
-        source_id = str(data.get("id", "")).strip()
-        url = str(data.get("url", "")).strip()
-        if not source_id:
-            raise BundlerError("A catalog source is missing its 'id'.")
-        if not url:
-            raise BundlerError(f"Catalog source '{source_id}' is missing its 'url'.")
-        priority = data.get("priority")
-        if priority is None:
-            raise BundlerError(f"Catalog source '{source_id}' is missing its 'priority'.")
-        if isinstance(priority, bool) or not isinstance(priority, (int, str)):
-            raise BundlerError(
-                f"Catalog source '{source_id}' has a non-integer priority: {priority!r}."
-            )
-        try:
-            priority_int = int(priority)
-        except (TypeError, ValueError):
-            raise BundlerError(
-                f"Catalog source '{source_id}' has a non-integer priority: {priority!r}."
-            ) from None
-        return cls(
-            id=source_id,
-            url=url,
-            priority=priority_int,
-            install_policy=InstallPolicy.parse(data.get("install_policy")),
-            scope=scope,
-        )
-
-    def to_dict(self) -> dict[str, Any]:
-        return {
-            "id": self.id,
-            "url": self.url,
-            "priority": self.priority,
-            "install_policy": self.install_policy.value,
-        }
-
-
-def _parse_tags(value: Any, entry_id: str) -> tuple[str, ...]:
-    """Coerce a catalog entry's ``tags`` into a tuple of strings.
-
-    Catalogs are untrusted input: a bare string would otherwise be iterated
-    character-by-character, so reject anything that is not a list/tuple.
-    """
-    if value is None:
-        return ()
-    if isinstance(value, (str, bytes)) or not isinstance(value, (list, tuple)):
-        raise BundlerError(
-            f"Catalog entry '{entry_id}': 'tags' must be a list of strings."
-        )
-    return tuple(str(t) for t in value)
-
-
-def _parse_verified(value: Any, entry_id: str) -> bool:
-    """Validate a catalog entry's ``verified`` flag is a real boolean.
-
-    ``bool("false")`` is truthy, so coercing arbitrary strings would silently
-    mark untrusted entries as verified; require an actual boolean instead.
-    """
-    if isinstance(value, bool):
-        return value
-    raise BundlerError(
-        f"Catalog entry '{entry_id}': 'verified' must be a boolean (true/false)."
-    )
-
-
-@dataclass(frozen=True)
-class CatalogEntry:
-    id: str
-    name: str
-    version: str
-    role: str
-    description: str
-    author: str
-    license: str
-    download_url: str
-    requires_speckit_version: str
-    provides: dict[str, int] = field(default_factory=dict)
-    repository: str | None = None
-    tags: tuple[str, ...] = ()
-    verified: bool = False
-    # Resolution provenance (filled in by the catalog stack at lookup time):
-    source_id: str | None = None
-    source_policy: InstallPolicy | None = None
-
-    @classmethod
-    def from_dict(cls, data: Any) -> "CatalogEntry":
-        if not isinstance(data, dict):
-            raise BundlerError("Each catalog entry must be a mapping.")
-        entry_id = str(data.get("id", "")).strip()
-        requires = data.get("requires") or {}
-        if not isinstance(requires, dict):
-            raise BundlerError(
-                f"Catalog entry '{entry_id or '<unknown>'}': 'requires' must be a "
-                "mapping when present."
-            )
-        provides_raw = data.get("provides") or {}
-        if not isinstance(provides_raw, dict):
-            raise BundlerError(
-                f"Catalog entry '{entry_id or '<unknown>'}': 'provides' must be a "
-                "mapping when present."
-            )
-        return cls(
-            id=entry_id,
-            name=str(data.get("name", "")).strip(),
-            version=str(data.get("version", "")).strip(),
-            role=str(data.get("role", "")).strip(),
-            description=str(data.get("description", "")).strip(),
-            author=str(data.get("author", "")).strip(),
-            license=str(data.get("license", "")).strip(),
-            download_url=str(data.get("download_url", "")).strip(),
-            requires_speckit_version=str(requires.get("speckit_version", "")).strip(),
-            provides=dict(provides_raw),
-            repository=(str(data["repository"]) if data.get("repository") else None),
-            tags=_parse_tags(data.get("tags"), entry_id),
-            verified=_parse_verified(data.get("verified", False), entry_id),
-        )
-
-    def with_provenance(self, source: CatalogSource) -> "CatalogEntry":
-        return CatalogEntry(
-            id=self.id, name=self.name, version=self.version, role=self.role,
-            description=self.description, author=self.author, license=self.license,
-            download_url=self.download_url,
-            requires_speckit_version=self.requires_speckit_version,
-            provides=self.provides, repository=self.repository, tags=self.tags,
-            verified=self.verified, source_id=source.id,
-            source_policy=source.install_policy,
-        )
-
-
-def load_catalog_payload(data: Any) -> dict[str, CatalogEntry]:
-    """Parse a catalog JSON payload into ``{bundle_id: CatalogEntry}``."""
-    if not isinstance(data, dict):
-        raise BundlerError("Catalog payload must be a JSON object.")
-    bundles_raw = data.get("bundles")
-    if not isinstance(bundles_raw, dict):
-        raise BundlerError("Catalog payload is missing a 'bundles' object.")
-    entries: dict[str, CatalogEntry] = {}
-    for bundle_id, entry_raw in bundles_raw.items():
-        key = str(bundle_id)
-        entry = CatalogEntry.from_dict(entry_raw)
-        # The enclosing key is the authoritative bundle id used by
-        # search/resolve/install. Reject entries whose own ``id`` is missing or
-        # disagrees with the key, so a malformed or malicious catalog can't list
-        # an id that resolves to a different (or no) bundle.
-        if not entry.id:
-            raise BundlerError(
-                f"Catalog entry for '{key}' is missing its 'id' field."
-            )
-        if entry.id != key:
-            raise BundlerError(
-                f"Catalog entry id mismatch: key '{key}' != entry id "
-                f"'{entry.id}'."
-            )
-        entries[key] = entry
-    return entries
-
-
-def load_source_stack(project_root: Path, user_config_dir: Path | None = None) -> list[CatalogSource]:
-    """Build the effective, priority-sorted source stack (project > user > built-in).
-
-    A source id present at a higher-precedence scope overrides the same id at a
-    lower scope. The built-in default stack is always the fallback.
-    """
-    by_id: dict[str, CatalogSource] = {}
-
-    # Lowest precedence first; later writes override earlier ones for the same id.
-    for raw in BUILTIN_DEFAULT_STACK:
-        src = CatalogSource.from_dict(raw, Scope.BUILTIN)
-        by_id[src.id] = src
-
-    if user_config_dir is not None:
-        _merge_config(by_id, Path(user_config_dir) / CONFIG_FILENAME, Scope.USER)
-
-    # Confine the project-scoped read: refuse a symlinked .specify/ that
-    # resolves outside the project root (consistent with other guarded reads).
-    project_config = Path(project_root) / ".specify" / CONFIG_FILENAME
-    if project_config.exists():
-        ensure_within(project_root, project_config)
-    _merge_config(by_id, project_config, Scope.PROJECT)
-
-    return sorted(by_id.values(), key=lambda s: (s.priority, s.id))
-
-
-def _merge_config(by_id: dict[str, CatalogSource], config_path: Path, scope: Scope) -> None:
-    if not config_path.exists():
-        return
-    data = load_yaml(config_path)
-    catalogs = data.get("catalogs") if isinstance(data, dict) else None
-    if not catalogs:
-        return
-    for raw in catalogs:
-        src = CatalogSource.from_dict(raw, scope)
-        by_id[src.id] = src

src/specify_cli/bundler/models/manifest.py

@@ -1,263 +0,0 @@
-"""Bundle manifest model (``bundle.yml``) — parsing and structural normalization.
-
-Mirrors ``contracts/bundle-manifest.schema.md``. Structural validation (shape,
-required fields, enum/semver checks) lives here; *reference* resolution against a
-catalog stack lives in the validator/resolver services.
-"""
-from __future__ import annotations
-
-import re
-from dataclasses import dataclass, field
-from pathlib import Path
-from typing import Any
-
-from .. import BundlerError
-from ..lib.versioning import is_semver
-from ..lib.yamlio import load_yaml
-
-SUPPORTED_SCHEMA_VERSIONS = {"1.0"}
-PRESET_STRATEGIES = {"replace", "prepend", "append", "wrap"}
-
-COMPONENT_KINDS = ("extensions", "presets", "steps", "workflows")
-
-# A bundle id must be a filesystem-safe slug: it is interpolated into artifact
-# filenames (e.g. ``<id>-<version>.zip``), so path separators or traversal
-# segments must never appear.
-_SAFE_BUNDLE_ID = re.compile(r"^[a-z0-9](?:[a-z0-9._-]*[a-z0-9])?$")
-
-
-@dataclass(frozen=True)
-class ComponentRef:
-    """A pointer to an existing Spec Kit primitive a bundle installs."""
-
-    kind: str  # one of COMPONENT_KINDS (singularized concept), stored plural-of-origin
-    id: str
-    version: str | None = None
-    source: str | None = None
-    priority: int | None = None  # presets only
-    strategy: str | None = None  # presets only
-
-    def label(self) -> str:
-        return f"{self.kind[:-1]}:{self.id}@{self.version or 'unpinned'}"
-
-
-@dataclass(frozen=True)
-class IntegrationRef:
-    id: str
-
-
-@dataclass(frozen=True)
-class Requires:
-    speckit_version: str
-    tools: tuple[str, ...] = ()
-    mcp: tuple[str, ...] = ()
-
-
-@dataclass(frozen=True)
-class BundleMeta:
-    id: str
-    name: str
-    version: str
-    role: str
-    description: str
-    author: str
-    license: str
-
-
-@dataclass
-class BundleManifest:
-    schema_version: str
-    bundle: BundleMeta
-    requires: Requires
-    integration: IntegrationRef | None = None
-    extensions: list[ComponentRef] = field(default_factory=list)
-    presets: list[ComponentRef] = field(default_factory=list)
-    steps: list[ComponentRef] = field(default_factory=list)
-    workflows: list[ComponentRef] = field(default_factory=list)
-    tags: tuple[str, ...] = ()
-    source_path: Path | None = None
-
-    @property
-    def components(self) -> list[ComponentRef]:
-        """All installable component references in deterministic order."""
-        return [*self.extensions, *self.presets, *self.steps, *self.workflows]
-
-    # -- construction ---------------------------------------------------------
-
-    @classmethod
-    def from_file(cls, path: Path) -> "BundleManifest":
-        data = load_yaml(path)
-        manifest = cls.from_dict(data)
-        manifest.source_path = Path(path)
-        return manifest
-
-    @classmethod
-    def from_dict(cls, data: Any) -> "BundleManifest":
-        if not isinstance(data, dict):
-            raise BundlerError("Manifest must be a YAML mapping at the top level.")
-
-        schema_version = str(data.get("schema_version", "")).strip()
-
-        bundle_raw = data.get("bundle")
-        if not isinstance(bundle_raw, dict):
-            raise BundlerError("Manifest is missing the required 'bundle' mapping.")
-        meta = BundleMeta(
-            id=str(bundle_raw.get("id", "")).strip(),
-            name=str(bundle_raw.get("name", "")).strip(),
-            version=str(bundle_raw.get("version", "")).strip(),
-            role=str(bundle_raw.get("role", "")).strip(),
-            description=str(bundle_raw.get("description", "")).strip(),
-            author=str(bundle_raw.get("author", "")).strip(),
-            license=str(bundle_raw.get("license", "")).strip(),
-        )
-
-        requires_raw = data.get("requires") or {}
-        if not isinstance(requires_raw, dict):
-            raise BundlerError("'requires' must be a mapping when present.")
-        requires = Requires(
-            speckit_version=str(requires_raw.get("speckit_version", "")).strip(),
-            tools=_parse_str_list(requires_raw.get("tools"), "requires.tools"),
-            mcp=_parse_str_list(requires_raw.get("mcp"), "requires.mcp"),
-        )
-
-        integration = None
-        integration_raw = data.get("integration")
-        if isinstance(integration_raw, dict) and integration_raw.get("id"):
-            integration = IntegrationRef(id=str(integration_raw["id"]).strip())
-
-        provides = data.get("provides") or {}
-        if not isinstance(provides, dict):
-            raise BundlerError("'provides' must be a mapping when present.")
-
-        tags_raw = data.get("tags")
-        if tags_raw is None:
-            tags_raw = []
-        else:
-            tags_raw = _parse_str_list(tags_raw, "tags")
-
-        manifest = cls(
-            schema_version=schema_version,
-            bundle=meta,
-            requires=requires,
-            integration=integration,
-            extensions=_parse_refs("extensions", provides.get("extensions")),
-            presets=_parse_refs("presets", provides.get("presets")),
-            steps=_parse_refs("steps", provides.get("steps")),
-            workflows=_parse_refs("workflows", provides.get("workflows")),
-            tags=tuple(str(t) for t in tags_raw),
-        )
-        return manifest
-
-    # -- structural validation ------------------------------------------------
-
-    def structural_errors(self) -> list[str]:
-        """Return a list of human-readable structural problems (empty == valid)."""
-        errors: list[str] = []
-
-        if self.schema_version not in SUPPORTED_SCHEMA_VERSIONS:
-            errors.append(
-                f"schema_version '{self.schema_version or '<missing>'}' is not supported "
-                f"(supported: {sorted(SUPPORTED_SCHEMA_VERSIONS)})."
-            )
-
-        required = {
-            "bundle.id": self.bundle.id,
-            "bundle.name": self.bundle.name,
-            "bundle.version": self.bundle.version,
-            "bundle.role": self.bundle.role,
-            "bundle.description": self.bundle.description,
-            "bundle.author": self.bundle.author,
-            "bundle.license": self.bundle.license,
-            "requires.speckit_version": self.requires.speckit_version,
-        }
-        for field_path, value in required.items():
-            if not value:
-                errors.append(f"Missing required field: {field_path}.")
-
-        if self.bundle.version and not is_semver(self.bundle.version):
-            errors.append(f"bundle.version '{self.bundle.version}' is not valid semver.")
-
-        if self.bundle.id and not _SAFE_BUNDLE_ID.match(self.bundle.id):
-            errors.append(
-                f"bundle.id '{self.bundle.id}' must be a slug "
-                "(lowercase letters, digits, '.', '_', '-'; no path separators)."
-            )
-
-        for ref in self.components:
-            if not ref.id:
-                errors.append(f"A {ref.kind[:-1]} entry is missing its 'id'.")
-            if ref.kind != "steps" and not ref.version:
-                errors.append(
-                    f"{ref.kind[:-1]} '{ref.id or '<unknown>'}' must be pinned to a 'version'."
-                )
-            if ref.version and not is_semver(ref.version):
-                errors.append(
-                    f"{ref.kind[:-1]} '{ref.id}' has invalid version '{ref.version}'."
-                )
-
-        for ref in self.presets:
-            if ref.priority is None:
-                errors.append(f"preset '{ref.id}' must declare an integer 'priority'.")
-            if ref.strategy is None or ref.strategy not in PRESET_STRATEGIES:
-                errors.append(
-                    f"preset '{ref.id}' has invalid strategy '{ref.strategy}' "
-                    f"(must be one of {sorted(PRESET_STRATEGIES)})."
-                )
-
-        return errors
-
-    def is_agnostic(self) -> bool:
-        """True when the bundle declares no integration (inherits the active one)."""
-        return self.integration is None
-
-
-def _parse_str_list(raw: Any, field_name: str) -> tuple[str, ...]:
-    """Coerce a manifest list-of-strings field into a tuple of strings.
-
-    Rejects a bare string/bytes (which would otherwise be iterated
-    character-by-character) and any non-list/tuple, matching the manifest
-    contract (``string[]``).
-    """
-    if raw is None:
-        return ()
-    if isinstance(raw, (str, bytes)) or not isinstance(raw, (list, tuple)):
-        raise BundlerError(f"'{field_name}' must be a list of strings when present.")
-    return tuple(str(item) for item in raw)
-
-
-def _parse_refs(kind: str, raw: Any) -> list[ComponentRef]:
-    if raw is None:
-        return []
-    if not isinstance(raw, list):
-        raise BundlerError(f"provides.{kind} must be a list when present.")
-    refs: list[ComponentRef] = []
-    for item in raw:
-        if not isinstance(item, dict):
-            raise BundlerError(f"Each provides.{kind} entry must be a mapping.")
-        priority = _parse_priority(kind, item.get("priority"))
-        refs.append(
-            ComponentRef(
-                kind=kind,
-                id=str(item.get("id", "")).strip(),
-                version=(str(item["version"]).strip() if item.get("version") else None),
-                source=(str(item["source"]).strip() if item.get("source") else None),
-                priority=priority,
-                strategy=(str(item["strategy"]).strip() if item.get("strategy") else None),
-            )
-        )
-    return refs
-
-
-def _parse_priority(kind: str, raw: Any) -> int | None:
-    if raw is None:
-        return None
-    if isinstance(raw, bool) or not isinstance(raw, (int, str)):
-        raise BundlerError(
-            f"provides.{kind} priority must be an integer, got {raw!r}."
-        )
-    try:
-        return int(raw)
-    except (TypeError, ValueError):
-        raise BundlerError(
-            f"provides.{kind} priority must be an integer, got {raw!r}."
-        ) from None

src/specify_cli/bundler/models/records.py

@@ -1,229 +0,0 @@
-"""Installed-bundle records — provenance for precise list/remove/update.
-
-Records are stored as JSON at ``.specify/bundle-records.json``. Each record
-captures exactly which components a bundle contributed so removal touches only
-that bundle's components and never collateral (FR-022, SC-004).
-"""
-from __future__ import annotations
-
-from dataclasses import dataclass
-from datetime import datetime, timezone
-from pathlib import Path
-from typing import Any
-
-from .. import BundlerError
-from ..lib.yamlio import dump_json, ensure_within, load_json
-from .manifest import COMPONENT_KINDS, ComponentRef
-
-RECORDS_FILENAME = "bundle-records.json"
-RECORDS_SCHEMA_VERSION = "1.0"
-
-
-@dataclass(frozen=True)
-class InstalledBundleRecord:
-    bundle_id: str
-    version: str
-    contributed_components: tuple[ComponentRef, ...]
-    installed_at: str
-
-    @classmethod
-    def create(
-        cls,
-        bundle_id: str,
-        version: str,
-        components: list[ComponentRef],
-        installed_at: str | None = None,
-    ) -> "InstalledBundleRecord":
-        return cls(
-            bundle_id=bundle_id,
-            version=version,
-            contributed_components=tuple(components),
-            installed_at=installed_at or _utc_now(),
-        )
-
-    def to_dict(self) -> dict[str, Any]:
-        return {
-            "bundle_id": self.bundle_id,
-            "version": self.version,
-            "installed_at": self.installed_at,
-            "contributed_components": [
-                _component_to_dict(c) for c in self.contributed_components
-            ],
-        }
-
-    @classmethod
-    def from_dict(cls, data: Any) -> "InstalledBundleRecord":
-        if not isinstance(data, dict):
-            raise BundlerError("Each installed-bundle record must be a mapping.")
-        components_raw = data.get("contributed_components") or []
-        if not isinstance(components_raw, list):
-            raise BundlerError(
-                "Corrupt record: 'contributed_components' must be a list."
-            )
-        bundle_id = str(data.get("bundle_id", "")).strip()
-        version = str(data.get("version", "")).strip()
-        if not bundle_id:
-            raise BundlerError(
-                "Corrupt records file: an installed-bundle record is missing "
-                "its 'bundle_id'."
-            )
-        if not version:
-            raise BundlerError(
-                f"Corrupt records file: record for bundle '{bundle_id}' is "
-                "missing its 'version'."
-            )
-        return cls(
-            bundle_id=bundle_id,
-            version=version,
-            installed_at=str(data.get("installed_at", "")).strip(),
-            contributed_components=tuple(
-                _component_from_dict(c) for c in components_raw
-            ),
-        )
-
-
-def records_path(project_root: Path) -> Path:
-    return Path(project_root) / ".specify" / RECORDS_FILENAME
-
-
-def _check_schema_version(value: Any, *, path: Path, required: bool) -> None:
-    """Reject a records file whose schema version we cannot safely parse.
-
-    A future incompatible format (or a corrupted file) must fail fast with an
-    actionable error rather than being silently mis-parsed, which could lead to
-    incorrect bundle attribution or removal. Forward-compatible minor bumps that
-    keep the same major version are accepted.
-    """
-    if value is None:
-        if required:
-            raise BundlerError(
-                f"Corrupt records file: {path} — missing 'schema_version'. "
-                f"Expected version {RECORDS_SCHEMA_VERSION}."
-            )
-        return
-    seen = str(value).strip()
-    if seen.split(".")[0] != RECORDS_SCHEMA_VERSION.split(".")[0]:
-        raise BundlerError(
-            f"Unsupported records schema version '{seen}' at {path}; this "
-            f"Spec Kit understands version {RECORDS_SCHEMA_VERSION}. The file may "
-            "have been written by a newer version or is corrupt."
-        )
-
-
-def load_records(project_root: Path) -> list[InstalledBundleRecord]:
-    # Defense in depth (mirrors the write path's within= confinement): refuse to
-    # read through a symlinked or traversal-escaping ``.specify`` that resolves
-    # outside project_root.
-    path = ensure_within(project_root, records_path(project_root))
-    if not path.exists():
-        return []
-    data = load_json(path)
-    if not isinstance(data, dict):
-        raise BundlerError(f"Corrupt records file: {path}")
-    _check_schema_version(data.get("schema_version"), path=path, required=True)
-    bundles = data.get("bundles") or []
-    if not isinstance(bundles, list):
-        raise BundlerError(
-            f"Corrupt records file: {path} — 'bundles' must be a list."
-        )
-    return [InstalledBundleRecord.from_dict(item) for item in bundles]
-
-
-def save_records(project_root: Path, records: list[InstalledBundleRecord]) -> None:
-    payload = {
-        "schema_version": RECORDS_SCHEMA_VERSION,
-        "updated_at": _utc_now(),
-        "bundles": [r.to_dict() for r in records],
-    }
-    dump_json(records_path(project_root), payload, within=project_root)
-
-
-def find_record(
-    records: list[InstalledBundleRecord], bundle_id: str
-) -> InstalledBundleRecord | None:
-    for record in records:
-        if record.bundle_id == bundle_id:
-            return record
-    return None
-
-
-def upsert_record(
-    records: list[InstalledBundleRecord], record: InstalledBundleRecord
-) -> list[InstalledBundleRecord]:
-    """Return a new list with *record* replacing any same-id record (append otherwise)."""
-    updated = [r for r in records if r.bundle_id != record.bundle_id]
-    updated.append(record)
-    return updated
-
-
-def remove_record(
-    records: list[InstalledBundleRecord], bundle_id: str
-) -> list[InstalledBundleRecord]:
-    return [r for r in records if r.bundle_id != bundle_id]
-
-
-def components_still_needed(
-    records: list[InstalledBundleRecord], exclude_bundle_id: str
-) -> set[tuple[str, str]]:
-    """Set of ``(kind, id)`` component keys required by bundles other than the excluded one."""
-    needed: set[tuple[str, str]] = set()
-    for record in records:
-        if record.bundle_id == exclude_bundle_id:
-            continue
-        for component in record.contributed_components:
-            needed.add((component.kind, component.id))
-    return needed
-
-
-def _component_to_dict(ref: ComponentRef) -> dict[str, Any]:
-    data: dict[str, Any] = {"kind": ref.kind, "id": ref.id}
-    if ref.version is not None:
-        data["version"] = ref.version
-    if ref.source is not None:
-        data["source"] = ref.source
-    if ref.priority is not None:
-        data["priority"] = ref.priority
-    if ref.strategy is not None:
-        data["strategy"] = ref.strategy
-    return data
-
-
-def _component_from_dict(data: Any) -> ComponentRef:
-    if not isinstance(data, dict):
-        raise BundlerError("Each contributed component must be a mapping.")
-    kind = str(data.get("kind", "")).strip()
-    cid = str(data.get("id", "")).strip()
-    if kind not in COMPONENT_KINDS:
-        raise BundlerError(
-            f"Corrupt records file: component 'kind' must be one of "
-            f"{list(COMPONENT_KINDS)}, got {kind or '<missing>'!r}."
-        )
-    if not cid:
-        raise BundlerError(
-            "Corrupt records file: a contributed component is missing its 'id'."
-        )
-    return ComponentRef(
-        kind=kind,
-        id=cid,
-        version=(str(data["version"]) if data.get("version") else None),
-        source=(str(data["source"]) if data.get("source") else None),
-        priority=_parse_priority(data.get("priority")),
-        strategy=(str(data["strategy"]) if data.get("strategy") else None),
-    )
-
-
-def _parse_priority(raw: Any) -> int | None:
-    if raw is None:
-        return None
-    if isinstance(raw, bool) or not isinstance(raw, (int, str)):
-        raise BundlerError(f"Component priority must be an integer, got {raw!r}.")
-    try:
-        return int(raw)
-    except (TypeError, ValueError):
-        raise BundlerError(
-            f"Component priority must be an integer, got {raw!r}."
-        ) from None
-
-
-def _utc_now() -> str:
-    return datetime.now(timezone.utc).strftime("%Y-%m-%dT%H:%M:%SZ")

src/specify_cli/bundler/services/__init__.py

@@ -1,2 +0,0 @@
-"""Bundler services (catalog stack, resolver, installer, conflict, validator, packager)."""
-from __future__ import annotations

src/specify_cli/bundler/services/adapters.py

@@ -1,193 +0,0 @@
-"""Concrete adapters: catalog fetching and primitive installation.
-
-These wire the bundler's injectable seams to the real environment:
-
-* :func:`make_catalog_fetcher` returns an offline-first fetcher that reads
-  built-in catalogs and local/pinned file URLs without network, and falls back
-  to a timeout-bounded HTTP GET only for ``http(s)://`` sources.
-* :class:`DefaultPrimitiveInstaller` dispatches component install/remove to the
-  existing Spec Kit primitive machinery in-process.
-"""
-from __future__ import annotations
-
-import re
-from pathlib import Path
-from urllib.parse import ParseResult, urlparse
-from urllib.request import url2pathname
-
-from .. import BundlerError
-from ..lib.yamlio import loads_json
-from ..models.catalog import CatalogSource
-from ..models.manifest import ComponentRef
-
-# Built-in catalog payloads ship empty by default; a host distribution can
-# replace these with curated content. Keeping them here makes ``search``/``info``
-# work fully offline against the default stack.
-_BUILTIN_CATALOGS: dict[str, dict] = {
-    "builtin://default": {
-        "schema_version": "1.0",
-        "catalog_url": "builtin://default",
-        "bundles": {},
-    },
-    "builtin://community": {
-        "schema_version": "1.0",
-        "catalog_url": "builtin://community",
-        "bundles": {},
-    },
-}
-
-HTTP_TIMEOUT_SECONDS = 10
-
-# Windows absolute paths like ``C:\catalog.json`` parse with a single-letter
-# ``scheme`` under urlparse; treat them as local files rather than URLs.
-_WINDOWS_DRIVE_RE = re.compile(r"^[A-Za-z]:[\\/]")
-
-
-def _is_windows_drive_path(url: str) -> bool:
-    return bool(_WINDOWS_DRIVE_RE.match(url))
-
-
-def _file_url_to_path(parsed: ParseResult) -> Path:
-    """Convert a ``file://`` URL to a local path.
-
-    Uses ``url2pathname`` for percent-decoding and OS-correct separators, and
-    preserves ``netloc`` so UNC paths (``file://server/share``) and Windows
-    drive URLs (``file:///C:/x``) resolve correctly instead of dropping host
-    or producing ``/C:/x``.
-    """
-    netloc = parsed.netloc
-    if netloc and netloc.lower() != "localhost":
-        # UNC share: file://server/share/... -> \\server\share\...
-        return Path(url2pathname(f"//{netloc}{parsed.path}"))
-    return Path(url2pathname(parsed.path))
-
-
-def _validate_remote_url(source_id: str, url: str) -> None:
-    """Restrict remote catalogs to HTTPS (HTTP only for localhost) with a host.
-
-    Mirrors ``specify_cli.catalogs`` URL validation to avoid MITM/downgrade
-    issues before any network call.
-    """
-    parsed = urlparse(url)
-    is_localhost = parsed.hostname in ("localhost", "127.0.0.1", "::1")
-    if parsed.scheme != "https" and not (parsed.scheme == "http" and is_localhost):
-        raise BundlerError(
-            f"Catalog '{source_id}' URL must use HTTPS (got {parsed.scheme}://). "
-            "HTTP is only allowed for localhost."
-        )
-    if not parsed.netloc:
-        raise BundlerError(
-            f"Catalog '{source_id}' URL must be a valid URL with a host: {url}"
-        )
-
-
-def make_catalog_fetcher(*, allow_network: bool = True):
-    """Return a fetcher callable suitable for :class:`CatalogStack`.
-
-    When *allow_network* is False, ``http(s)://`` sources raise instead of
-    touching the network (used by offline tests and ``--offline`` flows).
-    """
-
-    def fetch(source: CatalogSource) -> dict:
-        url = source.url
-        parsed = urlparse(url)
-        scheme = parsed.scheme.lower()
-
-        if scheme == "builtin":
-            payload = _BUILTIN_CATALOGS.get(url)
-            if payload is None:
-                raise BundlerError(f"Unknown built-in catalog '{url}'.")
-            return payload
-
-        if scheme == "file":
-            path = _file_url_to_path(parsed)
-            if not path.exists():
-                raise BundlerError(f"Catalog file not found: {path}")
-            return loads_json(path.read_text(encoding="utf-8"), origin=str(path))
-
-        if scheme == "" or _is_windows_drive_path(url):
-            path = Path(url)
-            if not path.exists():
-                raise BundlerError(f"Catalog file not found: {path}")
-            return loads_json(path.read_text(encoding="utf-8"), origin=str(path))
-
-        if scheme in ("http", "https"):
-            if not allow_network:
-                raise BundlerError(
-                    f"Network access disabled; cannot fetch catalog '{source.id}' "
-                    f"from {url}."
-                )
-            _validate_remote_url(source.id, url)
-            return _http_get_json(source.id, url)
-
-        raise BundlerError(f"Unsupported catalog URL scheme: {url}")
-
-    return fetch
-
-
-def _http_get_json(source_id: str, url: str) -> dict:
-    """Fetch catalog JSON over HTTP(S) via the shared authenticated client.
-
-    Routing through :func:`specify_cli.authentication.http.open_url` gives
-    ``auth.json`` token support and strips the ``Authorization`` header when a
-    redirect leaves the entry's trusted hosts or downgrades the scheme. We also
-    reject any redirect that leaves HTTPS (the ``redirect_validator`` runs
-    *before* each hop) and re-validate the final URL after redirects, so the
-    HTTPS/host guarantee from ``_validate_remote_url`` is preserved end to end
-    rather than only on the initial URL.
-    """
-    from ...authentication.http import open_url
-
-    def _validate_redirect(_old_url: str, new_url: str) -> None:
-        _validate_remote_url(source_id, new_url)
-
-    try:
-        with open_url(
-            url,
-            timeout=HTTP_TIMEOUT_SECONDS,
-            redirect_validator=_validate_redirect,
-        ) as response:
-            final_url = response.geturl()
-            _validate_remote_url(source_id, final_url)
-            raw = response.read().decode("utf-8")
-    except BundlerError:
-        raise
-    except Exception as exc:  # noqa: BLE001
-        raise BundlerError(f"Failed to fetch catalog from {url}: {exc}") from exc
-    return loads_json(raw, origin=final_url)
-
-
-class DefaultPrimitiveInstaller:
-    """Dispatch component install/remove to existing primitive machinery.
-
-    This adapter is intentionally thin: it owns no install logic of its own,
-    delegating entirely to the per-primitive managers so the bundler honours
-    Principle I (no duplicated primitive logic).
-
-    *allow_network* mirrors the bundle command's ``--offline`` flag: when False,
-    component kinds that can only be sourced from a remote catalog refuse rather
-    than touching the network. Bundled presets/extensions still install offline.
-    """
-
-    def __init__(self, *, allow_network: bool = True) -> None:
-        self._allow_network = allow_network
-
-    def is_installed(self, project_root: Path, component: ComponentRef) -> bool:
-        manager = self._manager_for(component, project_root)
-        return manager.is_installed(component)
-
-    def install(self, project_root: Path, component: ComponentRef) -> None:
-        manager = self._manager_for(component, project_root)
-        manager.install(component)
-
-    def remove(self, project_root: Path, component: ComponentRef) -> None:
-        manager = self._manager_for(component, project_root)
-        manager.remove(component)
-
-    def _manager_for(self, component: ComponentRef, project_root: Path):
-        # Lazy import to avoid import cycles and keep startup cheap (Principle IV).
-        from .primitives import primitive_manager
-
-        return primitive_manager(
-            component.kind, project_root, allow_network=self._allow_network
-        )

src/specify_cli/bundler/services/catalog_stack.py

@@ -1,114 +0,0 @@
-"""Catalog stack: aggregate bundle entries across sources with precedence + policy.
-
-Loads each source's catalog payload (via an injectable fetcher so tests stay
-offline), then resolves a bundle id to the highest-precedence entry while
-recording whether installation is permitted by that source's policy.
-"""
-from __future__ import annotations
-
-from dataclasses import dataclass
-from pathlib import Path
-from typing import Callable
-
-from .. import BundlerError
-from ..models.catalog import (
-    CatalogEntry,
-    CatalogSource,
-    load_catalog_payload,
-    load_source_stack,
-)
-
-# A fetcher returns the raw JSON payload (a dict) for a given source.
-CatalogFetcher = Callable[[CatalogSource], dict]
-
-
-@dataclass
-class ResolvedBundle:
-    entry: CatalogEntry
-    source: CatalogSource
-
-    @property
-    def install_allowed(self) -> bool:
-        return self.source.install_allowed
-
-
-class CatalogStack:
-    def __init__(
-        self,
-        sources: list[CatalogSource],
-        fetcher: CatalogFetcher,
-    ) -> None:
-        # Highest precedence (lowest priority number) first.
-        self._sources = sorted(sources, key=lambda s: (s.priority, s.id))
-        self._fetcher = fetcher
-        self._payloads: dict[str, dict[str, CatalogEntry]] = {}
-
-    @classmethod
-    def load(
-        cls,
-        project_root: Path,
-        fetcher: CatalogFetcher,
-        user_config_dir: Path | None = None,
-    ) -> "CatalogStack":
-        sources = load_source_stack(project_root, user_config_dir)
-        return cls(sources, fetcher)
-
-    @property
-    def sources(self) -> list[CatalogSource]:
-        return list(self._sources)
-
-    def _entries_for(self, source: CatalogSource) -> dict[str, CatalogEntry]:
-        if source.id not in self._payloads:
-            try:
-                raw = self._fetcher(source)
-            except BundlerError:
-                raise
-            except Exception as exc:  # noqa: BLE001 - surface as chained BundlerError
-                raise BundlerError(
-                    f"Failed to load catalog '{source.id}' ({source.url}): {exc}"
-                ) from exc
-            self._payloads[source.id] = load_catalog_payload(raw)
-        return self._payloads[source.id]
-
-    def resolve(self, bundle_id: str) -> ResolvedBundle:
-        """Return the highest-precedence entry for *bundle_id* or raise."""
-        for source in self._sources:
-            entries = self._entries_for(source)
-            entry = entries.get(bundle_id)
-            if entry is not None:
-                return ResolvedBundle(entry=entry.with_provenance(source), source=source)
-        raise BundlerError(
-            f"Bundle '{bundle_id}' was not found in any configured catalog."
-        )
-
-    def search(self, query: str = "") -> list[ResolvedBundle]:
-        """Return entries matching *query* (substring over id/name/role/tags/description).
-
-        Each bundle id appears once, resolved at its highest-precedence source.
-        Results are sorted by bundle id for deterministic output.
-        """
-        needle = query.strip().lower()
-        seen: dict[str, ResolvedBundle] = {}
-        for source in self._sources:
-            for bundle_id, entry in self._entries_for(source).items():
-                if bundle_id in seen:
-                    continue
-                if needle and not _matches(entry, needle):
-                    continue
-                seen[bundle_id] = ResolvedBundle(
-                    entry=entry.with_provenance(source), source=source
-                )
-        return [seen[k] for k in sorted(seen)]
-
-
-def _matches(entry: CatalogEntry, needle: str) -> bool:
-    haystack = " ".join(
-        [
-            entry.id,
-            entry.name,
-            entry.role,
-            entry.description,
-            " ".join(entry.tags),
-        ]
-    ).lower()
-    return needle in haystack

src/specify_cli/bundler/services/conflict.py

@@ -1,54 +0,0 @@
-"""Conflict detection across the installed-bundle stack.
-
-The single cross-bundle conflict point is the active integration (FR-019).
-Component-level overlaps (same preset id at different priorities, etc.) are
-resolved by the existing primitive machinery's own precedence rules, so the
-bundler only needs to guard the integration invariant and surface informational
-overlaps.
-"""
-from __future__ import annotations
-
-from dataclasses import dataclass, field
-
-from ..models.manifest import BundleManifest
-from ..models.records import InstalledBundleRecord
-
-
-@dataclass
-class ConflictReport:
-    integration_clash: str | None = None  # message when a hard clash exists
-    overlaps: list[str] = field(default_factory=list)  # components already provided
-
-    @property
-    def has_blocking_conflict(self) -> bool:
-        return self.integration_clash is not None
-
-
-def detect_conflicts(
-    manifest: BundleManifest,
-    active_integration: str | None,
-    installed: list[InstalledBundleRecord],
-) -> ConflictReport:
-    report = ConflictReport()
-
-    if manifest.integration is not None and active_integration:
-        if manifest.integration.id != active_integration:
-            report.integration_clash = (
-                f"Bundle targets integration '{manifest.integration.id}' but the "
-                f"project's active integration is '{active_integration}'."
-            )
-
-    already: dict[tuple[str, str], str] = {}
-    for record in installed:
-        for component in record.contributed_components:
-            already[(component.kind, component.id)] = record.bundle_id
-
-    for component in manifest.components:
-        owner = already.get((component.kind, component.id))
-        if owner and owner != manifest.bundle.id:
-            report.overlaps.append(
-                f"{component.kind[:-1]} '{component.id}' is already provided by "
-                f"bundle '{owner}'."
-            )
-
-    return report

src/specify_cli/bundler/services/installer.py

@@ -1,210 +0,0 @@
-"""Installer: apply an :class:`InstallPlan` via existing primitive machinery.
-
-The actual component installation (extensions, presets, steps, workflows) is
-delegated to a :class:`PrimitiveInstaller` so the bundler never re-implements
-primitive logic (Principle I) and integration tests can inject a deterministic,
-offline fake (Principle II/IV). The real adapter dispatches in-process to the
-existing extension/preset/step/workflow machinery.
-
-Installation is idempotent and stops on first failure with no partial record
-write (FR-018, SC partial-failure-stop).
-"""
-from __future__ import annotations
-
-from dataclasses import dataclass, field
-from pathlib import Path
-from typing import Protocol
-
-from .. import BundlerError
-from ..models.manifest import BundleManifest, ComponentRef
-from ..models.records import (
-    InstalledBundleRecord,
-    components_still_needed,
-    find_record,
-    load_records,
-    remove_record,
-    save_records,
-    upsert_record,
-)
-from .conflict import detect_conflicts
-from .resolver import InstallPlan
-
-
-class PrimitiveInstaller(Protocol):
-    """Adapter over the existing Spec Kit primitive install/remove machinery."""
-
-    def is_installed(self, project_root: Path, component: ComponentRef) -> bool: ...
-
-    def install(self, project_root: Path, component: ComponentRef) -> None: ...
-
-    def remove(self, project_root: Path, component: ComponentRef) -> None: ...
-
-
-@dataclass
-class InstallResult:
-    bundle_id: str
-    installed: list[ComponentRef] = field(default_factory=list)
-    skipped: list[ComponentRef] = field(default_factory=list)
-    refreshed: list[ComponentRef] = field(default_factory=list)
-    uninstalled: list[ComponentRef] = field(default_factory=list)
-
-    @property
-    def changed(self) -> bool:
-        return bool(self.installed or self.refreshed)
-
-
-def install_bundle(
-    project_root: Path,
-    plan: InstallPlan,
-    installer: PrimitiveInstaller,
-    manifest: BundleManifest | None = None,
-    refresh: bool = False,
-) -> InstallResult:
-    """Execute *plan*, recording provenance. Idempotent, with bounded rollback.
-
-    Atomicity is scoped, not global: on failure only the components newly
-    installed during *this* call are rolled back, and the provenance record is
-    written solely on full success (a failure records nothing). Components that
-    were already installed beforehand — including those re-applied when *refresh*
-    is True — are never rolled back.
-
-    When *refresh* is True (used by ``specify bundle update``), components that
-    are already installed are re-applied through the primitive machinery so they
-    are brought up to the plan's pinned versions, rather than skipped. Primitive
-    config (e.g. preset priority overrides) is preserved by the underlying
-    machinery.
-
-    Version-pin enforcement is install-time only. The primitive ``is_installed``
-    checks are id-based (they do not compare versions), so when a component is
-    already present and *refresh* is False it is skipped without verifying that
-    the on-disk version matches the manifest pin. Pins are therefore only
-    guaranteed to be applied when the bundler actually performs an install or a
-    refresh; running ``specify bundle update`` re-applies every owned component
-    at its pinned version.
-    """
-    records = load_records(project_root)
-
-    if manifest is not None:
-        report = detect_conflicts(manifest, plan.effective_integration, records)
-        if report.has_blocking_conflict:
-            raise BundlerError(report.integration_clash)
-
-    result = InstallResult(bundle_id=plan.bundle_id)
-    existing = find_record(records, plan.bundle_id)
-    prior_ours = {
-        (c.kind, c.id) for c in existing.contributed_components
-    } if existing is not None else set()
-    # Components already attributed to a *different* installed bundle: these are
-    # legitimately shareable (refcounted on removal), so this bundle may also
-    # claim them. A component that is installed on disk but tracked by no bundle
-    # was installed independently and must NOT be attributed here — otherwise
-    # removing this bundle would uninstall it (collateral removal, FR-022).
-    other_tracked = {
-        (c.kind, c.id)
-        for r in records
-        if r.bundle_id != plan.bundle_id
-        for c in r.contributed_components
-    }
-
-    contributed: list[ComponentRef] = []
-    done: list[ComponentRef] = []
-    try:
-        for component in plan.components:
-            key = (component.kind, component.id)
-            if installer.is_installed(project_root, component):
-                # A component is "ours" only when this bundle (or a sibling
-                # bundle) already owns it. Independently-installed components
-                # are never attributed and — crucially — never refreshed, so
-                # ``bundle update`` cannot make collateral changes to things it
-                # does not own (FR-022).
-                owned = key in prior_ours or key in other_tracked
-                if refresh and owned:
-                    _refresh_component(project_root, installer, component)
-                    result.refreshed.append(component)
-                else:
-                    result.skipped.append(component)
-                if owned:
-                    contributed.append(component)
-                continue
-            installer.install(project_root, component)
-            done.append(component)
-            result.installed.append(component)
-            contributed.append(component)
-    except BundlerError:
-        _rollback(project_root, installer, done)
-        raise
-    except Exception as exc:  # noqa: BLE001
-        _rollback(project_root, installer, done)
-        raise BundlerError(
-            f"Failed to install bundle '{plan.bundle_id}': {exc}. "
-            "No changes were recorded."
-        ) from exc
-
-    record = InstalledBundleRecord.create(
-        bundle_id=plan.bundle_id,
-        version=plan.version,
-        components=contributed,
-        # Preserve the original install time across refresh/update so
-        # ``bundle list`` keeps reporting when the bundle was first installed.
-        installed_at=existing.installed_at if existing is not None else None,
-    )
-    save_records(project_root, upsert_record(records, record))
-    return result
-
-
-def remove_bundle(
-    project_root: Path,
-    bundle_id: str,
-    installer: PrimitiveInstaller,
-) -> InstallResult:
-    """Remove a bundle, uninstalling only components no other bundle still needs."""
-    records = load_records(project_root)
-    target = next((r for r in records if r.bundle_id == bundle_id), None)
-    if target is None:
-        raise BundlerError(f"Bundle '{bundle_id}' is not installed.")
-
-    still_needed = components_still_needed(records, exclude_bundle_id=bundle_id)
-    result = InstallResult(bundle_id=bundle_id)
-
-    for component in target.contributed_components:
-        key = (component.kind, component.id)
-        if key in still_needed:
-            result.skipped.append(component)
-            continue
-        if installer.is_installed(project_root, component):
-            installer.remove(project_root, component)
-            result.uninstalled.append(component)
-        else:
-            result.skipped.append(component)
-
-    save_records(project_root, remove_record(records, bundle_id))
-    return result
-
-
-def _refresh_component(
-    project_root: Path,
-    installer: PrimitiveInstaller,
-    component: ComponentRef,
-) -> None:
-    """Re-apply an already-installed component to bring it up to its pinned version.
-
-    Prefers a primitive-provided ``refresh`` hook when available; otherwise falls
-    back to a re-install through the existing idempotent install path.
-    """
-    op = getattr(installer, "refresh", None)
-    if callable(op):
-        op(project_root, component)
-    else:
-        installer.install(project_root, component)
-
-
-def _rollback(
-    project_root: Path,
-    installer: PrimitiveInstaller,
-    done: list[ComponentRef],
-) -> None:
-    for component in reversed(done):
-        try:
-            installer.remove(project_root, component)
-        except Exception:  # noqa: BLE001 - best-effort rollback
-            continue

src/specify_cli/bundler/services/packager.py

@@ -1,145 +0,0 @@
-"""Packager: produce a single versioned distributable artifact from a bundle dir.
-
-``specify bundle build`` zips the manifest, README, and any local assets into
-``<id>-<version>.zip``. Build refuses on an invalid manifest, pointing the
-author to ``validate``. All file reads are confined within the bundle source
-directory (Principle V path confinement).
-"""
-from __future__ import annotations
-
-import os
-import re
-import zipfile
-from dataclasses import dataclass
-from pathlib import Path
-
-from .. import BundlerError
-from ..lib.yamlio import ensure_within
-from ..models.manifest import BundleManifest
-from .validator import validate_manifest
-
-# Files/dirs never included in an artifact.
-EXCLUDE_NAMES = {".git", "__pycache__", ".DS_Store"}
-
-# Fixed member timestamp (zip epoch) for reproducible, byte-stable artifacts.
-_FIXED_TIMESTAMP = (1980, 1, 1, 0, 0, 0)
-
-
-@dataclass
-class BuildResult:
-    artifact_path: Path
-    file_count: int
-
-
-def build_bundle(
-    bundle_dir: Path,
-    output_dir: Path | None = None,
-) -> BuildResult:
-    bundle_dir = Path(bundle_dir).resolve()
-    manifest_path = bundle_dir / "bundle.yml"
-    if not manifest_path.exists():
-        raise BundlerError(f"No bundle.yml found in '{bundle_dir}'.")
-
-    # The artifact contract requires a human-facing README.md alongside the
-    # manifest; refuse early rather than publish a bundle with no description.
-    if not (bundle_dir / "README.md").exists():
-        raise BundlerError(
-            f"No README.md found in '{bundle_dir}'. Every bundle must ship a "
-            "README.md describing it."
-        )
-
-    manifest = BundleManifest.from_file(manifest_path)
-    report = validate_manifest(manifest)
-    if not report.ok:
-        raise BundlerError(
-            "Refusing to build an invalid manifest. Run 'specify bundle validate' "
-            "and fix:\n  - " + "\n  - ".join(report.errors)
-        )
-
-    out_dir = Path(output_dir).resolve() if output_dir else bundle_dir
-    out_dir.mkdir(parents=True, exist_ok=True)
-    artifact_name = f"{manifest.bundle.id}-{manifest.bundle.version}.zip"
-    artifact_path = out_dir / artifact_name
-    # Defense in depth: even though validate_manifest() rejects unsafe ids, make
-    # sure a crafted id cannot push the artifact outside the output directory.
-    ensure_within(out_dir, artifact_path)
-
-    # If the output dir lives inside the bundle, skip its whole subtree so
-    # previously-built artifacts are never re-packaged (keeps builds
-    # reproducible and bounded).
-    skip_dir = out_dir if out_dir != bundle_dir and _is_within(bundle_dir, out_dir) else None
-    # Also skip any prior build artifact for this bundle (e.g. an older
-    # <id>-<version>.zip sitting next to bundle.yml), not just the current one.
-    # Match only a semver-looking version segment so legitimate assets that
-    # merely start with the bundle id (e.g. <id>-assets.zip) are still packaged.
-    artifact_re = re.compile(
-        rf"^{re.escape(manifest.bundle.id)}-"
-        r"\d+\.\d+\.\d+(?:-[0-9A-Za-z.-]+)?(?:\+[0-9A-Za-z.-]+)?\.zip$"
-    )
-    files = _collect_files(
-        bundle_dir, skip=artifact_path, skip_dir=skip_dir, artifact_re=artifact_re
-    )
-    with zipfile.ZipFile(artifact_path, "w", zipfile.ZIP_DEFLATED) as archive:
-        for file_path in files:
-            # Confinement: every packaged file must live under bundle_dir.
-            ensure_within(bundle_dir, file_path)
-            arcname = file_path.relative_to(bundle_dir).as_posix()
-            # Fixed timestamp so identical inputs yield a byte-for-byte
-            # identical artifact (reproducible builds).
-            info = zipfile.ZipInfo(filename=arcname, date_time=_FIXED_TIMESTAMP)
-            info.compress_type = zipfile.ZIP_DEFLATED
-            # Reproducible, normalized permissions: preserve executability so
-            # bundled scripts (e.g. extension hook scripts) stay runnable after
-            # extraction, but collapse to two canonical modes (0755 when any
-            # execute bit is set on the source, otherwise 0644) so identical
-            # inputs yield a byte-for-byte identical artifact.
-            mode = 0o755 if file_path.stat().st_mode & 0o111 else 0o644
-            info.external_attr = mode << 16
-            archive.writestr(info, file_path.read_bytes())
-
-    return BuildResult(artifact_path=artifact_path, file_count=len(files))
-
-
-def _is_within(parent: Path, child: Path) -> bool:
-    try:
-        child.relative_to(parent)
-        return True
-    except ValueError:
-        return False
-
-
-def _collect_files(
-    bundle_dir: Path,
-    skip: Path,
-    skip_dir: Path | None = None,
-    artifact_re: re.Pattern[str] | None = None,
-) -> list[Path]:
-    collected: list[Path] = []
-    # followlinks=False so a symlinked directory is never descended into,
-    # which would otherwise pull in out-of-tree files and then fail at
-    # ensure_within(). Symlinked dirs are pruned from traversal explicitly.
-    for root, dirnames, filenames in os.walk(bundle_dir, followlinks=False):
-        root_path = Path(root)
-        # Prune directories we must not descend into (in-place edit of dirnames).
-        dirnames[:] = [
-            d
-            for d in dirnames
-            if d not in EXCLUDE_NAMES and not (root_path / d).is_symlink()
-        ]
-        if skip_dir is not None and _is_within(skip_dir, root_path):
-            dirnames[:] = []
-            continue
-        for name in filenames:
-            path = root_path / name
-            if path == skip:
-                continue
-            if name in EXCLUDE_NAMES:
-                continue
-            if artifact_re is not None and artifact_re.match(name):
-                # A prior build artifact for this bundle — never re-package it.
-                continue
-            if path.is_symlink():
-                # Skip symlinked files to avoid escaping the bundle directory.
-                continue
-            collected.append(path)
-    return sorted(collected)

src/specify_cli/bundler/services/primitives.py

@@ -1,345 +0,0 @@
-"""Bridge from bundler component kinds to existing primitive managers.
-
-The bundler does not own install logic; it routes each component to the
-existing Spec Kit primitive machinery so a bundle install behaves exactly as a
-sequence of ``specify <primitive> add`` calls would (Principle I: never
-reimplement or fake primitive behaviour).
-
-Routing strategy per kind:
-
-* **presets** / **extensions** — wired through their reusable managers
-  (``install_from_directory`` / ``install_from_zip``). Bundled assets shipped
-  with Spec Kit install fully offline; catalog assets are fetched only when
-  network access is permitted.
-* **workflows** / **steps** — their install/remove orchestration lives in the
-  CLI command layer rather than a reusable service method, so the bundler
-  delegates to those existing command callables in-process (with the project
-  root as the working directory) instead of duplicating their download and
-  validation logic.
-"""
-from __future__ import annotations
-
-import contextlib
-import os
-from pathlib import Path
-from typing import Protocol
-
-from .. import BundlerError
-from ..models.manifest import ComponentRef
-
-DEFAULT_PRIORITY = 10
-
-
-def _assert_pinned_version(
-    kind: str, component_id: str, pinned: str | None, advertised: object
-) -> None:
-    """Refuse to install when the catalog version differs from the manifest pin.
-
-    Bundle manifests pin component versions for reproducibility; installing
-    whatever the active catalog currently serves would silently violate the
-    pin. When the catalog advertises no version we cannot enforce the pin, so
-    installation proceeds (the catalog, not the bundler, owns that gap).
-    """
-    if not pinned or advertised is None:
-        return
-    actual = str(advertised).strip()
-    if not actual:
-        return
-    from ..lib.versioning import parse_version
-
-    try:
-        matches = parse_version(actual) == parse_version(pinned)
-    except BundlerError:
-        matches = actual == str(pinned).strip()
-    if not matches:
-        raise BundlerError(
-            f"{kind} '{component_id}' is pinned to version {pinned} in the bundle "
-            f"manifest, but the active catalog serves {actual}. Update the bundle's "
-            "pinned version or the catalog before installing."
-        )
-
-
-class _KindManager(Protocol):
-    def is_installed(self, component: ComponentRef) -> bool: ...
-
-    def install(self, component: ComponentRef) -> None: ...
-
-    def remove(self, component: ComponentRef) -> None: ...
-
-
-def primitive_manager(
-    kind: str, project_root: Path, *, allow_network: bool = True
-) -> _KindManager:
-    if kind == "presets":
-        return _PresetKindManager(project_root, allow_network)
-    if kind == "extensions":
-        return _ExtensionKindManager(project_root, allow_network)
-    if kind == "workflows":
-        return _WorkflowKindManager(project_root, allow_network)
-    if kind == "steps":
-        return _StepKindManager(project_root, allow_network)
-    raise BundlerError(f"Unknown component kind '{kind}'.")
-
-
-@contextlib.contextmanager
-def _chdir(path: Path):
-    """Temporarily switch the working directory.
-
-    The delegated workflow/step command callables resolve the project via
-    ``Path.cwd()``; this makes that resolution land on *path*.
-    """
-    previous = Path.cwd()
-    os.chdir(path)
-    try:
-        yield
-    finally:
-        os.chdir(previous)
-
-
-def _delegate_command(action: str, label: str, call) -> None:
-    """Run a delegated CLI command callable, translating its exit into errors."""
-    import typer
-
-    try:
-        call()
-    except typer.Exit as exc:  # raised by the delegated command on failure
-        code = getattr(exc, "exit_code", 0) or 0
-        if code != 0:
-            raise BundlerError(f"Failed to {action} {label}.") from exc
-    except SystemExit as exc:  # pragma: no cover - defensive
-        if exc.code not in (0, None):
-            raise BundlerError(f"Failed to {action} {label}.") from exc
-
-
-class _PresetKindManager:
-    def __init__(self, project_root: Path, allow_network: bool) -> None:
-        from ...presets import PresetManager
-
-        self._root = project_root
-        self._allow_network = allow_network
-        self._manager = PresetManager(project_root)
-
-    def is_installed(self, component: ComponentRef) -> bool:
-        try:
-            return self._manager.get_pack(component.id) is not None
-        except Exception:  # noqa: BLE001
-            return False
-
-    def install(self, component: ComponentRef) -> None:
-        from ... import get_speckit_version
-        from ..._assets import _locate_bundled_preset
-
-        speckit_version = get_speckit_version()
-        priority = DEFAULT_PRIORITY if component.priority is None else component.priority
-
-        bundled = _locate_bundled_preset(component.id)
-        if bundled is not None:
-            self._manager.install_from_directory(bundled, speckit_version, priority)
-            return
-
-        if not self._allow_network:
-            raise BundlerError(
-                f"Preset '{component.id}' is not bundled and network access is "
-                f"disabled; re-run without --offline or install it first with "
-                f"'specify preset add {component.id}'."
-            )
-
-        from ...presets import PresetCatalog
-
-        catalog = PresetCatalog(self._root)
-        info = catalog.get_pack_info(component.id)
-        if not info:
-            raise BundlerError(f"Preset '{component.id}' not found in any catalog.")
-        if not info.get("_install_allowed", True):
-            raise BundlerError(
-                f"Preset '{component.id}' is from a discovery-only catalog; "
-                "installation is not allowed."
-            )
-        _assert_pinned_version(
-            "Preset", component.id, component.version, info.get("version")
-        )
-        zip_path = catalog.download_pack(component.id)
-        try:
-            self._manager.install_from_zip(zip_path, speckit_version, priority)
-        finally:
-            with contextlib.suppress(Exception):
-                if zip_path.exists():
-                    zip_path.unlink()
-
-    def remove(self, component: ComponentRef) -> None:
-        try:
-            self._manager.remove(component.id)
-        except Exception as exc:  # noqa: BLE001
-            raise BundlerError(
-                f"Failed to remove preset '{component.id}': {exc}"
-            ) from exc
-
-
-class _ExtensionKindManager:
-    def __init__(self, project_root: Path, allow_network: bool) -> None:
-        from ...extensions import ExtensionManager
-
-        self._root = project_root
-        self._allow_network = allow_network
-        self._manager = ExtensionManager(project_root)
-
-    def is_installed(self, component: ComponentRef) -> bool:
-        try:
-            return self._manager.registry.is_installed(component.id)
-        except Exception:  # noqa: BLE001
-            return False
-
-    def install(self, component: ComponentRef) -> None:
-        from ... import get_speckit_version
-        from ..._assets import _locate_bundled_extension
-
-        speckit_version = get_speckit_version()
-        priority = DEFAULT_PRIORITY if component.priority is None else component.priority
-
-        bundled = _locate_bundled_extension(component.id)
-        if bundled is not None:
-            self._manager.install_from_directory(
-                bundled, speckit_version, priority=priority
-            )
-            return
-
-        if not self._allow_network:
-            raise BundlerError(
-                f"Extension '{component.id}' is not bundled and network access is "
-                f"disabled; re-run without --offline or install it first with "
-                f"'specify extension add {component.id}'."
-            )
-
-        from ...extensions import ExtensionCatalog
-
-        catalog = ExtensionCatalog(self._root)
-        info = catalog.get_extension_info(component.id)
-        if not info:
-            raise BundlerError(
-                f"Extension '{component.id}' not found in any catalog."
-            )
-        if not info.get("_install_allowed", True):
-            raise BundlerError(
-                f"Extension '{component.id}' is from a discovery-only catalog; "
-                "installation is not allowed."
-            )
-        _assert_pinned_version(
-            "Extension", component.id, component.version, info.get("version")
-        )
-        zip_path = catalog.download_extension(component.id)
-        try:
-            self._manager.install_from_zip(
-                zip_path, speckit_version, priority=priority
-            )
-        finally:
-            with contextlib.suppress(Exception):
-                if zip_path.exists():
-                    zip_path.unlink()
-
-    def remove(self, component: ComponentRef) -> None:
-        try:
-            self._manager.remove(component.id)
-        except Exception as exc:  # noqa: BLE001
-            raise BundlerError(
-                f"Failed to remove extension '{component.id}': {exc}"
-            ) from exc
-
-
-class _WorkflowKindManager:
-    def __init__(self, project_root: Path, allow_network: bool) -> None:
-        from ...workflows.catalog import WorkflowRegistry
-
-        self._root = project_root
-        self._allow_network = allow_network
-        self._registry = WorkflowRegistry(project_root)
-
-    def is_installed(self, component: ComponentRef) -> bool:
-        try:
-            return self._registry.is_installed(component.id)
-        except Exception:  # noqa: BLE001
-            return False
-
-    def install(self, component: ComponentRef) -> None:
-        if not self._allow_network and not self._is_bundled(component.id):
-            raise BundlerError(
-                f"Workflow '{component.id}' installs from a catalog and network "
-                f"access is disabled; re-run without --offline or install it first "
-                f"with 'specify workflow add {component.id}'."
-            )
-        self._assert_pinned_version(component)
-        from ... import workflow_add
-
-        with _chdir(self._root):
-            _delegate_command(
-                "install", f"workflow '{component.id}'",
-                lambda: workflow_add(component.id),
-            )
-
-    def _assert_pinned_version(self, component: ComponentRef) -> None:
-        if not component.version:
-            return
-        try:
-            from ...workflows.catalog import WorkflowCatalog
-
-            info = WorkflowCatalog(self._root).get_workflow_info(component.id)
-        except Exception:  # noqa: BLE001 - catalog unreachable: cannot enforce
-            return
-        if info:
-            _assert_pinned_version(
-                "Workflow", component.id, component.version, info.get("version")
-            )
-
-    @staticmethod
-    def _is_bundled(workflow_id: str) -> bool:
-        # A workflow that ships with Spec Kit installs fully offline.
-        from ..._assets import _locate_bundled_workflow
-
-        return _locate_bundled_workflow(workflow_id) is not None
-
-    def remove(self, component: ComponentRef) -> None:
-        from ... import workflow_remove
-
-        with _chdir(self._root):
-            _delegate_command(
-                "remove", f"workflow '{component.id}'",
-                lambda: workflow_remove(component.id),
-            )
-
-
-class _StepKindManager:
-    def __init__(self, project_root: Path, allow_network: bool) -> None:
-        from ...workflows.catalog import StepRegistry
-
-        self._root = project_root
-        self._allow_network = allow_network
-        self._registry = StepRegistry(project_root)
-
-    def is_installed(self, component: ComponentRef) -> bool:
-        try:
-            return self._registry.is_installed(component.id)
-        except Exception:  # noqa: BLE001
-            return False
-
-    def install(self, component: ComponentRef) -> None:
-        if not self._allow_network:
-            raise BundlerError(
-                f"Step '{component.id}' installs from a catalog and network access "
-                f"is disabled; re-run without --offline or install it first with "
-                f"'specify workflow step add {component.id}'."
-            )
-        from ... import workflow_step_add
-
-        with _chdir(self._root):
-            _delegate_command(
-                "install", f"step '{component.id}'",
-                lambda: workflow_step_add(component.id),
-            )
-
-    def remove(self, component: ComponentRef) -> None:
-        from ... import workflow_step_remove
-
-        with _chdir(self._root):
-            _delegate_command(
-                "remove", f"step '{component.id}'",
-                lambda: workflow_step_remove(component.id),
-            )

src/specify_cli/bundler/services/references.py

@@ -1,114 +0,0 @@
-"""Resolve bundle component references against real, available components.
-
-Used by ``specify bundle validate`` (FR-005 / SC-007) to confirm that every
-declared component points at something installable. Resolution is offline-first:
-a reference resolves when the component is bundled with Spec Kit or already
-installed in the project; catalog sources are consulted only when network access
-is permitted. Offline runs that cannot confirm a reference downgrade to a
-warning rather than a false failure, while definitively-unknown references
-always error.
-"""
-from __future__ import annotations
-
-from pathlib import Path
-
-from ..models.manifest import ComponentRef
-
-
-def _resolved_locally(root: Path, component: ComponentRef) -> bool:
-    kind = component.kind
-    try:
-        if kind == "presets":
-            from ..._assets import _locate_bundled_preset
-            from ...presets import PresetManager
-
-            if _locate_bundled_preset(component.id) is not None:
-                return True
-            return PresetManager(root).get_pack(component.id) is not None
-        if kind == "extensions":
-            from ..._assets import _locate_bundled_extension
-            from ...extensions import ExtensionManager
-
-            if _locate_bundled_extension(component.id) is not None:
-                return True
-            return ExtensionManager(root).registry.is_installed(component.id)
-        if kind == "workflows":
-            from ..._assets import _locate_bundled_workflow
-            from ...workflows.catalog import WorkflowRegistry
-
-            if _locate_bundled_workflow(component.id) is not None:
-                return True
-            return WorkflowRegistry(root).is_installed(component.id)
-        if kind == "steps":
-            from ...workflows.catalog import StepRegistry
-
-            return StepRegistry(root).is_installed(component.id)
-    except Exception:  # noqa: BLE001 - resolution is best-effort
-        return False
-    return False
-
-
-def _resolved_in_catalog(root: Path, component: ComponentRef) -> bool | None:
-    """Return True/False if a catalog could be consulted, or None on failure."""
-    kind = component.kind
-    try:
-        if kind == "presets":
-            from ...presets import PresetCatalog
-
-            return PresetCatalog(root).get_pack_info(component.id) is not None
-        if kind == "extensions":
-            from ...extensions import ExtensionCatalog
-
-            return ExtensionCatalog(root).get_extension_info(component.id) is not None
-        if kind == "workflows":
-            from ...workflows.catalog import WorkflowCatalog
-
-            return WorkflowCatalog(root).get_workflow_info(component.id) is not None
-        if kind == "steps":
-            from ...workflows.catalog import StepCatalog
-
-            return StepCatalog(root).get_step_info(component.id) is not None
-    except Exception:  # noqa: BLE001 - catalog may be unreachable/misconfigured
-        return None
-    return None
-
-
-def make_reference_checker(
-    project_root: Path,
-    *,
-    allow_network: bool,
-    warnings: list[str],
-):
-    """Build a ``ReferenceChecker`` for :func:`validate_manifest`.
-
-    Returns an error string for a reference that is definitively unresolvable,
-    ``None`` otherwise. Unverifiable references (offline, or an unreachable
-    catalog) append a note to *warnings* and pass.
-    """
-
-    def check(component: ComponentRef) -> str | None:
-        if _resolved_locally(project_root, component):
-            return None
-
-        if allow_network:
-            in_catalog = _resolved_in_catalog(project_root, component)
-            if in_catalog is True:
-                return None
-            if in_catalog is False:
-                return (
-                    f"{component.kind[:-1]} '{component.id}' is not bundled, "
-                    "installed, or present in any active catalog."
-                )
-            warnings.append(
-                f"Could not verify {component.kind[:-1]} '{component.id}' "
-                "(catalog unreachable); reference left unchecked."
-            )
-            return None
-
-        warnings.append(
-            f"Could not verify {component.kind[:-1]} '{component.id}' offline "
-            "(not bundled or installed); re-run validate online to check catalogs."
-        )
-        return None
-
-    return check

src/specify_cli/bundler/services/resolver.py

@@ -1,122 +0,0 @@
-"""Resolver: expand a bundle manifest into a concrete, ordered install plan.
-
-The plan the resolver produces is the single source of truth shared by
-``info`` (preview) and ``install`` (execution) so the two never diverge
-(SC-002 transparency). Resolution also enforces the SpecKit version gate
-(FR-016) and the integration-compatibility check (FR-019).
-"""
-from __future__ import annotations
-
-from dataclasses import dataclass, field
-from pathlib import Path
-
-from .. import BundlerError
-from ..lib.versioning import satisfies
-from ..models.manifest import BundleManifest, ComponentRef
-
-
-@dataclass
-class InstallPlan:
-    bundle_id: str
-    version: str
-    role: str
-    effective_integration: str | None
-    components: list[ComponentRef] = field(default_factory=list)
-    warnings: list[str] = field(default_factory=list)
-
-    @property
-    def component_count(self) -> int:
-        return len(self.components)
-
-    def grouped(self) -> dict[str, list[ComponentRef]]:
-        groups: dict[str, list[ComponentRef]] = {
-            "extensions": [],
-            "presets": [],
-            "steps": [],
-            "workflows": [],
-        }
-        for component in self.components:
-            groups.setdefault(component.kind, []).append(component)
-        return groups
-
-
-def resolve_install_plan(
-    manifest: BundleManifest,
-    *,
-    speckit_version: str,
-    active_integration: str | None,
-    integration_explicit: bool = False,
-    enforce_version: bool = True,
-) -> InstallPlan:
-    """Expand *manifest* into an :class:`InstallPlan`, enforcing gates.
-
-    Raises :class:`BundlerError` when a hard gate fails (version gate,
-    integration clash). Soft issues are collected in ``plan.warnings``.
-
-    *integration_explicit* signals that ``active_integration`` came from an
-    explicit ``--integration`` override rather than project auto-detection. When
-    a bundle pins an integration but the project's active integration cannot be
-    determined (``active_integration is None``) and the caller did not supply an
-    explicit override, resolution fails instead of silently adopting the
-    bundle's required integration (FR-019 guard).
-    """
-    structural = manifest.structural_errors()
-    if structural:
-        raise BundlerError(
-            "Cannot resolve an invalid manifest:\n  - " + "\n  - ".join(structural)
-        )
-
-    # FR-016: SpecKit version gate — refuse incompatible installs.
-    if enforce_version and manifest.requires.speckit_version:
-        if not satisfies(speckit_version, manifest.requires.speckit_version):
-            raise BundlerError(
-                f"Bundle '{manifest.bundle.id}' requires Spec Kit "
-                f"{manifest.requires.speckit_version}, but this project uses "
-                f"{speckit_version}. Update Spec Kit or choose a compatible bundle."
-            )
-
-    # FR-019: integration-compatibility — a bundle that pins a different
-    # integration than the project's active one halts (no silent change).
-    effective_integration = active_integration
-    if manifest.integration is not None:
-        required = manifest.integration.id
-        if active_integration and required != active_integration:
-            raise BundlerError(
-                f"Bundle '{manifest.bundle.id}' targets integration '{required}', "
-                f"but this project's active integration is '{active_integration}'. "
-                "Installing it would conflict; aborting with no changes."
-            )
-        if active_integration is None and not integration_explicit:
-            raise BundlerError(
-                f"Bundle '{manifest.bundle.id}' targets integration '{required}', "
-                "but this project's active integration could not be determined "
-                "(missing or unreadable .specify/integration.json). Re-run with "
-                "'--integration' to confirm the target, or repair the project "
-                "before installing."
-            )
-        effective_integration = required
-
-    warnings: list[str] = []
-    if manifest.requires.tools:
-        warnings.append(
-            "Requires external tools: " + ", ".join(manifest.requires.tools)
-        )
-    if manifest.requires.mcp:
-        warnings.append("Requires MCP servers: " + ", ".join(manifest.requires.mcp))
-
-    return InstallPlan(
-        bundle_id=manifest.bundle.id,
-        version=manifest.bundle.version,
-        role=manifest.bundle.role,
-        effective_integration=effective_integration,
-        components=list(manifest.components),
-        warnings=warnings,
-    )
-
-
-def load_manifest_from_dir(bundle_dir: Path) -> BundleManifest:
-    """Load ``bundle.yml`` from a bundle directory."""
-    manifest_path = Path(bundle_dir) / "bundle.yml"
-    if not manifest_path.exists():
-        raise BundlerError(f"No bundle.yml found in '{bundle_dir}'.")
-    return BundleManifest.from_file(manifest_path)

src/specify_cli/bundler/services/validator.py

@@ -1,60 +0,0 @@
-"""Validator: structural + reference validation for a bundle manifest.
-
-``specify bundle validate`` reports whether a manifest is well-formed and all
-component references are resolvable. Structural checks come from the manifest
-model; reference resolution is optional (requires a resolver callback) so the
-command can run fully offline against pinned/local references.
-"""
-from __future__ import annotations
-
-from dataclasses import dataclass, field
-from typing import Callable
-
-from .. import BundlerError
-from ..lib.versioning import parse_constraint
-from ..models.manifest import BundleManifest, ComponentRef
-
-# A reference checker returns None when resolvable, or an error string.
-ReferenceChecker = Callable[[ComponentRef], str | None]
-
-
-@dataclass
-class ValidationReport:
-    errors: list[str] = field(default_factory=list)
-    warnings: list[str] = field(default_factory=list)
-
-    @property
-    def ok(self) -> bool:
-        return not self.errors
-
-    def merge(self, other: "ValidationReport") -> None:
-        self.errors.extend(other.errors)
-        self.warnings.extend(other.warnings)
-
-
-def validate_manifest(
-    manifest: BundleManifest,
-    reference_checker: ReferenceChecker | None = None,
-) -> ValidationReport:
-    report = ValidationReport()
-
-    report.errors.extend(manifest.structural_errors())
-
-    if manifest.requires.speckit_version:
-        try:
-            parse_constraint(manifest.requires.speckit_version)
-        except BundlerError as exc:
-            report.errors.append(
-                f"requires.speckit_version '{manifest.requires.speckit_version}' "
-                f"is not a valid constraint: {exc}"
-            )
-
-    if reference_checker is not None:
-        for component in manifest.components:
-            problem = reference_checker(component)
-            if problem:
-                report.errors.append(
-                    f"Unresolved reference {component.label()}: {problem}"
-                )
-
-    return report

src/specify_cli/commands/bundle/__init__.py

@@ -1,834 +0,0 @@
-"""``specify bundle`` command group — discover, install, author Spec Kit bundles.
-
-This module is the CLI/UX layer only (Principle I: thin commands over services).
-Each command resolves a project, builds a catalog stack, delegates to a bundler
-service, and renders Rich output. ``--json`` emits machine-readable data on
-stdout; human logs go to stderr/console.
-"""
-from __future__ import annotations
-
-import json as _json
-import re
-from pathlib import Path
-
-import typer
-
-from ..._console import console
-from ...bundler import BundlerError
-from ...bundler.lib.project import (
-    active_integration,
-    find_project_root,
-    require_project_root,
-)
-from ...bundler.models.records import load_records
-
-bundle_app = typer.Typer(
-    name="bundle",
-    help="Discover, install, and author Spec Kit bundles",
-    add_completion=False,
-)
-
-bundle_catalog_app = typer.Typer(
-    name="catalog",
-    help="Manage bundle catalog sources",
-    add_completion=False,
-)
-bundle_app.add_typer(bundle_catalog_app, name="catalog")
-
-
-# ===== helpers =====
-
-
-def _fail(message: str) -> None:
-    """Print an actionable error to stderr and exit non-zero."""
-    console.print(f"[red]Error:[/red] {message}", style=None)
-    raise typer.Exit(code=1)
-
-
-def _user_config_dir() -> Path:
-    # User-scope Spec Kit config lives under ~/.specify (same convention as
-    # auth.json, extension/preset catalogs). Passing this through to the source
-    # stack is what makes the documented project > user > built-in precedence
-    # reachable from the CLI.
-    return Path.home() / ".specify"
-
-
-def _build_stack(project_root: Path, *, offline: bool):
-    from ...bundler.services.adapters import make_catalog_fetcher
-    from ...bundler.services.catalog_stack import CatalogStack
-
-    fetcher = make_catalog_fetcher(allow_network=not offline)
-    return CatalogStack.load(project_root, fetcher, user_config_dir=_user_config_dir())
-
-
-def _speckit_version() -> str:
-    from ..._assets import get_speckit_version
-
-    return get_speckit_version()
-
-
-def _trust_level(verified: bool) -> str:
-    """Trust framing for a catalog entry (FR-010): org-curated vs community."""
-    return "verified" if verified else "community"
-
-
-def _trust_badge(verified: bool) -> str:
-    return (
-        "[green]✔ verified[/green]"
-        if verified
-        else "[yellow]community[/yellow]"
-    )
-
-
-def _default_script_type() -> str:
-    """OS-appropriate default script flavor (FR-013)."""
-    import os
-
-    return "ps" if os.name == "nt" else "sh"
-
-
-def _run_init(integration: str, *, script_type: str, offline: bool = False) -> None:
-    """Idempotently scaffold a Spec Kit project here via the existing ``init`` machinery.
-
-    Reuses the real ``specify init`` command callback in-process (Principle I)
-    with ``--here --force`` so it is non-interactive and merges into the current
-    directory.
-    """
-    from ... import app
-
-    init_cb = next(
-        c.callback
-        for c in app.registered_commands
-        if c.callback and c.callback.__name__ == "init"
-    )
-    try:
-        init_cb(
-            project_name=None,
-            script_type=script_type,
-            ignore_agent_tools=True,
-            here=True,
-            force=True,
-            skip_tls=False,
-            debug=False,
-            github_token=None,
-            offline=offline,
-            preset=None,
-            integration=integration,
-            integration_options=None,
-        )
-    except typer.Exit as exc:
-        if exc.exit_code:
-            raise BundlerError(
-                f"Failed to initialize a Spec Kit project (integration '{integration}')."
-            ) from exc
-
-
-def _resolve_init_integration(override: str | None, manifest) -> str:
-    """Precedence (FR-013): explicit override → bundle-declared → default."""
-    from ..._agent_config import DEFAULT_INIT_INTEGRATION
-
-    if override:
-        return override
-    if manifest is not None and manifest.integration is not None:
-        return manifest.integration.id
-    return DEFAULT_INIT_INTEGRATION
-
-
-# ===== Consume =====
-
-
-@bundle_app.command("search")
-def bundle_search(
-    query: str = typer.Argument("", help="Optional text query"),
-    offline: bool = typer.Option(False, "--offline", help="Do not access the network"),
-    as_json: bool = typer.Option(False, "--json", help="Emit JSON to stdout"),
-) -> None:
-    """List matching bundles across the active catalog stack."""
-    try:
-        project_root = find_project_root() or Path.cwd()
-        stack = _build_stack(project_root, offline=offline)
-        results = stack.search(query)
-    except BundlerError as exc:
-        _fail(str(exc))
-        return
-
-    if as_json:
-        payload = [
-            {
-                "id": r.entry.id,
-                "name": r.entry.name,
-                "role": r.entry.role,
-                "version": r.entry.version,
-                "description": r.entry.description,
-                "source": r.source.id,
-                "install_policy": r.source.install_policy.value,
-                "verified": r.entry.verified,
-                "trust": _trust_level(r.entry.verified),
-            }
-            for r in results
-        ]
-        print(_json.dumps(payload, indent=2))
-        return
-
-    if not results:
-        console.print("[yellow]No matching bundles found.[/yellow]")
-        return
-
-    console.print("\n[bold cyan]Bundles:[/bold cyan]\n")
-    for r in results:
-        policy = (
-            "[dim](discovery-only)[/dim]"
-            if not r.source.install_allowed
-            else ""
-        )
-        console.print(
-            f"  [bold]{r.entry.id}[/bold] v{r.entry.version} — {r.entry.name} "
-            f"[dim]({r.entry.role})[/dim] {_trust_badge(r.entry.verified)} {policy}"
-        )
-        console.print(f"    {r.entry.description}")
-        console.print(f"    [dim]source: {r.source.id}[/dim]")
-
-
-@bundle_app.command("info")
-def bundle_info(
-    bundle_id: str = typer.Argument(..., help="Bundle id to inspect"),
-    offline: bool = typer.Option(False, "--offline", help="Do not access the network"),
-    as_json: bool = typer.Option(False, "--json", help="Emit JSON to stdout"),
-) -> None:
-    """Show full metadata and the fully expanded component set (== what install adds)."""
-    try:
-        project_root = find_project_root() or Path.cwd()
-        stack = _build_stack(project_root, offline=offline)
-        resolved = stack.resolve(bundle_id)
-        # `info` must show the fully expanded component set that `install` would
-        # apply (contracts/cli-commands.md). Expansion happens regardless of
-        # install policy — discovery-only bundles stay inspectable; only
-        # `install` is refused. But if the manifest itself can't be resolved
-        # (e.g. --offline against an https:// download_url, or a download
-        # failure), fail loudly and exit non-zero rather than silently
-        # degrading to catalog `provides` counts, so users never mistake an
-        # unverifiable bundle for a known/installable one.
-        manifest = _download_manifest(resolved, offline=offline)
-    except BundlerError as exc:
-        _fail(str(exc))
-        return
-
-    overlaps = _bundle_overlaps(project_root, manifest, offline=offline)
-    components = _manifest_component_view(manifest)
-
-    entry = resolved.entry
-    if as_json:
-        payload = {
-            "id": entry.id,
-            "name": entry.name,
-            "version": entry.version,
-            "role": entry.role,
-            "description": entry.description,
-            "author": entry.author,
-            "license": entry.license,
-            "source": resolved.source.id,
-            "install_policy": resolved.source.install_policy.value,
-            "provides": entry.provides,
-            "requires": {"speckit_version": entry.requires_speckit_version},
-            "verified": entry.verified,
-            "trust": _trust_level(entry.verified),
-            "integration": (manifest.integration.id if manifest and manifest.integration else None),
-            "components": components,
-            "overlaps": overlaps,
-        }
-        print(_json.dumps(payload, indent=2))
-        return
-
-    console.print(f"\n[bold cyan]{entry.id}[/bold cyan] v{entry.version} — {entry.name}")
-    console.print(f"  Role: {entry.role}")
-    console.print(f"  {entry.description}")
-    console.print(f"  Author: {entry.author}   License: {entry.license}")
-    console.print(f"  Source: {resolved.source.id} ({resolved.source.install_policy.value})")
-    console.print(f"  Trust: {_trust_badge(entry.verified)}")
-    if entry.requires_speckit_version:
-        console.print(f"  Requires Spec Kit: {entry.requires_speckit_version}")
-    if manifest and manifest.integration:
-        console.print(f"  Integration: {manifest.integration.id}")
-
-    if components:
-        console.print("\n  [bold]Components[/bold] (added on install):")
-        for kind in ("extensions", "presets", "steps", "workflows"):
-            items = [c for c in components if c["kind"] == kind]
-            if not items:
-                continue
-            console.print(f"    [bold]{kind}:[/bold]")
-            for item in items:
-                console.print(f"      - {_format_component(item)}")
-    else:
-        console.print("\n  [bold]Provides:[/bold]")
-        for kind in ("extensions", "presets", "steps", "workflows"):
-            count = entry.provides.get(kind, 0)
-            if count:
-                console.print(f"    {kind}: {count}")
-
-    if overlaps:
-        console.print("\n  [yellow]Overlaps with already-installed bundles:[/yellow]")
-        for overlap in overlaps:
-            console.print(f"    [yellow]-[/yellow] {overlap}")
-
-    if not resolved.install_allowed:
-        console.print(
-            "\n  [yellow]This source is discovery-only; the bundle cannot be "
-            "installed from here.[/yellow]"
-        )
-
-
-@bundle_app.command("list")
-def bundle_list(
-    as_json: bool = typer.Option(False, "--json", help="Emit JSON to stdout"),
-) -> None:
-    """List bundles currently installed in the project with versions."""
-    try:
-        project_root = require_project_root()
-        records = load_records(project_root)
-    except BundlerError as exc:
-        _fail(str(exc))
-        return
-
-    if as_json:
-        print(_json.dumps([r.to_dict() for r in records], indent=2))
-        return
-
-    if not records:
-        console.print("[yellow]No bundles installed.[/yellow]")
-        console.print("\nInstall one with: [cyan]specify bundle install <id>[/cyan]")
-        return
-
-    console.print("\n[bold cyan]Installed bundles:[/bold cyan]\n")
-    for record in records:
-        console.print(
-            f"  [bold]{record.bundle_id}[/bold] v{record.version} "
-            f"[dim]({len(record.contributed_components)} components, "
-            f"installed {record.installed_at})[/dim]"
-        )
-
-
-@bundle_app.command("install")
-def bundle_install(
-    bundle_id: str = typer.Argument(
-        ...,
-        help="Bundle id (from the catalog stack) or a local path to a .zip "
-        "artifact, bundle directory, or bundle.yml",
-    ),
-    integration: str = typer.Option(None, "--integration", help="Override integration"),
-    offline: bool = typer.Option(False, "--offline", help="Do not access the network"),
-) -> None:
-    """Install a bundle's full component set through each primitive's machinery.
-
-    ``bundle_id`` may be a catalog bundle id, or a local path to a built
-    artifact (``.zip``), a bundle directory, or a ``bundle.yml`` file. Local
-    sources install directly without consulting the catalog stack.
-    """
-    try:
-        from ...bundler.lib.project import find_project_root
-        from ...bundler.services.adapters import DefaultPrimitiveInstaller
-        from ...bundler.services.installer import install_bundle
-        from ...bundler.services.resolver import resolve_install_plan
-
-        project_root = find_project_root()
-
-        local_manifest = _local_manifest_source(bundle_id)
-        if local_manifest is not None:
-            manifest = local_manifest
-        else:
-            stack = _build_stack(project_root or Path.cwd(), offline=offline)
-            resolved = stack.resolve(bundle_id)
-
-            if not resolved.install_allowed:
-                raise BundlerError(
-                    f"Bundle '{bundle_id}' resolves only from a discovery-only source "
-                    f"('{resolved.source.id}'); it cannot be installed from there."
-                )
-            manifest = _download_manifest(resolved, offline=offline)
-
-        if project_root is None:
-            init_integration = _resolve_init_integration(integration, manifest)
-            console.print(
-                f"[cyan]No Spec Kit project here; initializing with integration "
-                f"'{init_integration}'…[/cyan]"
-            )
-            _run_init(init_integration, script_type=_default_script_type(), offline=offline)
-            project_root = require_project_root()
-
-        for overlap in _bundle_overlaps(project_root, manifest, offline=offline):
-            console.print(f"[yellow]![/yellow] {overlap}")
-
-        # For an already-initialized project, the project's recorded active
-        # integration is authoritative — an explicit --integration must not be
-        # able to bypass the FR-019 integration-clash guard. The override only
-        # selects the integration at init time (handled above) or confirms the
-        # target when the active integration cannot be determined.
-        detected = active_integration(project_root)
-        plan = resolve_install_plan(
-            manifest,
-            speckit_version=_speckit_version(),
-            active_integration=detected if detected is not None else integration,
-            integration_explicit=bool(integration) and detected is None,
-        )
-        for warning in plan.warnings:
-            console.print(f"[yellow]![/yellow] {warning}")
-
-        result = install_bundle(
-            project_root,
-            plan,
-            DefaultPrimitiveInstaller(allow_network=not offline),
-            manifest=manifest,
-        )
-    except BundlerError as exc:
-        _fail(str(exc))
-        return
-
-    console.print(
-        f"[green]✓[/green] Installed '{result.bundle_id}' "
-        f"({len(result.installed)} added, {len(result.skipped)} already present)."
-    )
-
-
-@bundle_app.command("update")
-def bundle_update(
-    bundle_id: str = typer.Argument(None, help="Bundle id, or omit with --all"),
-    all_bundles: bool = typer.Option(False, "--all", help="Update every installed bundle"),
-    integration: str = typer.Option(None, "--integration", help="Override integration"),
-    offline: bool = typer.Option(False, "--offline", help="Do not access the network"),
-) -> None:
-    """Re-resolve and refresh a bundle's components via each primitive's update path."""
-    try:
-        project_root = require_project_root()
-        records = load_records(project_root)
-        if not all_bundles and not bundle_id:
-            raise BundlerError("Specify a bundle id or use --all.")
-        targets = (
-            [r.bundle_id for r in records]
-            if all_bundles
-            else [bundle_id]
-        )
-        if not targets:
-            console.print("[yellow]No installed bundles to update.[/yellow]")
-            return
-
-        stack = _build_stack(project_root, offline=offline)
-        from ...bundler.services.adapters import DefaultPrimitiveInstaller
-        from ...bundler.services.installer import install_bundle
-        from ...bundler.services.resolver import resolve_install_plan
-
-        installer = DefaultPrimitiveInstaller(allow_network=not offline)
-        for target in targets:
-            if not any(r.bundle_id == target for r in records):
-                raise BundlerError(f"Bundle '{target}' is not installed.")
-            resolved = stack.resolve(target)
-            if not resolved.install_allowed:
-                raise BundlerError(
-                    f"Bundle '{target}' resolves only from a discovery-only source "
-                    f"('{resolved.source.id}'); it cannot be updated from there. "
-                    "Update requires an install-allowed source (FR-025)."
-                )
-            manifest = _download_manifest(resolved, offline=offline)
-            detected = active_integration(project_root)
-            plan = resolve_install_plan(
-                manifest,
-                speckit_version=_speckit_version(),
-                active_integration=detected if detected is not None else integration,
-                integration_explicit=bool(integration) and detected is None,
-            )
-            install_bundle(project_root, plan, installer, manifest=manifest, refresh=True)
-            console.print(f"[green]✓[/green] Updated '{target}' to v{plan.version}.")
-    except BundlerError as exc:
-        _fail(str(exc))
-        return
-
-
-@bundle_app.command("remove")
-def bundle_remove(
-    bundle_id: str = typer.Argument(..., help="Installed bundle id to remove"),
-) -> None:
-    """Uninstall only the components this bundle contributed (no collateral removals)."""
-    try:
-        project_root = require_project_root()
-        from ...bundler.services.adapters import DefaultPrimitiveInstaller
-        from ...bundler.services.installer import remove_bundle
-
-        result = remove_bundle(project_root, bundle_id, DefaultPrimitiveInstaller())
-    except BundlerError as exc:
-        _fail(str(exc))
-        return
-
-    console.print(
-        f"[green]✓[/green] Removed '{result.bundle_id}' "
-        f"({len(result.uninstalled)} uninstalled, {len(result.skipped)} kept for other bundles)."
-    )
-
-
-# ===== Author =====
-
-
-@bundle_app.command("validate")
-def bundle_validate(
-    path: Path = typer.Option(
-        None, "--path", help="Bundle directory or bundle.yml (default: cwd)"
-    ),
-    offline: bool = typer.Option(
-        False,
-        "--offline",
-        help="Do not access catalogs; verify references against bundled/installed only",
-    ),
-) -> None:
-    """Report whether the manifest is well-formed and references resolve."""
-    try:
-        manifest_path = _resolve_manifest_path(path)
-        from ...bundler.lib.project import find_project_root
-        from ...bundler.models.manifest import BundleManifest
-        from ...bundler.services.references import make_reference_checker
-        from ...bundler.services.validator import validate_manifest
-
-        manifest = BundleManifest.from_file(manifest_path)
-        ref_root = find_project_root(manifest_path.parent) or Path.cwd()
-        ref_warnings: list[str] = []
-        checker = make_reference_checker(
-            ref_root, allow_network=not offline, warnings=ref_warnings
-        )
-        report = validate_manifest(manifest, reference_checker=checker)
-        report.warnings.extend(ref_warnings)
-    except BundlerError as exc:
-        _fail(str(exc))
-        return
-
-    for warning in report.warnings:
-        console.print(f"[yellow]![/yellow] {warning}")
-    if not report.ok:
-        console.print("[red]Manifest is invalid:[/red]")
-        for error in report.errors:
-            console.print(f"  [red]-[/red] {error}")
-        raise typer.Exit(code=1)
-    console.print(f"[green]✓[/green] {manifest.bundle.id} is well-formed and valid.")
-
-
-@bundle_app.command("build")
-def bundle_build(
-    path: Path = typer.Option(
-        None, "--path", help="Bundle directory (default: cwd)"
-    ),
-    output: Path = typer.Option(None, "--output", help="Output directory for the artifact"),
-) -> None:
-    """Produce a single versioned distributable artifact (.zip)."""
-    try:
-        bundle_dir = (path or Path.cwd()).resolve()
-        if bundle_dir.is_file():
-            bundle_dir = bundle_dir.parent
-        from ...bundler.services.packager import build_bundle
-
-        result = build_bundle(bundle_dir, output_dir=output)
-    except BundlerError as exc:
-        _fail(str(exc))
-        return
-
-    console.print(
-        f"[green]✓[/green] Built {result.artifact_path.name} "
-        f"({result.file_count} files) → {result.artifact_path}"
-    )
-
-
-@bundle_app.command("init")
-def bundle_init(
-    bundle: str = typer.Argument(None, help="Optional bundle to install after init"),
-    integration: str = typer.Option(None, "--integration", help="Integration override"),
-    offline: bool = typer.Option(False, "--offline", help="Do not access the network"),
-) -> None:
-    """Ensure the project is initialized (idempotent), then optionally install a bundle."""
-    from ...bundler.lib.project import find_project_root
-
-    try:
-        project_root = find_project_root()
-        if project_root is None:
-            init_integration = _resolve_init_integration(integration, None)
-            console.print(
-                f"[cyan]Initializing a Spec Kit project with integration "
-                f"'{init_integration}'…[/cyan]"
-            )
-            _run_init(init_integration, script_type=_default_script_type(), offline=offline)
-            project_root = require_project_root()
-    except BundlerError as exc:
-        _fail(str(exc))
-        return
-
-    console.print(f"[green]✓[/green] Spec Kit project ready at {project_root}.")
-    if bundle:
-        bundle_install(bundle, integration=integration, offline=offline)
-
-
-# ===== Catalog management =====
-
-
-@bundle_catalog_app.command("list")
-def catalog_list() -> None:
-    """Print the active, priority-ordered catalog stack with scope and policy."""
-    try:
-        project_root = require_project_root()
-        from ...bundler.models.catalog import Scope, load_source_stack
-
-        sources = load_source_stack(project_root, user_config_dir=_user_config_dir())
-    except BundlerError as exc:
-        _fail(str(exc))
-        return
-
-    console.print("\n[bold cyan]Catalog stack[/bold cyan] (highest precedence first):\n")
-    only_builtin = all(s.scope == Scope.BUILTIN for s in sources)
-    for source in sources:
-        console.print(
-            f"  [bold]{source.id}[/bold]  priority={source.priority}  "
-            f"policy={source.install_policy.value}  scope={source.scope.value}"
-        )
-        console.print(f"    [dim]{source.url}[/dim]")
-    if only_builtin:
-        console.print("\n[dim]Using the built-in default stack.[/dim]")
-
-
-@bundle_catalog_app.command("add")
-def catalog_add(
-    url: str = typer.Argument(..., help="Catalog URL"),
-    policy: str = typer.Option(
-        "install-allowed", "--policy", help="install-allowed | discovery-only"
-    ),
-    priority: int = typer.Option(10, "--priority", help="Source priority (lower = higher)"),
-    source_id: str = typer.Option(None, "--id", help="Explicit source id"),
-) -> None:
-    """Register a project-scoped catalog source and persist it."""
-    try:
-        project_root = require_project_root()
-        from ...bundler.commands_impl.catalog_config import add_source
-
-        source = add_source(project_root, url, policy=policy, priority=priority, source_id=source_id)
-    except BundlerError as exc:
-        _fail(str(exc))
-        return
-
-    console.print(
-        f"[green]✓[/green] Added catalog '{source.id}' "
-        f"(priority {source.priority}, {source.install_policy.value})."
-    )
-
-
-@bundle_catalog_app.command("remove")
-def catalog_remove(
-    id_or_url: str = typer.Argument(..., help="Source id or url to remove"),
-) -> None:
-    """Remove a project-scoped catalog source (built-in defaults can't be deleted)."""
-    try:
-        project_root = require_project_root()
-        from ...bundler.commands_impl.catalog_config import remove_source
-
-        removed = remove_source(project_root, id_or_url)
-    except BundlerError as exc:
-        _fail(str(exc))
-        return
-
-    console.print(f"[green]✓[/green] Removed catalog source '{removed}'.")
-
-
-# ===== internal helpers =====
-
-
-def _manifest_component_view(manifest) -> list[dict]:
-    """Flatten a manifest's components to JSON-friendly dicts (id, version, ...)."""
-    if manifest is None:
-        return []
-    view: list[dict] = []
-    for component in manifest.components:
-        item = {
-            "kind": component.kind,
-            "id": component.id,
-            "version": component.version,
-        }
-        if component.priority is not None:
-            item["priority"] = component.priority
-        if component.strategy is not None:
-            item["strategy"] = component.strategy
-        view.append(item)
-    return view
-
-
-def _format_component(item: dict) -> str:
-    label = f"{item['id']} v{item['version']}" if item.get("version") else item["id"]
-    extras = []
-    if item.get("priority") is not None:
-        extras.append(f"priority={item['priority']}")
-    if item.get("strategy") is not None:
-        extras.append(f"strategy={item['strategy']}")
-    if extras:
-        label += f" ({', '.join(extras)})"
-    return label
-
-
-def _bundle_overlaps(project_root: Path, manifest, *, offline: bool) -> list[str]:
-    """Return informational overlaps between *manifest* and installed bundles."""
-    if manifest is None:
-        return []
-    try:
-        from ...bundler.services.conflict import detect_conflicts
-
-        report = detect_conflicts(
-            manifest,
-            active_integration(project_root),
-            load_records(project_root),
-        )
-        return list(report.overlaps)
-    except BundlerError:
-        return []
-
-
-def _local_manifest_source(arg: str):
-    """Return a :class:`BundleManifest` if *arg* points at a local bundle.
-
-    Supports a built ``.zip`` artifact, a bundle directory, or a ``bundle.yml``
-    file. Returns ``None`` when *arg* is not an existing path, so callers fall
-    back to catalog-stack resolution by bundle id.
-    """
-    from ...bundler.models.manifest import BundleManifest
-
-    candidate = Path(arg).expanduser()
-    if not candidate.exists():
-        return None
-
-    if candidate.is_dir():
-        manifest_path = candidate / "bundle.yml"
-        if not manifest_path.exists():
-            raise BundlerError(f"No bundle.yml found in '{candidate}'.")
-        return BundleManifest.from_file(manifest_path)
-
-    if candidate.suffix == ".zip":
-        import io
-        import zipfile
-
-        import yaml as _yaml
-
-        with zipfile.ZipFile(candidate) as archive:
-            try:
-                raw = archive.read("bundle.yml")
-            except KeyError as exc:
-                raise BundlerError(
-                    f"Artifact '{candidate}' does not contain a bundle.yml."
-                ) from exc
-        data = _yaml.safe_load(io.BytesIO(raw))
-        return BundleManifest.from_dict(data)
-
-    if candidate.name == "bundle.yml" or candidate.suffix in (".yml", ".yaml"):
-        return BundleManifest.from_file(candidate)
-
-    raise BundlerError(
-        f"'{candidate}' is not a recognised bundle source (.zip artifact, bundle "
-        "directory, or bundle.yml)."
-    )
-
-
-def _resolve_manifest_path(path: Path | None) -> Path:
-    target = (path or Path.cwd()).resolve()
-    if target.is_dir():
-        target = target / "bundle.yml"
-    if not target.exists():
-        raise BundlerError(f"No bundle.yml found at '{target}'.")
-    return target
-
-
-def _download_manifest(resolved, *, offline: bool):
-    """Resolve a bundle's manifest from its catalog ``download_url``.
-
-    Local/``file://`` URLs always work offline and may point at a ``.zip``
-    artifact, a bundle directory, or a ``bundle.yml`` (handled by
-    :func:`_local_manifest_source`). Remote ``https://`` URLs are fetched with
-    the shared authenticated, redirect-validated HTTP client, and only when not
-    ``--offline``.
-    """
-    from urllib.parse import urlparse
-
-    url = resolved.entry.download_url
-    if not url:
-        raise BundlerError(
-            f"Catalog entry '{resolved.entry.id}' has no download_url; cannot resolve "
-            "its manifest."
-        )
-    parsed = urlparse(url)
-    scheme = parsed.scheme.lower()
-
-    # On Windows an absolute path like ``C:\bundle.yml`` parses with a
-    # single-letter ``scheme``; treat it as a local file, not a URL scheme.
-    if scheme in ("", "file") or re.match(r"^[A-Za-z]:[\\/]", url):
-        local = Path(parsed.path if scheme == "file" else url)
-        manifest = _local_manifest_source(str(local))
-        if manifest is None:
-            raise BundlerError(f"Bundle manifest not found: {local}")
-        return manifest
-
-    if scheme in ("http", "https"):
-        if offline:
-            raise BundlerError(
-                f"Network access disabled; cannot download bundle '{resolved.entry.id}' "
-                f"from {url}."
-            )
-        return _download_remote_manifest(resolved.entry.id, url)
-
-    raise BundlerError(
-        f"Unsupported download_url scheme for bundle '{resolved.entry.id}': {url}"
-    )
-
-
-def _require_https(label: str, url: str) -> None:
-    from urllib.parse import urlparse
-
-    parsed = urlparse(url)
-    is_localhost = parsed.hostname in ("localhost", "127.0.0.1", "::1")
-    if parsed.scheme != "https" and not (parsed.scheme == "http" and is_localhost):
-        raise BundlerError(
-            f"Refusing to download {label} over non-HTTPS URL: {url}"
-        )
-    if not parsed.hostname:
-        raise BundlerError(f"Refusing to download {label} from URL with no host: {url}")
-
-
-def _download_remote_manifest(entry_id: str, url: str):
-    """Fetch a remote bundle artifact over HTTPS and extract its manifest."""
-    import io
-    import tempfile
-
-    from ...authentication.http import open_url
-
-    def _validate_redirect(old_url: str, new_url: str) -> None:
-        _require_https(f"bundle '{entry_id}'", new_url)
-
-    _require_https(f"bundle '{entry_id}'", url)
-    try:
-        with open_url(url, timeout=30, redirect_validator=_validate_redirect) as resp:
-            _require_https(f"bundle '{entry_id}'", resp.geturl())
-            raw = resp.read()
-    except BundlerError:
-        raise
-    except Exception as exc:  # noqa: BLE001
-        raise BundlerError(f"Failed to download bundle '{entry_id}' from {url}: {exc}") from exc
-
-    # A .zip artifact is written to a temp file and parsed via the local-source
-    # path (which extracts bundle.yml); any other payload is treated as YAML.
-    if url.lower().endswith(".zip"):
-        with tempfile.TemporaryDirectory() as tmp:
-            artifact = Path(tmp) / "bundle.zip"
-            artifact.write_bytes(raw)
-            manifest = _local_manifest_source(str(artifact))
-            if manifest is None:
-                raise BundlerError(
-                    f"Downloaded artifact for bundle '{entry_id}' is not a valid bundle."
-                )
-            return manifest
-
-    import yaml as _yaml
-
-    from ...bundler.models.manifest import BundleManifest
-
-    data = _yaml.safe_load(io.BytesIO(raw))
-    return BundleManifest.from_dict(data)
-
-
-def register(app: typer.Typer) -> None:
-    """Attach the bundle command group to the root Typer app."""
-    app.add_typer(bundle_app, name="bundle")

src/specify_cli/commands/init.py

@@ -693,7 +693,6 @@ def register(app: typer.Typer) -> None:
         ) or getattr(resolved_integration, "_skills_mode", False)
 
         codex_skill_mode = selected_ai == "codex" and _is_skills_integration
-        zcode_skill_mode = selected_ai == "zcode" and _is_skills_integration
         claude_skill_mode = selected_ai == "claude" and _is_skills_integration
         kimi_skill_mode = selected_ai == "kimi"
         agy_skill_mode = selected_ai == "agy" and _is_skills_integration
@@ -707,7 +706,6 @@ def register(app: typer.Typer) -> None:
         cline_skill_mode = selected_ai == "cline"
         native_skill_mode = (
             codex_skill_mode
-            or zcode_skill_mode
             or claude_skill_mode
             or kimi_skill_mode
             or agy_skill_mode
@@ -723,11 +721,6 @@ def register(app: typer.Typer) -> None:
                 f"{step_num}. Start Codex in this project directory; spec-kit skills were installed to [cyan].agents/skills[/cyan]"
             )
             step_num += 1
-        if zcode_skill_mode:
-            steps_lines.append(
-                f"{step_num}. Start ZCode in this project directory; spec-kit skills were installed to [cyan].zcode/skills[/cyan]"
-            )
-            step_num += 1
         if claude_skill_mode:
             steps_lines.append(
                 f"{step_num}. Start Claude in this project directory; spec-kit skills were installed to [cyan].claude/skills[/cyan]"
@@ -750,10 +743,7 @@ def register(app: typer.Typer) -> None:
             step_num += 1
         usage_label = "skills" if native_skill_mode else "slash commands"
 
-        from .._invocation_style import (
-            is_dollar_skills_agent as _is_dollar_skills_agent,
-            is_slash_skills_agent as _is_slash_skills_agent,
-        )
+        from .._invocation_style import is_slash_skills_agent as _is_slash_skills_agent
 
         # `_is_skills_integration` means the integration is installed in
         # skills mode, which is the semantic equivalent of `ai_skills_enabled`
@@ -761,7 +751,7 @@ def register(app: typer.Typer) -> None:
         _ai_skills_enabled = _is_skills_integration
 
         def _display_cmd(name: str) -> str:
-            if _is_dollar_skills_agent(selected_ai, _ai_skills_enabled):
+            if codex_skill_mode:
                 return f"$speckit-{name}"
             if kimi_skill_mode:
                 return f"/skill:speckit-{name}"

src/specify_cli/extensions.py

@@ -26,11 +26,11 @@ import yaml
 from packaging import version as pkg_version
 from packaging.specifiers import InvalidSpecifier, SpecifierSet
 
-from .._init_options import is_ai_skills_enabled
-from .._invocation_style import is_dollar_skills_agent, is_slash_skills_agent
-from .._utils import dump_frontmatter, relative_extension_path_violation
-from ..catalogs import CatalogEntry as BaseCatalogEntry
-from ..catalogs import CatalogStackBase
+from ._init_options import is_ai_skills_enabled
+from ._invocation_style import is_slash_skills_agent
+from ._utils import dump_frontmatter
+from .catalogs import CatalogEntry as BaseCatalogEntry
+from .catalogs import CatalogStackBase
 
 _FALLBACK_CORE_COMMAND_NAMES = frozenset(
     {
@@ -290,18 +290,6 @@ class ExtensionManifest:
             if "name" not in cmd or "file" not in cmd:
                 raise ValidationError("Command missing 'name' or 'file'")
 
-            # Validate the 'file' field at manifest-load time using the single
-            # shared policy in relative_extension_path_violation(), so manifest
-            # validation cannot drift from the runtime registrar guard. This is
-            # defense-in-depth: the command/skill/preset readers also contain
-            # the resolved path, but rejecting an unsafe value here surfaces a
-            # clear error instead of silently skipping the command.
-            cmd_file = cmd["file"]
-            reason = relative_extension_path_violation(cmd_file)
-            if reason:
-                label = repr(cmd_file) if isinstance(cmd_file, str) else f"for command '{cmd.get('name')}'"
-                raise ValidationError(f"Invalid command 'file' {label}: {reason}")
-
             # Validate command name format
             if not EXTENSION_COMMAND_NAME_PATTERN.match(cmd["name"]):
                 corrected = self._try_correct_command_name(cmd["name"], ext["id"])
@@ -905,7 +893,7 @@ class ExtensionManager:
         be created due to symlink, containment, or permission issues so
         that callers can fall back gracefully.
         """
-        from .. import (
+        from . import (
             _print_cli_warning,
             load_init_options,
             resolve_active_skills_dir,
@@ -948,7 +936,7 @@ class ExtensionManager:
         if not isinstance(selected_ai, str) or not selected_ai:
             return _ensure_usable(skills_dir)
 
-        from ..agents import CommandRegistrar
+        from .agents import CommandRegistrar
 
         registrar = CommandRegistrar()
         agent_config = registrar.AGENT_CONFIGS.get(selected_ai)
@@ -985,9 +973,9 @@ class ExtensionManager:
         if not skills_dir:
             return []
 
-        from .. import load_init_options
-        from ..agents import CommandRegistrar
-        from ..integrations import get_integration
+        from . import load_init_options
+        from .agents import CommandRegistrar
+        from .integrations import get_integration
 
         written: List[str] = []
         opts = load_init_options(self.project_root)
@@ -1073,10 +1061,20 @@ class ExtensionManager:
             )
             # Preserve the command's argument-hint in the generated skill,
             # mirroring the core template path (ClaudeIntegration.setup injects
-            # it for built-in commands). See CommandRegistrar.apply_argument_hint
-            # for why the value is added to the dict before serialization rather
-            # than via the string-based inject_argument_hint helper.
-            registrar.apply_argument_hint(frontmatter, frontmatter_data, integration)
+            # it for built-in commands). The value is added to the frontmatter
+            # dict before serialization — rather than via the string-based
+            # inject_argument_hint helper — so that a folded multi-line
+            # description cannot be split by the inserted line. Gated on the
+            # integration exposing inject_argument_hint so only argument-hint
+            # aware agents receive the key, leaving build_skill_frontmatter's
+            # shared shape unchanged for every other agent.
+            argument_hint = frontmatter.get("argument-hint")
+            if (
+                argument_hint
+                and integration is not None
+                and hasattr(integration, "inject_argument_hint")
+            ):
+                frontmatter_data["argument-hint"] = str(argument_hint)
             frontmatter_text = dump_frontmatter(frontmatter_data)
 
             # Derive a human-friendly title from the command name
@@ -1201,7 +1199,7 @@ class ExtensionManager:
                 shutil.rmtree(skill_subdir)
         else:
             # Fallback: scan all possible agent skills directories
-            from .. import AGENT_CONFIG, DEFAULT_SKILLS_DIR
+            from . import AGENT_CONFIG, DEFAULT_SKILLS_DIR
 
             candidate_dirs: set[Path] = set()
             for cfg in AGENT_CONFIG.values():
@@ -1616,7 +1614,7 @@ class ExtensionManager:
         # Resolve the skills directory for the specific agent so cleanup is
         # agent-scoped and does not depend on the currently-active agent in
         # init-options.  Use the same helper that extension install uses.
-        from .. import _get_skills_dir as resolve_skills_dir
+        from . import _get_skills_dir as resolve_skills_dir
 
         agent_skills_dir = resolve_skills_dir(self.project_root, agent_name)
 
@@ -1678,17 +1676,21 @@ class ExtensionManager:
     def register_enabled_extensions_for_agent(self, agent_name: str) -> None:
         """Register installed, enabled extensions for ``agent_name``.
 
-        Command-file registration is scoped to the explicit ``agent_name``
-        argument, so this method can be used after install, upgrade, or switch.
-        Extension skill rendering is still scoped to the active ``ai`` /
-        ``ai_skills`` settings in init-options, so non-active skills-mode
-        targets receive command files here. Per-agent skills parity is tracked
-        separately in #2948.
+        This is intended to be called after switching integrations. Command
+        registration is scoped to the explicit ``agent_name`` argument, but some
+        behavior still depends on the current init-options state (for example,
+        skills-mode handling uses the active ``ai`` / ``ai_skills`` settings).
+
+        Callers should therefore pass the agent that has just been made active
+        in init-options; in normal use, ``agent_name`` is expected to match the
+        current ``ai`` value. This mirrors extension install behavior while
+        avoiding stale default-mode command directories when that active agent
+        is running in skills mode (notably Copilot ``--skills``).
         """
         if not agent_name:
             return
 
-        from .. import load_init_options
+        from . import load_init_options
 
         registrar = CommandRegistrar()
         agent_config = registrar.AGENT_CONFIGS.get(agent_name)
@@ -1740,53 +1742,38 @@ class ExtensionManager:
                     if new_registered != registered_commands:
                         updates["registered_commands"] = new_registered
 
-                # Extension *skills* are only ever rendered for the active agent:
-                # `_register_extension_skills` resolves the skills dir and
-                # frontmatter from init-options["ai"], ignoring ``agent_name``.
-                # When this method runs for a non-active agent — as install/upgrade
-                # now do for a secondary integration (#2886) — the skills pass would
-                # re-render the *active* agent's extension skills as a side effect,
-                # resurrecting skill files the user deliberately deleted. Skip it
-                # unless the target is the active agent; `switch` is unaffected
-                # because it activates the target before registering. (Rendering
-                # skills for a non-active target is tracked separately in #2948.)
-                if agent_name == active_agent:
-                    try:
-                        registered_skills = self._register_extension_skills(
-                            manifest, ext_dir
-                        )
-                    except Exception as skills_err:
-                        # Skills are a companion artifact.  If command registration
-                        # already succeeded, still persist it so later cleanup can
-                        # find those command files.
-                        from .. import _print_cli_warning
+                try:
+                    registered_skills = self._register_extension_skills(manifest, ext_dir)
+                except Exception as skills_err:
+                    # Skills are a companion artifact.  If command registration
+                    # already succeeded, still persist it so later cleanup can
+                    # find those command files.
+                    from . import _print_cli_warning
 
-                        _print_cli_warning(
-                            "register extension skills for",
-                            "extension",
-                            ext_id,
-                            skills_err,
-                            continuing=(
-                                "Continuing with available registration results for this "
-                                "extension and the remaining extensions."
-                            ),
+                    _print_cli_warning(
+                        "register extension skills for",
+                        "extension",
+                        ext_id,
+                        skills_err,
+                        continuing=(
+                            "Continuing with available registration results for this "
+                            "extension and the remaining extensions."
+                        ),
+                    )
+                else:
+                    if registered_skills:
+                        existing_skills = self._valid_name_list(
+                            metadata.get("registered_skills", [])
                         )
-                    else:
-                        if registered_skills:
-                            existing_skills = self._valid_name_list(
-                                metadata.get("registered_skills", [])
-                            )
-                            merged_skills = list(
-                                dict.fromkeys(existing_skills + registered_skills)
-                            )
-                            updates["registered_skills"] = merged_skills
+                        merged_skills = list(dict.fromkeys(existing_skills + registered_skills))
+                        updates["registered_skills"] = merged_skills
 
                 if updates:
                     self.registry.update(ext_id, updates)
             except Exception as ext_err:
                 # Best-effort per extension: warn and move on so a single bad
                 # extension cannot silently drop the others. See #2950.
-                from .. import _print_cli_warning
+                from . import _print_cli_warning
 
                 _print_cli_warning(
                     "register extension artifacts for",
@@ -1893,31 +1880,31 @@ class CommandRegistrar:
     """
 
     # Re-export AGENT_CONFIGS at class level for direct attribute access
-    from ..agents import CommandRegistrar as _AgentRegistrar
+    from .agents import CommandRegistrar as _AgentRegistrar
 
     AGENT_CONFIGS = _AgentRegistrar.AGENT_CONFIGS
 
     def __init__(self):
-        from ..agents import CommandRegistrar as _Registrar
+        from .agents import CommandRegistrar as _Registrar
 
         self._registrar = _Registrar()
 
     # Delegate static/utility methods
     @staticmethod
     def parse_frontmatter(content: str) -> tuple[dict, str]:
-        from ..agents import CommandRegistrar as _Registrar
+        from .agents import CommandRegistrar as _Registrar
 
         return _Registrar.parse_frontmatter(content)
 
     @staticmethod
     def render_frontmatter(fm: dict) -> str:
-        from ..agents import CommandRegistrar as _Registrar
+        from .agents import CommandRegistrar as _Registrar
 
         return _Registrar.render_frontmatter(fm)
 
     @staticmethod
     def _write_copilot_prompt(project_root, cmd_name: str) -> None:
-        from ..agents import CommandRegistrar as _Registrar
+        from .agents import CommandRegistrar as _Registrar
 
         _Registrar.write_copilot_prompt(project_root, cmd_name)
 
@@ -2868,7 +2855,7 @@ class HookExecutor:
         instance to avoid repeated filesystem reads during hook rendering.
         """
         if self._init_options_cache is None:
-            from .. import load_init_options
+            from . import load_init_options
 
             payload = load_init_options(self.project_root)
             self._init_options_cache = payload if isinstance(payload, dict) else {}
@@ -2897,17 +2884,17 @@ class HookExecutor:
         selected_ai = init_options.get("ai")
         ai_skills_enabled = is_ai_skills_enabled(init_options)
 
-        dollar_skill_mode = is_dollar_skills_agent(selected_ai, ai_skills_enabled)
+        codex_skill_mode = selected_ai == "codex" and ai_skills_enabled
         kimi_skill_mode = selected_ai == "kimi"
         cline_mode = selected_ai == "cline"
 
         skill_name = self._skill_name_from_command(command_id)
-        if dollar_skill_mode and skill_name:
+        if codex_skill_mode and skill_name:
             return f"${skill_name}"
         if kimi_skill_mode and skill_name:
             return f"/skill:{skill_name}"
         if cline_mode:
-            from ..integrations.cline import format_cline_command_name
+            from .integrations.cline import format_cline_command_name
 
             return f"/{format_cline_command_name(command_id)}"
 

src/specify_cli/integrations/__init__.py

@@ -58,7 +58,6 @@ def _register_builtins() -> None:
     from .copilot import CopilotIntegration
     from .cursor_agent import CursorAgentIntegration
     from .devin import DevinIntegration
-    from .firebender import FirebenderIntegration
     from .forge import ForgeIntegration
     from .gemini import GeminiIntegration
     from .generic import GenericIntegration
@@ -81,7 +80,6 @@ def _register_builtins() -> None:
     from .trae import TraeIntegration
     from .vibe import VibeIntegration
     from .windsurf import WindsurfIntegration
-    from .zcode import ZcodeIntegration
     from .zed import ZedIntegration
 
     # -- Registration (alphabetical) --------------------------------------
@@ -96,7 +94,6 @@ def _register_builtins() -> None:
     _register(CopilotIntegration())
     _register(CursorAgentIntegration())
     _register(DevinIntegration())
-    _register(FirebenderIntegration())
     _register(ForgeIntegration())
     _register(GeminiIntegration())
     _register(GenericIntegration())
@@ -119,7 +116,6 @@ def _register_builtins() -> None:
     _register(TraeIntegration())
     _register(VibeIntegration())
     _register(WindsurfIntegration())
-    _register(ZcodeIntegration())
     _register(ZedIntegration())
 
 

src/specify_cli/integrations/_helpers.py

@@ -3,7 +3,7 @@ from __future__ import annotations
 
 import os
 from pathlib import Path
-from typing import Any, Callable
+from typing import Any
 
 import typer
 
@@ -131,7 +131,7 @@ def _clear_init_options_for_integration(project_root: Path, integration_key: str
         ext_cfg_path = project_root / _AGENT_CTX_EXT_CONFIG
         if ext_cfg_path.exists():
             _update_agent_context_config_file(
-                project_root, "", preserve_markers=True, preserve_context_files=False
+                project_root, "", preserve_markers=True
             )
     elif has_legacy_context_keys:
         save_init_options(project_root, opts)
@@ -277,14 +277,12 @@ def _update_init_options_for_integration(
     """Update init-options.json and the agent-context extension config to
     reflect *integration* as the active one.
 
-    ``context_file``, ``context_files``, and ``context_markers`` are stored in the agent-context
+    ``context_file`` and ``context_markers`` are stored in the agent-context
     extension config (``.specify/extensions/agent-context/agent-context-config.yml``),
     not in ``init-options.json``.  Existing user-customised markers are
-    always preserved when the config already exists. Existing ``context_files``
-    lists are also preserved so projects can keep multi-agent context anchors
-    during integration switches. Invalid marker values are
-    silently ignored at runtime by ``_resolve_context_markers()`` which falls
-    back to the class-level defaults.
+    always preserved when the config already exists; invalid marker values
+    are silently ignored at runtime by ``_resolve_context_markers()`` which
+    falls back to the class-level defaults.
     """
     from .. import (
         _AGENT_CTX_EXT_CONFIG,
@@ -387,93 +385,6 @@ def _set_default_integration_or_exit(*args: Any, **kwargs: Any) -> None:
         raise typer.Exit(1)
 
 
-# ---------------------------------------------------------------------------
-# Extension (un)registration helpers (shared by use / switch / upgrade)
-# ---------------------------------------------------------------------------
-
-def _best_effort_extension_op(
-    project_root: Path,
-    agent_key: str,
-    op: Callable[[Any, str], None],
-    *,
-    phase: str,
-    continuing: str,
-) -> None:
-    """Run a best-effort ``ExtensionManager`` operation for ``agent_key``.
-
-    ``op`` receives the ``ExtensionManager`` and ``agent_key``. Any failure is
-    surfaced as a warning via ``_print_cli_warning`` and never aborts the
-    surrounding integration operation. ``continuing`` describes what already
-    succeeded so the warning makes the partial outcome clear.
-    """
-    try:
-        from ..extensions import ExtensionManager
-
-        ext_mgr = ExtensionManager(project_root)
-        op(ext_mgr, agent_key)
-    except Exception as ext_err:
-        from .. import _print_cli_warning
-
-        _print_cli_warning(phase, "integration", agent_key, ext_err, continuing=continuing)
-
-
-def _register_extensions_for_agent(
-    project_root: Path,
-    agent_key: str,
-    *,
-    continuing: str,
-) -> None:
-    """Register all enabled extensions' commands/skills for ``agent_key``.
-
-    ``use`` / ``switch`` re-register enabled extensions for the agent they
-    activate; ``upgrade`` backfills them for the refreshed agent. Plain
-    ``install`` deliberately does not call this helper so adding a secondary
-    integration has no extension side effects until it is selected or upgraded.
-    See issue #2886.
-
-    Known limitation: extension *skill* rendering is scoped to the active
-    agent (init-options track a single ``ai`` / ``ai_skills`` pair). A
-    skills-mode agent registered while it is *not* the active agent (e.g.
-    Copilot ``--skills`` registered while non-active) therefore
-    receives command files rather than skills here — matching ``extension
-    add``'s multi-agent behavior. ``use`` / ``switch`` avoid this because they
-    make the target the active agent first. Per-agent skills parity is tracked in
-    #2948.
-
-    Best-effort: never aborts the surrounding integration operation. Callers
-    invoke it *after* the use/upgrade/switch transaction has committed so a
-    failure here cannot trigger a rollback.
-    """
-    _best_effort_extension_op(
-        project_root,
-        agent_key,
-        lambda mgr, key: mgr.register_enabled_extensions_for_agent(key),
-        phase="register extension artifacts for",
-        continuing=continuing,
-    )
-
-
-def _unregister_extensions_for_agent(
-    project_root: Path,
-    agent_key: str,
-    *,
-    continuing: str,
-) -> None:
-    """Best-effort removal of ``agent_key``'s extension artifacts.
-
-    Used by ``switch`` when uninstalling the previous integration so its
-    extension command/skill files don't linger as orphans in the old agent's
-    directory.
-    """
-    _best_effort_extension_op(
-        project_root,
-        agent_key,
-        lambda mgr, key: mgr.unregister_agent_artifacts(key),
-        phase="clean up extension artifacts for",
-        continuing=continuing,
-    )
-
-
 # ---------------------------------------------------------------------------
 # CLI formatting helpers (re-exported from _commands.py)
 # ---------------------------------------------------------------------------

src/specify_cli/integrations/_migrate_commands.py

@@ -27,14 +27,12 @@ from ._helpers import (
     _get_speckit_version,
     _read_integration_json,
     _refresh_init_options_speckit_version,
-    _register_extensions_for_agent,
     _remove_integration_json,
     _resolve_integration_options,
     _resolve_integration_script_type,
     _resolve_script_type,
     _set_default_integration,
     _set_default_integration_or_exit,
-    _unregister_extensions_for_agent,
     _update_init_options_for_integration,
     _write_integration_json,
 )
@@ -122,14 +120,6 @@ def integration_switch(
             parsed_options=parsed_options,
             refresh_templates_force=force,
         )
-        _register_extensions_for_agent(
-            project_root,
-            target,
-            continuing=(
-                "The integration switch succeeded, but installed extensions may "
-                "need re-registration."
-            ),
-        )
         console.print(f"\n[green]✓[/green] Default integration set to [bold]{target}[/bold].")
         raise typer.Exit(0)
 
@@ -181,11 +171,19 @@ def integration_switch(
 
         # Unregister extension commands for the old agent so they don't
         # remain as orphans in the old agent's directory.
-        _unregister_extensions_for_agent(
-            project_root,
-            installed_key,
-            continuing="Continuing with integration switch; old extension artifacts may need manual cleanup.",
-        )
+        try:
+            from ..extensions import ExtensionManager
+
+            ext_mgr = ExtensionManager(project_root)
+            ext_mgr.unregister_agent_artifacts(installed_key)
+        except Exception as ext_err:
+            _print_cli_warning(
+                "clean up extension artifacts for",
+                "integration",
+                installed_key,
+                ext_err,
+                continuing="Continuing with integration switch; old extension artifacts may need manual cleanup.",
+            )
 
         # Clear metadata so a failed Phase 2 doesn't leave stale references
         installed_keys = [installed for installed in installed_keys if installed != installed_key]
@@ -272,6 +270,22 @@ def integration_switch(
             parsed_options=parsed_options,
         )
 
+        # Re-register extension commands for the new agent so that
+        # previously-installed extensions are available in the new integration.
+        try:
+            from ..extensions import ExtensionManager
+
+            ext_mgr = ExtensionManager(project_root)
+            ext_mgr.register_enabled_extensions_for_agent(target)
+        except Exception as ext_err:
+            _print_cli_warning(
+                "register extension artifacts for",
+                "integration",
+                target,
+                ext_err,
+                continuing="The integration switch succeeded, but installed extensions may need re-registration.",
+            )
+
     except Exception as exc:
         # Attempt rollback of any files written by setup
         try:
@@ -319,15 +333,6 @@ def integration_switch(
         )
         raise typer.Exit(1)
 
-    # Re-register extension commands for the new agent so previously-installed
-    # extensions are available in it. Done after the try/except (the switch has
-    # committed) so this best-effort step can never trigger the rollback above.
-    _register_extensions_for_agent(
-        project_root,
-        target,
-        continuing="The integration switch succeeded, but installed extensions may need re-registration.",
-    )
-
     name = (target_integration.config or {}).get("name", target)
     console.print(f"\n[green]✓[/green] Switched to integration '{name}'")
 
@@ -491,17 +496,5 @@ def integration_upgrade(
         if stale_removed:
             console.print(f"  Removed {len(stale_removed)} stale file(s) from previous install")
 
-    # Re-register enabled extensions for the upgraded agent so its extension
-    # commands are (re)created — including agents installed before this
-    # back-fill existed. Mirrors switch for command registration; see #2886.
-    # Done after the upgrade has fully settled (Phase 2 included) and outside
-    # the try/except above so this best-effort step cannot affect upgrade
-    # success.
-    _register_extensions_for_agent(
-        project_root,
-        key,
-        continuing="The integration was upgraded, but installed extensions may need re-registration.",
-    )
-
     name = (integration.config or {}).get("name", key)
     console.print(f"\n[green]✓[/green] Integration '{name}' upgraded successfully")

src/specify_cli/integrations/_query_commands.py

@@ -17,7 +17,6 @@ from ..integration_state import (
 from ._commands import integration_app, integration_catalog_app
 from ._helpers import (
     _read_integration_json,
-    _register_extensions_for_agent,
     _resolve_integration_options,
     _set_default_integration_or_exit,
 )
@@ -243,11 +242,6 @@ def integration_use(
             f"[cyan]specify integration use {key} --force[/cyan]."
         ),
     )
-    _register_extensions_for_agent(
-        project_root,
-        key,
-        continuing="The integration was selected, but installed extensions may need re-registration.",
-    )
     console.print(f"[green]✓[/green] Default integration set to [bold]{key}[/bold].")
 
 

src/specify_cli/integrations/base.py

@@ -20,7 +20,7 @@ import shlex
 import shutil
 from abc import ABC
 from dataclasses import dataclass
-from pathlib import Path, PureWindowsPath
+from pathlib import Path
 from typing import TYPE_CHECKING, Any
 
 import yaml
@@ -93,11 +93,6 @@ class IntegrationBase(ABC):
 
     * ``context_file``     — path (relative to project root) of the agent
                              context/instructions file (e.g. ``"CLAUDE.md"``)
-
-    Projects may additionally opt into managing multiple context files by
-    setting ``context_files`` in the agent-context extension config. The
-    integration class still declares one default ``context_file`` for backwards
-    compatibility and command-template rendering.
     """
 
     # -- Must be set by every subclass ------------------------------------
@@ -637,11 +632,6 @@ class IntegrationBase(ABC):
             return True
         return entry.get("enabled", True) is not False
 
-    @staticmethod
-    def _context_file_dedupe_key(path: str) -> str:
-        """Return the comparison key for context file de-duplication."""
-        return path.casefold() if os.name == "nt" else path
-
     def _resolve_context_markers(self, project_root: Path) -> tuple[str, str]:
         """Return the (start, end) context markers to use for *project_root*.
 
@@ -691,156 +681,51 @@ class IntegrationBase(ABC):
                 end = cm_end  # type: ignore[assignment]
         return start, end
 
-    @staticmethod
-    def _validate_context_file_path(project_root: Path, context_file: str) -> str:
-        """Return a safe project-relative context file path.
-
-        The agent-context scripts reject paths that can escape the project
-        root; the Python integration path must apply the same guard before
-        setup or teardown touches context files.
-        """
-        candidate = context_file.strip()
-        if not candidate:
-            raise ValueError("agent-context: context file path must not be empty")
-
-        win_path = PureWindowsPath(candidate)
-        if Path(candidate).is_absolute() or win_path.drive or win_path.root:
-            raise ValueError(
-                "agent-context: context files must be project-relative paths; "
-                f"got {candidate!r}"
-            )
-        if "\\" in candidate:
-            raise ValueError(
-                "agent-context: context files must not contain backslash "
-                f"separators; got {candidate!r}"
-            )
-
-        parts = [part for part in re.split(r"[\\/]+", candidate) if part]
-        if ".." in parts:
-            raise ValueError(
-                "agent-context: context files must not contain '..' path "
-                f"segments; got {candidate!r}"
-            )
-
-        root = project_root.resolve()
-        target = (root / candidate).resolve(strict=False)
-        try:
-            target.relative_to(root)
-        except ValueError as exc:
-            raise ValueError(
-                "agent-context: context file path resolves outside the project "
-                f"root; got {candidate!r}"
-            ) from exc
-
-        return candidate
-
-    @classmethod
-    def _resolve_context_file_values(
-        cls,
+    def upsert_context_section(
+        self,
         project_root: Path,
-        cfg: dict[str, Any] | None,
-        *,
-        fallback_context_file: Any = None,
-        legacy_context_file: Any = None,
-        include_context_files: bool = True,
-        validate: bool = True,
-    ) -> list[str]:
-        """Resolve context file config with shared precedence and de-duplication."""
-        files: list[str] = []
-        seen: set[str] = set()
+        plan_path: str = "",
+    ) -> Path | None:
+        """Create or update the managed section in the agent context file.
 
-        def add_context_file(value: Any) -> None:
-            if not isinstance(value, str):
-                return
-            candidate = value.strip()
-            if not candidate:
-                return
-            if validate:
-                candidate = cls._validate_context_file_path(project_root, candidate)
-            key = cls._context_file_dedupe_key(candidate)
-            if key in seen:
-                return
-            files.append(candidate)
-            seen.add(key)
+        If the context file does not exist it is created with just the
+        managed section.  If it exists, the content between the configured
+        start/end markers (default ``<!-- SPECKIT START -->`` /
+        ``<!-- SPECKIT END -->``) is replaced, or appended when no markers
+        are found. Markers are read from the agent-context extension config
+        (``.specify/extensions/agent-context/agent-context-config.yml``)
+        when present, falling back to the class-level constants.
 
-        if isinstance(cfg, dict) and include_context_files:
-            configured = cfg.get("context_files")
-            if isinstance(configured, list):
-                for value in configured:
-                    add_context_file(value)
-                if files:
-                    return files
-
-        if isinstance(cfg, dict):
-            add_context_file(cfg.get("context_file"))
-            if files:
-                return files
-
-        add_context_file(fallback_context_file)
-        if files:
-            return files
-
-        add_context_file(legacy_context_file)
-        return files
-
-    @staticmethod
-    def _format_context_file_values(context_files: list[str]) -> str:
-        """Return context file targets as the template display string."""
-        return ", ".join(context_files)
-
-    def _resolve_context_files(self, project_root: Path) -> list[str]:
-        """Return project-relative context files managed for *project_root*.
-
-        ``context_files`` in the agent-context extension config, when present
-        and non-empty, takes precedence over the config's singular
-        ``context_file``. The integration class default is used only when the
-        extension config has no context file target.
-        Raises ``ValueError`` when a configured path can escape the project
-        root.
+        Returns the path to the context file, or ``None`` when
+        ``context_file`` is not set or the ``agent-context`` extension is
+        disabled.
         """
-        config_path = (
-            project_root
-            / ".specify"
-            / "extensions"
-            / "agent-context"
-            / "agent-context-config.yml"
-        )
-        try:
-            raw = config_path.read_text(encoding="utf-8")
-            cfg = yaml.safe_load(raw)
-        except (OSError, UnicodeError, ValueError, yaml.YAMLError):
-            cfg = None
-        return self._resolve_context_file_values(
-            project_root,
-            cfg,
-            fallback_context_file=self.context_file,
-        )
+        if not self.context_file:
+            return None
 
-    def _context_file_display(self, project_root: Path) -> str:
-        """Return human-readable context file target(s) for templates."""
         if not self._agent_context_extension_enabled(project_root):
-            from .. import _load_agent_context_config
+            return None
 
-            context_files = self._resolve_context_file_values(
-                project_root,
-                _load_agent_context_config(project_root),
-                fallback_context_file=self.context_file,
-                include_context_files=False,
-                validate=False,
-            )
-            return context_files[0] if context_files else ""
-        return self._format_context_file_values(
-            self._resolve_context_files(project_root)
+        from .._console import console  # local import to avoid cycles
+
+        console.print(
+            "[yellow]Deprecation:[/yellow] Inline agent-context updates during "
+            "integration setup will be disabled in v0.12.0. Context file "
+            "management has moved to the bundled [bold]agent-context[/bold] "
+            "extension. Run [cyan]specify extension disable agent-context[/cyan] "
+            "to opt out early.",
+            highlight=False,
+        )
+
+        marker_start, marker_end = self._resolve_context_markers(project_root)
+
+        ctx_path = project_root / self.context_file
+        section = (
+            f"{marker_start}\n"
+            f"{self._build_context_section(plan_path)}\n"
+            f"{marker_end}\n"
         )
 
-    @staticmethod
-    def _upsert_context_file(
-        ctx_path: Path,
-        section: str,
-        marker_start: str,
-        marker_end: str,
-    ) -> None:
-        """Create or update one managed context section."""
         if ctx_path.exists():
             content = ctx_path.read_text(encoding="utf-8-sig")
             start_idx = content.find(marker_start)
@@ -880,70 +765,18 @@ class IntegrationBase(ABC):
 
             # Ensure .mdc files have required YAML frontmatter
             if ctx_path.suffix == ".mdc":
-                new_content = IntegrationBase._ensure_mdc_frontmatter(new_content)
+                new_content = self._ensure_mdc_frontmatter(new_content)
         else:
             ctx_path.parent.mkdir(parents=True, exist_ok=True)
             # Cursor .mdc files require YAML frontmatter to be loaded
             if ctx_path.suffix == ".mdc":
-                new_content = IntegrationBase._ensure_mdc_frontmatter(section)
+                new_content = self._ensure_mdc_frontmatter(section)
             else:
                 new_content = section
 
         normalized = new_content.replace("\r\n", "\n").replace("\r", "\n")
         ctx_path.write_bytes(normalized.encode("utf-8"))
-
-    def upsert_context_section(
-        self,
-        project_root: Path,
-        plan_path: str = "",
-    ) -> Path | None:
-        """Create or update the managed section in the agent context file.
-
-        If the context file does not exist it is created with just the
-        managed section.  If it exists, the content between the configured
-        start/end markers (default ``<!-- SPECKIT START -->`` /
-        ``<!-- SPECKIT END -->``) is replaced, or appended when no markers
-        are found. Markers are read from the agent-context extension config
-        (``.specify/extensions/agent-context/agent-context-config.yml``)
-        when present, falling back to the class-level constants.
-
-        Returns the path to the first context file, or ``None`` when no context
-        files are configured or the ``agent-context`` extension is
-        disabled.
-        """
-        if not self._agent_context_extension_enabled(project_root):
-            return None
-
-        context_files = self._resolve_context_files(project_root)
-        if not context_files:
-            return None
-
-        from .._console import console  # local import to avoid cycles
-
-        console.print(
-            "[yellow]Deprecation:[/yellow] Inline agent-context updates during "
-            "integration setup will be disabled in v0.12.0. Context file "
-            "management has moved to the bundled [bold]agent-context[/bold] "
-            "extension. Run [cyan]specify extension disable agent-context[/cyan] "
-            "to opt out early.",
-            highlight=False,
-        )
-
-        marker_start, marker_end = self._resolve_context_markers(project_root)
-
-        section = (
-            f"{marker_start}\n"
-            f"{self._build_context_section(plan_path)}\n"
-            f"{marker_end}\n"
-        )
-
-        first_path: Path | None = None
-        for context_file in context_files:
-            ctx_path = project_root / context_file
-            self._upsert_context_file(ctx_path, section, marker_start, marker_end)
-            if first_path is None:
-                first_path = ctx_path
-        return first_path
+        return ctx_path
 
     def remove_context_section(self, project_root: Path) -> bool:
         """Remove the managed section from the agent context file.
@@ -954,73 +787,68 @@ class IntegrationBase(ABC):
         (``.specify/extensions/agent-context/agent-context-config.yml``)
         when present, falling back to the class-level constants.
         """
+        if not self.context_file:
+            return False
+
         if not self._agent_context_extension_enabled(project_root):
             return False
 
-        context_files = self._resolve_context_files(project_root)
-        if not context_files:
+        ctx_path = project_root / self.context_file
+        if not ctx_path.exists():
             return False
 
         marker_start, marker_end = self._resolve_context_markers(project_root)
-        removed_any = False
 
-        for context_file in context_files:
-            ctx_path = project_root / context_file
-            if not ctx_path.exists():
-                continue
+        content = ctx_path.read_text(encoding="utf-8-sig")
+        start_idx = content.find(marker_start)
+        end_idx = content.find(
+            marker_end,
+            start_idx if start_idx != -1 else 0,
+        )
 
-            content = ctx_path.read_text(encoding="utf-8-sig")
-            start_idx = content.find(marker_start)
-            end_idx = content.find(
-                marker_end,
-                start_idx if start_idx != -1 else 0,
+        # Only remove a complete, well-ordered managed section. If either
+        # marker is missing, leave the file unchanged to avoid deleting
+        # unrelated user-authored content.
+        if start_idx == -1 or end_idx == -1 or end_idx <= start_idx:
+            return False
+
+        removal_start = start_idx
+        removal_end = end_idx + len(marker_end)
+
+        # Consume trailing line ending (CRLF or LF)
+        if removal_end < len(content) and content[removal_end] == "\r":
+            removal_end += 1
+        if removal_end < len(content) and content[removal_end] == "\n":
+            removal_end += 1
+
+        # Also strip a blank line before the section if present
+        if removal_start > 0 and content[removal_start - 1] == "\n":
+            if removal_start > 1 and content[removal_start - 2] == "\n":
+                removal_start -= 1
+
+        new_content = content[:removal_start] + content[removal_end:]
+
+        # Normalize line endings before comparisons
+        normalized = new_content.replace("\r\n", "\n").replace("\r", "\n")
+
+        # For .mdc files, treat Speckit-generated frontmatter-only content as empty
+        if ctx_path.suffix == ".mdc":
+            import re
+
+            # Delete the file if only YAML frontmatter remains (no body content)
+            frontmatter_only = re.match(
+                r"^---\n.*?\n---\s*$", normalized, re.DOTALL
             )
-
-            # Only remove a complete, well-ordered managed section. If either
-            # marker is missing, leave the file unchanged to avoid deleting
-            # unrelated user-authored content.
-            if start_idx == -1 or end_idx == -1 or end_idx <= start_idx:
-                continue
-
-            removal_start = start_idx
-            removal_end = end_idx + len(marker_end)
-
-            # Consume trailing line ending (CRLF or LF)
-            if removal_end < len(content) and content[removal_end] == "\r":
-                removal_end += 1
-            if removal_end < len(content) and content[removal_end] == "\n":
-                removal_end += 1
-
-            # Also strip a blank line before the section if present
-            if removal_start > 0 and content[removal_start - 1] == "\n":
-                if removal_start > 1 and content[removal_start - 2] == "\n":
-                    removal_start -= 1
-
-            new_content = content[:removal_start] + content[removal_end:]
-
-            # Normalize line endings before comparisons
-            normalized = new_content.replace("\r\n", "\n").replace("\r", "\n")
-
-            # For .mdc files, treat Speckit-generated frontmatter-only content as empty
-            if ctx_path.suffix == ".mdc":
-                import re
-
-                # Delete the file if only YAML frontmatter remains (no body content)
-                frontmatter_only = re.match(
-                    r"^---\n.*?\n---\s*$", normalized, re.DOTALL
-                )
-                if not normalized.strip() or frontmatter_only:
-                    ctx_path.unlink()
-                    removed_any = True
-                    continue
-
-            if not normalized.strip():
+            if not normalized.strip() or frontmatter_only:
                 ctx_path.unlink()
-            else:
-                ctx_path.write_bytes(normalized.encode("utf-8"))
-            removed_any = True
+                return True
 
-        return removed_any
+        if not normalized.strip():
+            ctx_path.unlink()
+        else:
+            ctx_path.write_bytes(normalized.encode("utf-8"))
+
+        return True
 
     @staticmethod
     def resolve_command_refs(content: str, separator: str = ".") -> str:
@@ -1291,13 +1119,12 @@ class MarkdownIntegration(IntegrationBase):
             else "$ARGUMENTS"
         )
         created: list[Path] = []
-        context_file_display = self._context_file_display(project_root)
 
         for src_file in templates:
             raw = src_file.read_text(encoding="utf-8")
             processed = self.process_template(
                 raw, self.key, script_type, arg_placeholder,
-                context_file=context_file_display,
+                context_file=self.context_file or "",
             )
             dst_name = self.command_filename(src_file.stem)
             dst_file = self.write_file_and_record(
@@ -1497,14 +1324,13 @@ class TomlIntegration(IntegrationBase):
             else "{{args}}"
         )
         created: list[Path] = []
-        context_file_display = self._context_file_display(project_root)
 
         for src_file in templates:
             raw = src_file.read_text(encoding="utf-8")
             description = self._extract_description(raw)
             processed = self.process_template(
                 raw, self.key, script_type, arg_placeholder,
-                context_file=context_file_display,
+                context_file=self.context_file or "",
             )
             _, body = self._split_frontmatter(processed)
             toml_content = self._render_toml(description, body)
@@ -1693,7 +1519,6 @@ class YamlIntegration(IntegrationBase):
             else "{{args}}"
         )
         created: list[Path] = []
-        context_file_display = self._context_file_display(project_root)
 
         for src_file in templates:
             raw = src_file.read_text(encoding="utf-8")
@@ -1709,7 +1534,7 @@ class YamlIntegration(IntegrationBase):
 
             processed = self.process_template(
                 raw, self.key, script_type, arg_placeholder,
-                context_file=context_file_display,
+                context_file=self.context_file or "",
             )
             _, body = self._split_frontmatter(processed)
             yaml_content = self._render_yaml(
@@ -1884,7 +1709,6 @@ class SkillsIntegration(IntegrationBase):
             else "$ARGUMENTS"
         )
         created: list[Path] = []
-        context_file_display = self._context_file_display(project_root)
 
         for src_file in templates:
             raw = src_file.read_text(encoding="utf-8")
@@ -1908,7 +1732,7 @@ class SkillsIntegration(IntegrationBase):
             # Process body through the standard template pipeline
             processed_body = self.process_template(
                 raw, self.key, script_type, arg_placeholder,
-                context_file=context_file_display,
+                context_file=self.context_file or "",
                 invoke_separator=self.invoke_separator,
             )
             # Strip the processed frontmatter — we rebuild it for skills.

src/specify_cli/integrations/copilot/__init__.py

@@ -354,14 +354,13 @@ class CopilotIntegration(IntegrationBase):
 
         script_type = opts.get("script_type", "sh")
         arg_placeholder = self.registrar_config.get("args", "$ARGUMENTS")
-        context_file_display = self._context_file_display(project_root)
 
         # 1. Process and write command files as .agent.md
         for src_file in templates:
             raw = src_file.read_text(encoding="utf-8")
             processed = self.process_template(
                 raw, self.key, script_type, arg_placeholder,
-                context_file=context_file_display,
+                context_file=self.context_file or "",
             )
             dst_name = self.command_filename(src_file.stem)
             dst_file = self.write_file_and_record(

src/specify_cli/integrations/firebender/__init__.py

@@ -1,33 +0,0 @@
-"""Firebender IDE integration.
-
-Firebender (https://firebender.com/) is an AI coding agent for Android Studio
-and IntelliJ. It reads project-local custom slash commands from
-``.firebender/commands/*.mdc`` and project rules from ``.firebender/rules/*.mdc``,
-so Spec Kit installs its command templates as ``.mdc`` command files and writes
-the managed context section into a ``.firebender/rules/`` rule file.
-"""
-
-from ..base import MarkdownIntegration
-
-
-class FirebenderIntegration(MarkdownIntegration):
-    key = "firebender"
-    config = {
-        "name": "Firebender",
-        "folder": ".firebender/",
-        "commands_subdir": "commands",
-        "install_url": "https://firebender.com/",
-        "requires_cli": False,
-    }
-    registrar_config = {
-        "dir": ".firebender/commands",
-        "format": "markdown",
-        "args": "$ARGUMENTS",
-        "extension": ".mdc",
-    }
-    context_file = ".firebender/rules/specify-rules.mdc"
-    multi_install_safe = True
-
-    def command_filename(self, template_name: str) -> str:
-        """Firebender reads custom slash commands from ``.firebender/commands/*.mdc``."""
-        return f"speckit.{template_name}.mdc"

src/specify_cli/integrations/forge/__init__.py

@@ -128,14 +128,13 @@ class ForgeIntegration(MarkdownIntegration):
         script_type = opts.get("script_type", "sh")
         arg_placeholder = self.registrar_config.get("args", "{{parameters}}")
         created: list[Path] = []
-        context_file_display = self._context_file_display(project_root)
 
         for src_file in templates:
             raw = src_file.read_text(encoding="utf-8")
             # Process template with standard MarkdownIntegration logic
             processed = self.process_template(
                 raw, self.key, script_type, arg_placeholder,
-                context_file=context_file_display,
+                context_file=self.context_file or "",
                 invoke_separator=self.invoke_separator,
             )
 

src/specify_cli/integrations/generic/__init__.py

@@ -119,13 +119,12 @@ class GenericIntegration(MarkdownIntegration):
         script_type = opts.get("script_type", "sh")
         arg_placeholder = "$ARGUMENTS"
         created: list[Path] = []
-        context_file_display = self._context_file_display(project_root)
 
         for src_file in templates:
             raw = src_file.read_text(encoding="utf-8")
             processed = self.process_template(
                 raw, self.key, script_type, arg_placeholder,
-                context_file=context_file_display,
+                context_file=self.context_file or "",
             )
             dst_name = self.command_filename(src_file.stem)
             dst_file = self.write_file_and_record(

src/specify_cli/integrations/hermes/__init__.py

@@ -114,7 +114,6 @@ class HermesIntegration(SkillsIntegration):
         global_skills_dir.mkdir(parents=True, exist_ok=True)
 
         created: list[Path] = []
-        context_file_display = self._context_file_display(project_root)
 
         for src_file in templates:
             raw = src_file.read_text(encoding="utf-8")
@@ -141,7 +140,7 @@ class HermesIntegration(SkillsIntegration):
                 self.key,
                 script_type,
                 arg_placeholder,
-                context_file=context_file_display,
+                context_file=self.context_file or "",
                 invoke_separator=self.invoke_separator,
             )
             # Strip the processed frontmatter — we rebuild it for skills.

src/specify_cli/integrations/manifest.py

@@ -232,30 +232,6 @@ class IntegrationManifest:
             # transition. ``discard`` is a no-op when the key is absent.
             self._recovered_files.discard(normalized)
 
-    def remove(self, rel_path: str | Path) -> bool:
-        """Drop *rel_path* from the tracked file set and any recovered marker.
-
-        Operates purely on the manifest's recorded key; it does NOT touch the
-        file on disk. Returns ``True`` if an entry was present and removed.
-        Used to keep the manifest consistent after a caller deletes a stale
-        managed file that the current install no longer ships.
-
-        Input is normalized through the same lexical pipeline as
-        ``record_existing`` / ``is_recovered``: absolute paths and paths
-        containing ``..`` segments are rejected (return ``False``) — such paths
-        can never be canonical manifest keys, so there is nothing to remove.
-        """
-        rel = Path(rel_path)
-        if rel.is_absolute() or ".." in rel.parts:
-            return False
-        try:
-            abs_path = _validate_rel_path(rel, self.project_root)
-            normalized = abs_path.relative_to(self.project_root).as_posix()
-        except ValueError:
-            return False
-        self._recovered_files.discard(normalized)
-        return self._files.pop(normalized, None) is not None
-
     # -- Querying ---------------------------------------------------------
 
     @property

src/specify_cli/integrations/zcode/__init__.py

@@ -1,43 +0,0 @@
-"""ZCode integration — skills-based agent (Z.AI).
-
-ZCode uses the ``.zcode/skills/speckit-<name>/SKILL.md`` layout, matching
-the Claude Code skill format. Skills are invoked in chat with
-``$speckit-<name>``. Z.AI recommends skills (over simple ``/`` commands)
-for template- and script-driven workflows such as spec-kit.
-"""
-
-from __future__ import annotations
-
-from ..base import IntegrationOption, SkillsIntegration
-
-
-class ZcodeIntegration(SkillsIntegration):
-    """Integration for ZCode CLI (Z.AI)."""
-
-    key = "zcode"
-    config = {
-        "name": "ZCode",
-        "folder": ".zcode/",
-        "commands_subdir": "skills",
-        "install_url": "https://zcode.z.ai/",
-        "requires_cli": True,
-    }
-    registrar_config = {
-        "dir": ".zcode/skills",
-        "format": "markdown",
-        "args": "$ARGUMENTS",
-        "extension": "/SKILL.md",
-    }
-    context_file = "ZCODE.md"
-    multi_install_safe = True
-
-    @classmethod
-    def options(cls) -> list[IntegrationOption]:
-        return [
-            IntegrationOption(
-                "--skills",
-                is_flag=True,
-                default=True,
-                help="Install as agent skills (default for ZCode)",
-            ),
-        ]

src/specify_cli/presets/__init__.py

@@ -1064,14 +1064,11 @@ class PresetManager:
                         body = self._resolve_skill_command_refs(
                             body, registrar, selected_ai
                         )
-                    from ..integrations import get_integration
-                    integration = get_integration(selected_ai) if isinstance(selected_ai, str) else None
                     fm_data = registrar.build_skill_frontmatter(
                         selected_ai if isinstance(selected_ai, str) else "",
                         skill_name, desc,
                         f"override:{cmd_name}",
                     )
-                    registrar.apply_argument_hint(fm, fm_data, integration)
                     fm_text = dump_frontmatter(fm_data)
                     skill_title = self._skill_title_from_command(cmd_name)
                     skill_content = (
@@ -1079,6 +1076,8 @@ class PresetManager:
                         f"# Speckit {skill_title} Skill\n\n{body}\n"
                     )
                     # Apply integration post-processing (e.g. Claude flags)
+                    from ..integrations import get_integration
+                    integration = get_integration(selected_ai) if isinstance(selected_ai, str) else None
                     if integration is not None and hasattr(integration, "post_process_skill_content"):
                         skill_content = integration.post_process_skill_content(skill_content)
                     skill_file.write_text(skill_content, encoding="utf-8")
@@ -1347,7 +1346,6 @@ class PresetManager:
                     enhanced_desc,
                     f"preset:{manifest.id}",
                 )
-                registrar.apply_argument_hint(frontmatter, frontmatter_data, integration)
                 frontmatter_text = dump_frontmatter(frontmatter_data)
                 skill_content = (
                     f"---\n"
@@ -1444,7 +1442,6 @@ class PresetManager:
                     enhanced_desc,
                     f"templates/commands/{short_name}.md",
                 )
-                registrar.apply_argument_hint(frontmatter, frontmatter_data, integration)
                 frontmatter_text = dump_frontmatter(frontmatter_data)
                 skill_title = self._skill_title_from_command(short_name)
                 skill_content = (
@@ -1482,7 +1479,6 @@ class PresetManager:
                     frontmatter.get("description", f"Extension command: {command_name}"),
                     extension_restore["source"],
                 )
-                registrar.apply_argument_hint(frontmatter, frontmatter_data, integration)
                 frontmatter_text = dump_frontmatter(frontmatter_data)
                 skill_content = (
                     f"---\n"
@@ -2707,7 +2703,7 @@ class PresetResolver:
         # (source-checkout / editable install).  This is the canonical home for
         # speckit's built-in command/template files and must always be checked
         # so that strategy:wrap presets can locate {CORE_TEMPLATE}.
-        from specify_cli import _locate_core_pack, _repo_root  # local import to avoid cycles
+        from specify_cli import _locate_core_pack  # local import to avoid cycles
         _core_pack = _locate_core_pack()
         if _core_pack is not None:
             # Wheel install path
@@ -2727,7 +2723,7 @@ class PresetResolver:
                 return candidate
         else:
             # Source-checkout / editable install: templates live at repo root
-            repo_root = _repo_root()
+            repo_root = Path(__file__).parent.parent.parent
             if template_type == "template":
                 candidate = repo_root / "templates" / f"{template_name}.md"
             elif template_type == "command":
@@ -3079,7 +3075,7 @@ class PresetResolver:
         ``.specify/templates/`` doesn't contain the core file.
         """
         try:
-            from specify_cli import _locate_core_pack, _repo_root
+            from specify_cli import _locate_core_pack
         except ImportError:
             return None
 
@@ -3102,7 +3098,7 @@ class PresetResolver:
                 if c.exists():
                     return c
         else:
-            repo_root = _repo_root()
+            repo_root = Path(__file__).parent.parent.parent
             for name in names:
                 if template_type == "template":
                     c = repo_root / "templates" / f"{name}.md"

src/specify_cli/shared_infra.py

@@ -304,7 +304,7 @@ def install_shared_infra(
     customization warning to tell the user which flag would overwrite their
     customizations.
     """
-    from .integrations.manifest import _sha256, _validate_rel_path
+    from .integrations.manifest import _sha256
 
     manifest = load_speckit_manifest(project_path, version=version, console=console)
     prior_hashes = dict(manifest.files)
@@ -325,11 +325,6 @@ def install_shared_infra(
     symlinked_files: list[str] = []
     planned_copies: list[tuple[Path, str, bytes, int]] = []
     planned_templates: list[tuple[Path, str, str]] = []
-    # Track every shared path the current bundle produces so we can detect
-    # manifest entries the core no longer ships (stale-script cleanup, #3076).
-    seen_rels: set[str] = set()
-    scripts_scanned = False
-    variant_dir = "bash" if script_type == "sh" else "powershell"
 
     def _decide_overwrite(rel: str, dst: Path) -> tuple[bool, str | None]:
         """Return (write, bucket) where bucket is 'skip', 'preserved', or None."""
@@ -384,6 +379,7 @@ def install_shared_infra(
     if scripts_src.is_dir():
         dest_scripts = project_path / ".specify" / "scripts"
         if _ensure_or_bucket_dir(dest_scripts):
+            variant_dir = "bash" if script_type == "sh" else "powershell"
             variant_src = scripts_src / variant_dir
             if variant_src.is_dir():
                 dest_variant = dest_scripts / variant_dir
@@ -391,18 +387,10 @@ def install_shared_infra(
                     for src_path in variant_src.rglob("*"):
                         if not src_path.is_file():
                             continue
-                        # Mark scanned only once a real source file is seen. An
-                        # empty (or symlink-skipped) variant keeps this False, so
-                        # stale-cleanup is skipped — otherwise it would treat every
-                        # tracked script as obsolete and delete it. (The safety
-                        # hinge is this flag, not ``seen_rels``, which also holds
-                        # template paths populated later.)
-                        scripts_scanned = True
 
                         rel_path = src_path.relative_to(variant_src)
                         dst_path = dest_variant / rel_path
                         rel = dst_path.relative_to(project_path).as_posix()
-                        seen_rels.add(rel)
                         if not _safe_dest_or_bucket(dst_path, rel, parent_must_exist=False):
                             continue
                         write, bucket = _decide_overwrite(rel, dst_path)
@@ -454,7 +442,6 @@ def install_shared_infra(
 
                 dst = dest_templates / src.name
                 rel = dst.relative_to(project_path).as_posix()
-                seen_rels.add(rel)
                 if not _safe_dest_or_bucket(dst, rel):
                     continue
                 write, bucket = _decide_overwrite(rel, dst)
@@ -534,63 +521,5 @@ def install_shared_infra(
         if refresh_hint:
             console.print(refresh_hint)
 
-    # Remove stale managed scripts: paths a previous install recorded that the
-    # current core no longer ships — e.g. the legacy
-    # ``scripts/<variant>/update-agent-context.sh`` superseded by the bundled
-    # agent-context extension. Left behind, such an orphan can crash when it
-    # sources a refreshed ``common.sh`` (#3076). Only run when the script source
-    # was actually scanned (so a missing/empty source never triggers mass
-    # deletion), scoped to the active variant, and only for *managed* copies —
-    # a user-customized file (hash diverges), a symlink, or a recovered entry is
-    # preserved by ``_is_managed``.
-    if scripts_scanned:
-        stale_removed: list[str] = []
-        script_prefix = f".specify/scripts/{variant_dir}/"
-        for rel in list(prior_hashes):
-            if rel in seen_rels or not rel.startswith(script_prefix):
-                continue
-            # Guard corrupted/hand-edited manifest keys BEFORE any filesystem
-            # access: absolute, ``..``, or (on Windows) drive-relative keys such
-            # as ``C:tmp`` are not ``is_absolute()`` yet discard the project root
-            # when joined. The lexical check is a fast reject; ``_validate_rel_path``
-            # resolves the join and confirms containment, catching the rest. A key
-            # that still escapes is *skipped*, never turned into an install-time
-            # hard failure. Mirrors IntegrationManifest.is_recovered / remove.
-            rel_path = Path(rel)
-            if rel_path.is_absolute() or ".." in rel_path.parts:
-                continue
-            try:
-                _validate_rel_path(rel_path, project_path)
-            except ValueError:
-                continue
-            dst = project_path / rel_path
-            # Already gone from disk but still tracked: drop the orphaned manifest
-            # entry so the manifest stays consistent (nothing to unlink).
-            if not dst.exists() and not dst.is_symlink():
-                manifest.remove(rel)
-                continue
-            if not _is_managed(rel, dst):
-                continue  # user-modified / symlink / recovered → preserve
-            # Never unlink through a symlinked ancestor (writes/deletes could
-            # escape the project root). The safe-destination check buckets such
-            # paths under ``symlinked_files`` and we leave them in place.
-            if not _safe_dest_or_bucket(dst, rel):
-                continue
-            try:
-                dst.unlink()
-            except OSError as exc:
-                console.print(f"[yellow]⚠[/yellow]  could not remove stale {rel}: {exc}")
-                continue
-            manifest.remove(rel)
-            stale_removed.append(rel)
-
-        if stale_removed:
-            console.print(
-                f"[yellow]⚠[/yellow]  Removed {len(stale_removed)} obsolete shared "
-                "script(s) left by a previous install:"
-            )
-            for path in stale_removed:
-                console.print(f"    {path}")
-
     manifest.save()
     return True

src/specify_cli/workflows/base.py

@@ -47,10 +47,9 @@ class StepContext:
     #: Resolved workflow inputs (from user prompts / defaults).
     inputs: dict[str, Any] = field(default_factory=dict)
 
-    #: Accumulated step results keyed by step ID. Each entry is the dict the
-    #: engine persists per step:
-    #: ``{"type": ..., "integration": ..., "model": ..., "options": ...,
-    #:   "input": ..., "output": ..., "status": ...}``.
+    #: Accumulated step results keyed by step ID.
+    #: Each entry is ``{"integration": ..., "model": ..., "options": ...,
+    #:   "input": ..., "output": ...}``.
     steps: dict[str, dict[str, Any]] = field(default_factory=dict)
 
     #: Current fan-out item (set only inside fan-out iterations).

src/specify_cli/workflows/engine.py

@@ -676,7 +676,6 @@ class WorkflowEngine:
 
             # Record step results — prefer resolved values from step output
             step_data = {
-                "type": step_type,
                 "integration": result.output.get("integration")
                 or step_config.get("integration")
                 or context.default_integration,

src/specify_cli/workflows/expressions.py

@@ -12,19 +12,6 @@ import re
 from typing import Any
 
 
-# The filters the expression evaluator recognizes. Used to tell a
-# *registered* filter used in an unsupported form (e.g. `| join` with no
-# argument) apart from a genuinely unknown filter name, so each raises an
-# error that names the real problem.
-_REGISTERED_FILTERS: tuple[str, ...] = (
-    "default",
-    "join",
-    "map",
-    "contains",
-    "from_json",
-)
-
-
 # -- Custom filters -------------------------------------------------------
 
 def _filter_default(value: Any, default_value: Any = "") -> Any:
@@ -205,27 +192,7 @@ def _evaluate_simple_expression(expr: str, namespace: dict[str, Any]) -> Any:
         filter_name = filter_expr.strip()
         if filter_name == "default":
             return _filter_default(value)
-        # No recognized filter matched. Fail loudly rather than silently
-        # returning the unfiltered value: a passthrough turns a mis-typed or
-        # unsupported filter into a wrong result with no signal. Mirrors the
-        # strict `from_json` handling above. Distinguish a *registered* filter
-        # used in an unsupported form (e.g. `| join` or `| map` with no
-        # argument) from a genuinely unknown filter name, so the message names
-        # the real problem instead of calling a known filter "unknown".
-        leading_name = re.match(r"\w+", filter_expr)
-        name = leading_name.group(0) if leading_name else filter_expr
-        expected = (
-            "expected one of default or default('x'), join('sep'), "
-            "map('attr'), contains('s'), or from_json"
-        )
-        if name in _REGISTERED_FILTERS:
-            raise ValueError(
-                f"filter '{name}' used in an unsupported form (got "
-                f"'| {filter_expr}'): {expected}"
-            )
-        raise ValueError(
-            f"unknown filter '{name}': {expected} (got '| {filter_expr}')"
-        )
+        return value
 
     # Boolean operators — parse 'or' first (lower precedence) so that
     # 'a or b and c' is evaluated as 'a or (b and c)'.

tests/bundler_helpers.py

@@ -1,125 +0,0 @@
-"""Shared helpers and fakes for bundler tests.
-
-Kept out of ``tests/conftest.py`` so the existing root fixtures are untouched.
-Import what you need explicitly, e.g.::
-
-    from tests.bundler_helpers import FakeInstaller, write_manifest
-"""
-from __future__ import annotations
-
-import json
-from pathlib import Path
-
-import yaml
-
-from specify_cli.bundler.models.manifest import ComponentRef
-
-
-def valid_manifest_dict(**overrides) -> dict:
-    """Return a structurally valid manifest dict; override any top-level key."""
-    data = {
-        "schema_version": "1.0",
-        "bundle": {
-            "id": "demo-bundle",
-            "name": "Demo Bundle",
-            "version": "1.2.0",
-            "role": "developer",
-            "description": "A demo bundle for tests.",
-            "author": "Spec Kit",
-            "license": "MIT",
-        },
-        "requires": {"speckit_version": ">=0.1.0"},
-        "provides": {
-            "extensions": [{"id": "ext-a", "version": "1.0.0"}],
-            "presets": [
-                {"id": "preset-a", "version": "2.0.0", "priority": 10, "strategy": "append"}
-            ],
-            "steps": [{"id": "step-a"}],
-            "workflows": [{"id": "wf-a", "version": "0.3.0"}],
-        },
-        "tags": ["demo", "test"],
-    }
-    data.update(overrides)
-    return data
-
-
-def write_manifest(directory: Path, data: dict | None = None) -> Path:
-    directory.mkdir(parents=True, exist_ok=True)
-    manifest_path = directory / "bundle.yml"
-    manifest_path.write_text(
-        yaml.safe_dump(data if data is not None else valid_manifest_dict()),
-        encoding="utf-8",
-    )
-    return manifest_path
-
-
-def make_project(root: Path) -> Path:
-    """Create a minimal Spec Kit project skeleton under *root*."""
-    (root / ".specify").mkdir(parents=True, exist_ok=True)
-    return root
-
-
-def catalog_payload(bundles: dict | None = None) -> dict:
-    return {
-        "schema_version": "1.0",
-        "updated_at": "2026-06-19T00:00:00Z",
-        "catalog_url": "file://test",
-        "bundles": bundles or {},
-    }
-
-
-def catalog_entry_dict(bundle_id: str = "demo-bundle", **overrides) -> dict:
-    entry = {
-        "id": bundle_id,
-        "name": "Demo Bundle",
-        "version": "1.2.0",
-        "role": "developer",
-        "description": "A demo bundle.",
-        "author": "Spec Kit",
-        "license": "MIT",
-        "download_url": "",
-        "requires": {"speckit_version": ">=0.1.0"},
-        "provides": {"extensions": 1, "presets": 1, "steps": 1, "workflows": 1},
-        "verified": True,
-    }
-    entry.update(overrides)
-    return entry
-
-
-def write_catalog_file(path: Path, bundles: dict) -> Path:
-    path.parent.mkdir(parents=True, exist_ok=True)
-    path.write_text(json.dumps(catalog_payload(bundles)), encoding="utf-8")
-    return path
-
-
-class FakeInstaller:
-    """Deterministic in-memory PrimitiveInstaller for offline integration tests."""
-
-    def __init__(self, *, fail_on: str | None = None) -> None:
-        self.installed: set[tuple[str, str]] = set()
-        self.install_calls: list[tuple[str, str]] = []
-        self.remove_calls: list[tuple[str, str]] = []
-        self.refresh_calls: list[tuple[str, str]] = []
-        self._fail_on = fail_on
-
-    def _key(self, component: ComponentRef) -> tuple[str, str]:
-        return (component.kind, component.id)
-
-    def is_installed(self, project_root: Path, component: ComponentRef) -> bool:
-        return self._key(component) in self.installed
-
-    def install(self, project_root: Path, component: ComponentRef) -> None:
-        from specify_cli.bundler import BundlerError
-
-        self.install_calls.append(self._key(component))
-        if self._fail_on is not None and component.id == self._fail_on:
-            raise BundlerError(f"Simulated failure installing {component.id}")
-        self.installed.add(self._key(component))
-
-    def remove(self, project_root: Path, component: ComponentRef) -> None:
-        self.remove_calls.append(self._key(component))
-        self.installed.discard(self._key(component))
-
-    def refresh(self, project_root: Path, component: ComponentRef) -> None:
-        self.refresh_calls.append(self._key(component))
-        self.installed.add(self._key(component))

tests/contract/test_bundle_cli.py

@@ -1,391 +0,0 @@
-"""Contract test for the `specify bundle` CLI surface (Typer integration).
-
-Exercises the wired commands end-to-end via CliRunner against a temp project,
-asserting exit codes and the cross-cutting error guarantees from
-contracts/cli-commands.md (offline, discovery-only refusal, not-a-project error).
-"""
-from __future__ import annotations
-
-import json
-from pathlib import Path
-
-import pytest
-import yaml
-from typer.testing import CliRunner
-
-from specify_cli import app
-from specify_cli.bundler.services.packager import build_bundle
-from tests.bundler_helpers import (
-    catalog_entry_dict,
-    valid_manifest_dict,
-    write_catalog_file,
-)
-
-runner = CliRunner()
-
-
-@pytest.fixture()
-def project(tmp_path: Path, monkeypatch) -> Path:
-    (tmp_path / ".specify").mkdir()
-    monkeypatch.chdir(tmp_path)
-    return tmp_path
-
-
-def test_bundle_help_lists_all_commands():
-    result = runner.invoke(app, ["bundle", "--help"])
-    assert result.exit_code == 0
-    for cmd in ("search", "info", "list", "install", "update", "remove",
-                "validate", "build", "init", "catalog"):
-        assert cmd in result.output
-
-
-def test_update_accepts_integration_override():
-    # Update must expose --integration so integration-pinned bundles can be
-    # updated in projects where the active integration can't be auto-detected.
-    # Rich may insert ANSI escapes between the two leading dashes, so match the
-    # un-split option word rather than the literal "--integration".
-    result = runner.invoke(app, ["bundle", "update", "--help"])
-    assert result.exit_code == 0
-    assert "integration" in result.output
-
-
-def test_list_empty_project(project: Path):
-    result = runner.invoke(app, ["bundle", "list"])
-    assert result.exit_code == 0
-    assert "No bundles installed" in result.output
-
-
-def test_commands_outside_project_fail_with_guidance(tmp_path: Path, monkeypatch):
-    monkeypatch.chdir(tmp_path)  # no .specify/
-    result = runner.invoke(app, ["bundle", "list"])
-    assert result.exit_code == 1
-    assert "Spec Kit project" in result.output
-
-
-def test_search_works_without_a_project(tmp_path: Path, monkeypatch):
-    # Discovery commands fall back to the built-in/user catalog stack and must
-    # not require a Spec Kit project (matches README/quickstart examples).
-    monkeypatch.chdir(tmp_path)  # no .specify/
-    result = runner.invoke(app, ["bundle", "search", "--offline", "--json"])
-    assert result.exit_code == 0, result.output
-    assert result.output.strip().startswith("[")
-
-
-def test_info_unknown_bundle_without_project_reports_not_found(tmp_path: Path, monkeypatch):
-    monkeypatch.chdir(tmp_path)  # no .specify/
-    result = runner.invoke(app, ["bundle", "info", "does-not-exist", "--offline"])
-    # Reaches catalog resolution (not the project gate) and reports a clean miss.
-    assert result.exit_code == 1
-    assert "Spec Kit project" not in result.output
-
-
-def test_catalog_list_shows_builtin_defaults(project: Path):
-    result = runner.invoke(app, ["bundle", "catalog", "list"])
-    assert result.exit_code == 0
-    assert "default" in result.output
-    assert "community" in result.output
-    assert "built-in default stack" in result.output
-
-
-def test_catalog_add_and_remove(project: Path):
-    catalog = project / "local-catalog.json"
-    write_catalog_file(catalog, {"demo": catalog_entry_dict("demo")})
-
-    added = runner.invoke(
-        app, ["bundle", "catalog", "add", str(catalog), "--id", "local"]
-    )
-    assert added.exit_code == 0, added.output
-
-    listed = runner.invoke(app, ["bundle", "catalog", "list"])
-    assert "local" in listed.output
-
-    removed = runner.invoke(app, ["bundle", "catalog", "remove", "local"])
-    assert removed.exit_code == 0
-
-
-def test_catalog_remove_builtin_is_refused(project: Path):
-    result = runner.invoke(app, ["bundle", "catalog", "remove", "default"])
-    assert result.exit_code == 1
-    assert "built-in" in result.output
-
-
-def test_validate_reports_invalid_manifest(project: Path):
-    data = valid_manifest_dict()
-    del data["bundle"]["license"]
-    (project / "bundle.yml").write_text(yaml.safe_dump(data), encoding="utf-8")
-    result = runner.invoke(app, ["bundle", "validate"])
-    assert result.exit_code == 1
-    assert "license" in result.output
-
-
-def test_validate_accepts_valid_manifest(project: Path):
-    (project / "bundle.yml").write_text(
-        yaml.safe_dump(valid_manifest_dict()), encoding="utf-8"
-    )
-    # Offline mode does not fail on references it cannot verify (synthetic ids
-    # here); they surface as warnings while structure is confirmed valid.
-    result = runner.invoke(app, ["bundle", "validate", "--offline"])
-    assert result.exit_code == 0, result.output
-    assert "valid" in result.output
-
-
-def test_validate_rejects_broken_reference(project: Path):
-    # Synthetic component ids resolve to nothing in any catalog → hard failure.
-    (project / "bundle.yml").write_text(
-        yaml.safe_dump(valid_manifest_dict()), encoding="utf-8"
-    )
-    result = runner.invoke(app, ["bundle", "validate"])
-    assert result.exit_code == 1
-    assert "preset-a" in result.output or "ext-a" in result.output
-
-
-def test_validate_accepts_bundled_reference(project: Path):
-    data = valid_manifest_dict()
-    data["provides"] = {"extensions": [{"id": "agent-context", "version": "1.0.0"}]}
-    (project / "bundle.yml").write_text(yaml.safe_dump(data), encoding="utf-8")
-    result = runner.invoke(app, ["bundle", "validate"])
-    assert result.exit_code == 0, result.output
-    assert "valid" in result.output
-
-
-def test_build_produces_artifact(project: Path):
-    (project / "bundle.yml").write_text(
-        yaml.safe_dump(valid_manifest_dict()), encoding="utf-8"
-    )
-    (project / "README.md").write_text("# Demo", encoding="utf-8")
-    result = runner.invoke(app, ["bundle", "build", "--output", str(project / "dist")])
-    assert result.exit_code == 0, result.output
-    artifacts = list((project / "dist").glob("*.zip"))
-    assert len(artifacts) == 1
-
-
-def test_info_expands_full_component_set(project: Path):
-    bundle_dir = project / "src-bundle"
-    bundle_dir.mkdir()
-    (bundle_dir / "bundle.yml").write_text(
-        yaml.safe_dump(valid_manifest_dict()), encoding="utf-8"
-    )
-    catalog = project / "local-catalog.json"
-    entry = catalog_entry_dict(
-        "demo-bundle", download_url=str(bundle_dir / "bundle.yml")
-    )
-    write_catalog_file(catalog, {"demo-bundle": entry})
-    added = runner.invoke(
-        app, ["bundle", "catalog", "add", str(catalog), "--id", "local"]
-    )
-    assert added.exit_code == 0, added.output
-
-    result = runner.invoke(app, ["bundle", "info", "demo-bundle", "--json", "--offline"])
-    assert result.exit_code == 0, result.output
-    payload = json.loads(result.output)
-    components = {(c["kind"], c["id"]): c for c in payload["components"]}
-    assert ("extensions", "ext-a") in components
-    preset = components[("presets", "preset-a")]
-    assert preset["version"] == "2.0.0"
-    assert preset["priority"] == 10
-    assert preset["strategy"] == "append"
-    assert payload["trust"] == "verified"
-
-    text = runner.invoke(app, ["bundle", "info", "demo-bundle", "--offline"])
-    assert "preset-a v2.0.0" in text.output
-    assert "Trust" in text.output
-
-
-def test_info_expands_discovery_only_bundle(project: Path):
-    # Discovery-only bundles must still be fully inspectable via `info`;
-    # only `install` is refused for them.
-    bundle_dir = project / "disc-bundle"
-    bundle_dir.mkdir()
-    (bundle_dir / "bundle.yml").write_text(
-        yaml.safe_dump(valid_manifest_dict()), encoding="utf-8"
-    )
-    catalog = project / "disc-catalog.json"
-    entry = catalog_entry_dict(
-        "demo-bundle", download_url=str(bundle_dir / "bundle.yml")
-    )
-    write_catalog_file(catalog, {"demo-bundle": entry})
-    config = {
-        "schema_version": "1.0",
-        "catalogs": [
-            {"id": "disc", "url": str(catalog), "priority": 1,
-             "install_policy": "discovery-only"}
-        ],
-    }
-    (project / ".specify" / "bundle-catalogs.yml").write_text(
-        yaml.safe_dump(config), encoding="utf-8"
-    )
-    result = runner.invoke(app, ["bundle", "info", "demo-bundle", "--json", "--offline"])
-    assert result.exit_code == 0, result.output
-    payload = json.loads(result.output)
-    components = {(c["kind"], c["id"]) for c in payload["components"]}
-    assert ("extensions", "ext-a") in components
-
-
-def test_info_resolves_local_zip_download_url(project: Path):
-    # A local .zip artifact as download_url is extracted to read bundle.yml.
-    bundle_dir = project / "zip-src"
-    bundle_dir.mkdir()
-    (bundle_dir / "bundle.yml").write_text(
-        yaml.safe_dump(valid_manifest_dict()), encoding="utf-8"
-    )
-    (bundle_dir / "README.md").write_text("# Demo", encoding="utf-8")
-    artifact = build_bundle(bundle_dir, output_dir=project / "dist").artifact_path
-    catalog = project / "zip-catalog.json"
-    write_catalog_file(
-        catalog,
-        {"demo-bundle": catalog_entry_dict("demo-bundle", download_url=str(artifact))},
-    )
-    added = runner.invoke(
-        app, ["bundle", "catalog", "add", str(catalog), "--id", "local"]
-    )
-    assert added.exit_code == 0, added.output
-    result = runner.invoke(app, ["bundle", "info", "demo-bundle", "--json", "--offline"])
-    assert result.exit_code == 0, result.output
-    payload = json.loads(result.output)
-    components = {(c["kind"], c["id"]) for c in payload["components"]}
-    assert ("extensions", "ext-a") in components
-
-
-def test_install_refuses_discovery_only_source(project: Path, monkeypatch):
-    # Point a discovery-only catalog at a local payload containing the bundle.
-    catalog = project / "disc.json"
-    write_catalog_file(catalog, {"demo": catalog_entry_dict("demo")})
-    config = {
-        "schema_version": "1.0",
-        "catalogs": [
-            {"id": "disc", "url": str(catalog), "priority": 1,
-             "install_policy": "discovery-only"}
-        ],
-    }
-    (project / ".specify" / "bundle-catalogs.yml").write_text(
-        yaml.safe_dump(config), encoding="utf-8"
-    )
-    result = runner.invoke(app, ["bundle", "install", "demo", "--offline"])
-    assert result.exit_code == 1
-    assert "discovery-only" in result.output
-
-
-def test_update_refuses_discovery_only_source(project: Path):
-    # An installed bundle whose only resolvable source is discovery-only must
-    # not be updatable from there (FR-025), mirroring the install policy gate.
-    from specify_cli.bundler.models.manifest import ComponentRef
-    from specify_cli.bundler.models.records import (
-        InstalledBundleRecord,
-        save_records,
-    )
-
-    save_records(
-        project,
-        [
-            InstalledBundleRecord.create(
-                "demo",
-                "1.0.0",
-                [ComponentRef(kind="extensions", id="ext-a", version=None)],
-            )
-        ],
-    )
-
-    catalog = project / "disc.json"
-    write_catalog_file(catalog, {"demo": catalog_entry_dict("demo")})
-    config = {
-        "schema_version": "1.0",
-        "catalogs": [
-            {"id": "disc", "url": str(catalog), "priority": 1,
-             "install_policy": "discovery-only"}
-        ],
-    }
-    (project / ".specify" / "bundle-catalogs.yml").write_text(
-        yaml.safe_dump(config), encoding="utf-8"
-    )
-
-    result = runner.invoke(app, ["bundle", "update", "demo", "--offline"])
-    assert result.exit_code == 1
-    assert "discovery-only" in result.output
-
-
-def test_info_fails_loudly_when_manifest_unresolvable_offline(project: Path):
-    # `info` must expand the real component set; if the manifest can't be
-    # resolved (here: --offline against an https download_url), it should error
-    # and exit non-zero rather than silently degrading to `provides` counts.
-    catalog = project / "remote-catalog.json"
-    entry = catalog_entry_dict(
-        "demo-bundle", download_url="https://example.com/demo-bundle.zip"
-    )
-    write_catalog_file(catalog, {"demo-bundle": entry})
-    added = runner.invoke(
-        app, ["bundle", "catalog", "add", str(catalog), "--id", "remote"]
-    )
-    assert added.exit_code == 0, added.output
-
-    result = runner.invoke(app, ["bundle", "info", "demo-bundle", "--offline"])
-    assert result.exit_code == 1
-    assert "Network access disabled" in result.output
-
-
-def test_search_json_offline(project: Path):
-    catalog = project / "c.json"
-    write_catalog_file(catalog, {"demo": catalog_entry_dict("demo")})
-    config = {
-        "schema_version": "1.0",
-        "catalogs": [
-            {"id": "c", "url": str(catalog), "priority": 1,
-             "install_policy": "install-allowed"}
-        ],
-    }
-    (project / ".specify" / "bundle-catalogs.yml").write_text(
-        yaml.safe_dump(config), encoding="utf-8"
-    )
-    result = runner.invoke(app, ["bundle", "search", "--offline", "--json"])
-    assert result.exit_code == 0
-    payload = json.loads(result.output)
-    assert payload[0]["id"] == "demo"
-    # Trust indicator is exposed on the discovery surface (FR-010 / FR-027).
-    assert payload[0]["verified"] is True
-    assert payload[0]["trust"] == "verified"
-
-
-def test_search_text_shows_trust(project: Path):
-    catalog = project / "c.json"
-    write_catalog_file(
-        catalog,
-        {
-            "verified-one": catalog_entry_dict("verified-one", verified=True),
-            "community-one": catalog_entry_dict("community-one", verified=False),
-        },
-    )
-    config = {
-        "schema_version": "1.0",
-        "catalogs": [
-            {"id": "c", "url": str(catalog), "priority": 1,
-             "install_policy": "install-allowed"}
-        ],
-    }
-    (project / ".specify" / "bundle-catalogs.yml").write_text(
-        yaml.safe_dump(config), encoding="utf-8"
-    )
-    result = runner.invoke(app, ["bundle", "search", "--offline"])
-    assert result.exit_code == 0, result.output
-    assert "verified" in result.output
-    assert "community" in result.output
-
-
-def test_install_integration_override_cannot_bypass_clash_guard(project: Path):
-    # An initialized project's recorded active integration is authoritative:
-    # passing --integration must not let a differently-pinned bundle install.
-    import json
-
-    (project / ".specify" / "integration.json").write_text(
-        json.dumps({"integration": "copilot"}), encoding="utf-8"
-    )
-    bundle_dir = project / "claude-bundle"
-    bundle_dir.mkdir()
-    data = valid_manifest_dict(integration={"id": "claude"})
-    (bundle_dir / "bundle.yml").write_text(yaml.safe_dump(data), encoding="utf-8")
-    (bundle_dir / "README.md").write_text("# Claude bundle", encoding="utf-8")
-
-    result = runner.invoke(
-        app,
-        ["bundle", "install", str(bundle_dir), "--integration", "claude", "--offline"],
-    )
-    assert result.exit_code == 1
-    assert "claude" in result.output and "copilot" in result.output

tests/contract/test_catalog_schema.py

@@ -1,147 +0,0 @@
-"""Contract tests for the catalog schema and source stack.
-
-Mirrors contracts/bundle-catalog.schema.md: source precedence project > user >
-built-in, install policy gating, payload parsing.
-"""
-from __future__ import annotations
-
-from pathlib import Path
-
-import yaml
-
-from specify_cli.bundler.models.catalog import (
-    BUILTIN_DEFAULT_STACK,
-    CatalogSource,
-    InstallPolicy,
-    Scope,
-    load_catalog_payload,
-    load_source_stack,
-)
-from specify_cli.bundler import BundlerError
-import pytest
-from tests.bundler_helpers import catalog_entry_dict, catalog_payload, make_project
-
-
-def test_non_integer_source_priority_raises_actionable_error():
-    with pytest.raises(BundlerError, match="non-integer priority"):
-        CatalogSource.from_dict(
-            {"id": "corp", "url": "https://corp/catalog.json", "priority": "high"},
-            Scope.PROJECT,
-        )
-
-
-def test_builtin_default_stack_when_no_config(tmp_path: Path):
-    make_project(tmp_path)
-    sources = load_source_stack(tmp_path)
-    ids = [s.id for s in sources]
-    assert ids == ["default", "community"]
-    assert sources[0].install_policy is InstallPolicy.INSTALL_ALLOWED
-    assert sources[1].install_policy is InstallPolicy.DISCOVERY_ONLY
-    assert all(s.scope is Scope.BUILTIN for s in sources)
-
-
-def test_project_config_overrides_same_id(tmp_path: Path):
-    make_project(tmp_path)
-    config = {
-        "schema_version": "1.0",
-        "catalogs": [
-            {"id": "default", "url": "file://local", "priority": 1,
-             "install_policy": "install-allowed"},
-            {"id": "corp", "url": "https://corp/catalog.json", "priority": 0,
-             "install_policy": "install-allowed"},
-        ],
-    }
-    (tmp_path / ".specify" / "bundle-catalogs.yml").write_text(
-        yaml.safe_dump(config), encoding="utf-8"
-    )
-    sources = load_source_stack(tmp_path)
-    by_id = {s.id: s for s in sources}
-    assert by_id["default"].scope is Scope.PROJECT
-    assert by_id["default"].url == "file://local"
-    # Highest precedence (lowest priority number) sorts first.
-    assert sources[0].id == "corp"
-
-
-def test_user_scope_between_builtin_and_project(tmp_path: Path):
-    make_project(tmp_path)
-    user_dir = tmp_path / "userconf"
-    user_dir.mkdir()
-    (user_dir / "bundle-catalogs.yml").write_text(
-        yaml.safe_dump(
-            {"catalogs": [
-                {"id": "community", "url": "https://u", "priority": 2,
-                 "install_policy": "install-allowed"}
-            ]}
-        ),
-        encoding="utf-8",
-    )
-    sources = load_source_stack(tmp_path, user_config_dir=user_dir)
-    by_id = {s.id: s for s in sources}
-    # User overrode the built-in community policy to install-allowed.
-    assert by_id["community"].scope is Scope.USER
-    assert by_id["community"].install_allowed is True
-
-
-def test_load_payload_parses_entries():
-    payload = catalog_payload({"demo-bundle": catalog_entry_dict()})
-    entries = load_catalog_payload(payload)
-    assert "demo-bundle" in entries
-    assert entries["demo-bundle"].version == "1.2.0"
-    assert entries["demo-bundle"].provides["presets"] == 1
-
-
-def test_builtin_default_stack_constant_shape():
-    ids = {raw["id"] for raw in BUILTIN_DEFAULT_STACK}
-    assert ids == {"default", "community"}
-
-
-def test_catalog_entry_rejects_string_tags():
-    from specify_cli.bundler.models.catalog import CatalogEntry
-
-    data = catalog_entry_dict("demo")
-    data["tags"] = "not-a-list"
-    with pytest.raises(BundlerError, match="'tags' must be a list"):
-        CatalogEntry.from_dict(data)
-
-
-def test_catalog_entry_rejects_non_boolean_verified():
-    from specify_cli.bundler.models.catalog import CatalogEntry
-
-    data = catalog_entry_dict("demo")
-    data["verified"] = "false"  # truthy string must not mark the entry verified
-    with pytest.raises(BundlerError, match="'verified' must be a boolean"):
-        CatalogEntry.from_dict(data)
-
-
-def test_load_payload_rejects_id_key_mismatch():
-    # The enclosing key is authoritative; an entry whose own id disagrees with
-    # the key must be rejected so a catalog can't list a spoofed/unresolvable id.
-    payload = catalog_payload({"demo-bundle": catalog_entry_dict("other-id")})
-    with pytest.raises(BundlerError, match="id mismatch"):
-        load_catalog_payload(payload)
-
-
-def test_load_payload_rejects_missing_entry_id():
-    entry = catalog_entry_dict("demo-bundle")
-    entry["id"] = ""
-    payload = catalog_payload({"demo-bundle": entry})
-    with pytest.raises(BundlerError, match="missing its 'id'"):
-        load_catalog_payload(payload)
-
-
-def test_catalog_entry_rejects_non_mapping_requires():
-    from specify_cli.bundler.models.catalog import CatalogEntry
-
-    data = catalog_entry_dict("demo")
-    data["requires"] = "speckit>=0.1"
-    with pytest.raises(BundlerError, match="'requires' must be a mapping"):
-        CatalogEntry.from_dict(data)
-
-
-def test_catalog_entry_rejects_non_mapping_provides():
-    from specify_cli.bundler.models.catalog import CatalogEntry
-
-    data = catalog_entry_dict("demo")
-    data["provides"] = "extensions"
-    with pytest.raises(BundlerError, match="'provides' must be a mapping"):
-        CatalogEntry.from_dict(data)

tests/contract/test_manifest_schema.py

@@ -1,126 +0,0 @@
-"""Contract tests for the bundle manifest schema (bundle.yml).
-
-Mirrors contracts/bundle-manifest.schema.md: required identity/metadata fields,
-semver pinning of components, preset priority+strategy, integration optionality.
-"""
-from __future__ import annotations
-
-import pytest
-
-from specify_cli.bundler import BundlerError
-from specify_cli.bundler.models.manifest import BundleManifest
-from tests.bundler_helpers import valid_manifest_dict
-
-
-def test_valid_manifest_has_no_structural_errors():
-    manifest = BundleManifest.from_dict(valid_manifest_dict())
-    assert manifest.structural_errors() == []
-    assert manifest.bundle.id == "demo-bundle"
-    assert manifest.is_agnostic() is True
-
-
-def test_missing_required_field_is_reported_by_name():
-    data = valid_manifest_dict()
-    del data["bundle"]["license"]
-    errors = BundleManifest.from_dict(data).structural_errors()
-    assert any("bundle.license" in e for e in errors)
-
-
-def test_unsupported_schema_version_is_rejected():
-    data = valid_manifest_dict(schema_version="9.9")
-    errors = BundleManifest.from_dict(data).structural_errors()
-    assert any("schema_version" in e for e in errors)
-
-
-def test_non_semver_bundle_version_is_rejected():
-    data = valid_manifest_dict()
-    data["bundle"]["version"] = "not-a-version"
-    errors = BundleManifest.from_dict(data).structural_errors()
-    assert any("semver" in e for e in errors)
-
-
-def test_preset_requires_priority_and_strategy():
-    data = valid_manifest_dict()
-    data["provides"]["presets"] = [{"id": "p", "version": "1.0.0"}]
-    errors = BundleManifest.from_dict(data).structural_errors()
-    assert any("priority" in e for e in errors)
-    assert any("strategy" in e for e in errors)
-
-
-def test_invalid_preset_strategy_is_rejected():
-    data = valid_manifest_dict()
-    data["provides"]["presets"][0]["strategy"] = "merge"
-    errors = BundleManifest.from_dict(data).structural_errors()
-    assert any("strategy" in e for e in errors)
-
-
-def test_non_integer_priority_raises_actionable_error():
-    data = valid_manifest_dict()
-    data["provides"]["presets"][0]["priority"] = "high"
-    with pytest.raises(BundlerError, match="priority must be an integer"):
-        BundleManifest.from_dict(data)
-
-
-def test_non_step_components_must_be_pinned():
-    data = valid_manifest_dict()
-    data["provides"]["extensions"] = [{"id": "ext-unpinned"}]
-    errors = BundleManifest.from_dict(data).structural_errors()
-    assert any("must be pinned" in e for e in errors)
-
-
-def test_steps_may_be_unpinned():
-    data = valid_manifest_dict()
-    data["provides"]["steps"] = [{"id": "step-x"}]
-    manifest = BundleManifest.from_dict(data)
-    assert manifest.structural_errors() == []
-
-
-def test_integration_makes_bundle_non_agnostic():
-    data = valid_manifest_dict(integration={"id": "copilot"})
-    manifest = BundleManifest.from_dict(data)
-    assert manifest.is_agnostic() is False
-    assert manifest.integration.id == "copilot"
-
-
-def test_components_property_orders_by_kind():
-    manifest = BundleManifest.from_dict(valid_manifest_dict())
-    kinds = [c.kind for c in manifest.components]
-    assert kinds == ["extensions", "presets", "steps", "workflows"]
-
-
-def test_string_tags_rejected_not_split_per_character():
-    # A bare string would otherwise be iterated character-by-character; the
-    # schema requires a list of strings.
-    data = valid_manifest_dict()
-    data["tags"] = "security"
-    with pytest.raises(BundlerError, match="'tags' must be a list of strings"):
-        BundleManifest.from_dict(data)
-
-
-def test_unsafe_bundle_id_flagged_by_structural_validation():
-    data = valid_manifest_dict()
-    data["bundle"]["id"] = "../evil"
-    manifest = BundleManifest.from_dict(data)
-    errors = manifest.structural_errors()
-    assert any("bundle.id" in e and "slug" in e for e in errors)
-
-
-def test_valid_slug_bundle_id_passes():
-    data = valid_manifest_dict()
-    data["bundle"]["id"] = "team-a.bundle_1"
-    manifest = BundleManifest.from_dict(data)
-    assert not any("bundle.id" in e for e in manifest.structural_errors())
-
-
-def test_string_tools_rejected_not_split_per_character():
-    data = valid_manifest_dict()
-    data["requires"]["tools"] = "docker"
-    with pytest.raises(BundlerError, match="'requires.tools' must be a list of strings"):
-        BundleManifest.from_dict(data)
-
-
-def test_string_mcp_rejected_not_split_per_character():
-    data = valid_manifest_dict()
-    data["requires"]["mcp"] = "github"
-    with pytest.raises(BundlerError, match="'requires.mcp' must be a list of strings"):
-        BundleManifest.from_dict(data)

tests/extensions/test_extension_agent_context.py

@@ -3,13 +3,8 @@
 from __future__ import annotations
 
 import json
-import os
-import shutil
-import subprocess
-import sys
 from pathlib import Path
 
-import pytest
 import yaml
 
 from specify_cli import (
@@ -18,25 +13,18 @@ from specify_cli import (
     load_init_options,
     save_init_options,
 )
-from specify_cli.agents import CommandRegistrar
 from specify_cli.integrations.base import IntegrationBase
 from specify_cli.integrations.claude import ClaudeIntegration
-from tests.conftest import requires_bash
 
 
 PROJECT_ROOT = Path(__file__).resolve().parent.parent.parent
 EXT_DIR = PROJECT_ROOT / "extensions" / "agent-context"
-BASH = shutil.which("bash")
-POWERSHELL = (
-    shutil.which("pwsh") or shutil.which("powershell.exe") or shutil.which("powershell")
-)
 
 
 def _write_ext_config(project_root: Path, **overrides: object) -> None:
     """Write a minimal agent-context extension config."""
     cfg: dict = {
         "context_file": overrides.get("context_file", ""),
-        "context_files": overrides.get("context_files", []),
         "context_markers": overrides.get(
             "context_markers",
             {
@@ -84,14 +72,6 @@ class TestExtensionLayout:
         assert cmd.is_file()
         assert "agent-context-config.yml" in cmd.read_text(encoding="utf-8")
 
-    def test_command_file_documents_context_file_constraints(self):
-        text = (
-            EXT_DIR / "commands" / "speckit.agent-context.update.md"
-        ).read_text(encoding="utf-8")
-        assert "context file(s)" in text
-        assert "Windows drive paths" in text
-        assert "backslash separators" in text
-
     def test_bundled_scripts_exist(self):
         assert (EXT_DIR / "scripts" / "bash" / "update-agent-context.sh").is_file()
         assert (EXT_DIR / "scripts" / "powershell" / "update-agent-context.ps1").is_file()
@@ -127,184 +107,6 @@ class _CtxIntegration(ClaudeIntegration):
     """Use Claude as a concrete integration with a context_file."""
 
 
-class _NoContextIntegration(IntegrationBase):
-    """Minimal integration with no context_file for base-class fallback tests."""
-
-
-def _install_agent_context_config(project_root: Path, **overrides: object) -> None:
-    _write_ext_config(project_root, **overrides)
-
-
-def _bash_posix_path(path: Path) -> str:
-    """Convert a Windows path to the POSIX form used by the available bash."""
-    resolved = str(path.resolve())
-    if os.name != "nt":
-        return resolved
-
-    if BASH:
-        converted = subprocess.run(
-            [
-                BASH,
-                "-lc",
-                "command -v cygpath >/dev/null 2>&1 && cygpath -u \"$1\"",
-                "bash",
-                resolved,
-            ],
-            capture_output=True,
-            text=True,
-            timeout=30,
-        )
-        if converted.returncode == 0 and converted.stdout.strip():
-            return converted.stdout.strip()
-
-    drive = path.drive.rstrip(":").lower()
-    posix = path.as_posix()
-    return f"/mnt/{drive}{posix[2:]}" if drive else posix
-
-
-def _ensure_test_python_on_path(project_root: Path) -> Path:
-    """Create python/python3 shims that run the current pytest interpreter."""
-    shim_dir = project_root / ".test-python-bin"
-    shim_dir.mkdir(exist_ok=True)
-    python_exe = Path(sys.executable).resolve()
-    shell_python = _bash_posix_path(python_exe)
-
-    for name in ("python", "python3"):
-        shell_shim = shim_dir / name
-        shell_shim.write_text(
-            f"#!/usr/bin/env sh\nexec {shlex_quote(shell_python)} \"$@\"\n",
-            encoding="utf-8",
-            newline="\n",
-        )
-        shell_shim.chmod(0o755)
-
-        if os.name == "nt":
-            cmd_shim = shim_dir / f"{name}.cmd"
-            cmd_shim.write_text(
-                f'@echo off\r\n"{python_exe}" %*\r\n',
-                encoding="utf-8",
-            )
-
-    return shim_dir
-
-
-def _current_pythonpath() -> str:
-    """Return sys.path entries needed by child script interpreters."""
-    entries = [
-        entry
-        for entry in sys.path
-        if isinstance(entry, str) and entry
-    ]
-    existing = os.environ.get("PYTHONPATH")
-    if existing:
-        entries.extend(entry for entry in existing.split(os.pathsep) if entry)
-    return os.pathsep.join(dict.fromkeys(entries))
-
-
-def _bundled_script_env(
-    project_root: Path,
-    *,
-    for_bash: bool = False,
-    speckit_python: str | None = None,
-) -> dict[str, str]:
-    env = os.environ.copy()
-    shim_dir = _ensure_test_python_on_path(project_root)
-    env["PATH"] = str(shim_dir) + os.pathsep + env.get("PATH", "")
-    env["SPECKIT_PYTHON"] = (
-        speckit_python
-        if speckit_python is not None
-        else (_bash_posix_path(Path(sys.executable)) if for_bash else sys.executable)
-    )
-    pythonpath = _current_pythonpath()
-    if pythonpath:
-        env["PYTHONPATH"] = pythonpath
-    return env
-
-
-def _run_bash_agent_context_script(
-    project_root: Path,
-    *,
-    speckit_python: str | None = None,
-) -> subprocess.CompletedProcess:
-    script = EXT_DIR / "scripts" / "bash" / "update-agent-context.sh"
-    env = _bundled_script_env(
-        project_root,
-        for_bash=True,
-        speckit_python=speckit_python,
-    )
-    if os.name == "nt":
-        root = _bash_posix_path(project_root)
-        script_path = _bash_posix_path(script)
-        shim_dir = _bash_posix_path(_ensure_test_python_on_path(project_root))
-        command = (
-            f"export PATH={shlex_quote(shim_dir)}:\"$PATH\"; "
-            f"cd {shlex_quote(root)} && {shlex_quote(script_path)}"
-        )
-        return subprocess.run(
-            [BASH, "-lc", command],
-            env=env,
-            capture_output=True,
-            text=True,
-            timeout=30,
-        )
-    return subprocess.run(
-        [BASH, str(script)],
-        cwd=project_root,
-        env=env,
-        capture_output=True,
-        text=True,
-        timeout=30,
-    )
-
-
-def shlex_quote(value: str) -> str:
-    return "'" + value.replace("'", "'\"'\"'") + "'"
-
-
-def _run_powershell_agent_context_script(project_root: Path) -> subprocess.CompletedProcess:
-    script = EXT_DIR / "scripts" / "powershell" / "update-agent-context.ps1"
-    env = _bundled_script_env(project_root)
-    return subprocess.run(
-        [
-            POWERSHELL,
-            "-NoProfile",
-            "-ExecutionPolicy",
-            "Bypass",
-            "-File",
-            str(script),
-        ],
-        cwd=project_root,
-        env=env,
-        capture_output=True,
-        text=True,
-        timeout=30,
-    )
-
-
-def _run_powershell_agent_context_script_with_env(
-    project_root: Path,
-    *,
-    speckit_python: str,
-) -> subprocess.CompletedProcess:
-    script = EXT_DIR / "scripts" / "powershell" / "update-agent-context.ps1"
-    env = _bundled_script_env(project_root, speckit_python=speckit_python)
-    return subprocess.run(
-        [
-            POWERSHELL,
-            "-NoProfile",
-            "-ExecutionPolicy",
-            "Bypass",
-            "-File",
-            str(script),
-        ],
-        cwd=project_root,
-        env=env,
-        capture_output=True,
-        text=True,
-        timeout=30,
-    )
-
-
 class TestContextMarkerResolution:
     def test_defaults_when_ext_config_missing(self, tmp_path):
         i = _CtxIntegration()
@@ -398,142 +200,6 @@ class TestUpsertWithCustomMarkers:
         assert text.startswith("# header\n")
         assert "footer" in text
 
-    def test_upsert_uses_configured_context_files(self, tmp_path):
-        _write_ext_config(
-            tmp_path,
-            context_file="CLAUDE.md",
-            context_files=["AGENTS.md", "CLAUDE.md"],
-        )
-        i = _CtxIntegration()
-        result = i.upsert_context_section(
-            tmp_path, plan_path="specs/001-foo/plan.md"
-        )
-        assert result == tmp_path / "AGENTS.md"
-        for name in ("AGENTS.md", "CLAUDE.md"):
-            text = (tmp_path / name).read_text(encoding="utf-8")
-            assert IntegrationBase.CONTEXT_MARKER_START in text
-            assert "specs/001-foo/plan.md" in text
-
-    def test_context_files_deduplicate_with_platform_semantics(self, tmp_path):
-        duplicate = "agents.md" if os.name == "nt" else "AGENTS.md"
-        _write_ext_config(
-            tmp_path,
-            context_file="CLAUDE.md",
-            context_files=["AGENTS.md", "CLAUDE.md", duplicate],
-        )
-
-        files = _CtxIntegration()._resolve_context_files(tmp_path)
-
-        assert files == ["AGENTS.md", "CLAUDE.md"]
-
-    def test_empty_context_files_falls_back_to_config_context_file(self, tmp_path):
-        _write_ext_config(
-            tmp_path,
-            context_file="AGENTS.md",
-            context_files=[],
-        )
-
-        files = _CtxIntegration()._resolve_context_files(tmp_path)
-
-        assert files == ["AGENTS.md"]
-
-    def test_config_context_file_takes_precedence_over_class_default(self, tmp_path):
-        _write_ext_config(
-            tmp_path,
-            context_file="AGENTS.md",
-        )
-
-        i = _CtxIntegration()
-        result = i.upsert_context_section(
-            tmp_path, plan_path="specs/001-foo/plan.md"
-        )
-
-        assert result == tmp_path / "AGENTS.md"
-        assert (tmp_path / "AGENTS.md").exists()
-        assert not (tmp_path / "CLAUDE.md").exists()
-
-    def test_config_context_file_fallback_rejects_invalid_path(self, tmp_path):
-        _write_ext_config(
-            tmp_path,
-            context_file="../outside.md",
-            context_files=[],
-        )
-
-        with pytest.raises(ValueError, match="project-relative|must not contain"):
-            _CtxIntegration()._resolve_context_files(tmp_path)
-
-    def test_remove_uses_configured_context_files(self, tmp_path):
-        _write_ext_config(
-            tmp_path,
-            context_file="CLAUDE.md",
-            context_files=["AGENTS.md", "CLAUDE.md"],
-        )
-        i = _CtxIntegration()
-        for name in ("AGENTS.md", "CLAUDE.md"):
-            (tmp_path / name).write_text(
-                f"head\n{IntegrationBase.CONTEXT_MARKER_START}\nbody\n"
-                f"{IntegrationBase.CONTEXT_MARKER_END}\ntail\n",
-                encoding="utf-8",
-            )
-        assert i.remove_context_section(tmp_path) is True
-        for name in ("AGENTS.md", "CLAUDE.md"):
-            text = (tmp_path / name).read_text(encoding="utf-8")
-            assert "body" not in text
-            assert "head" in text
-            assert "tail" in text
-
-    @pytest.mark.parametrize(
-        "bad_path",
-        [
-            "../outside.md",
-            "nested/../../outside.md",
-            "nested\\outside.md",
-            str(Path("/tmp/outside.md")),
-            "C:/tmp/outside.md",
-            "C:tmp/outside.md",
-        ],
-    )
-    def test_upsert_rejects_context_files_outside_project(self, tmp_path, bad_path):
-        _write_ext_config(
-            tmp_path,
-            context_file="CLAUDE.md",
-            context_files=["AGENTS.md", bad_path],
-        )
-        i = _CtxIntegration()
-        with pytest.raises(ValueError, match="project-relative|must not contain"):
-            i.upsert_context_section(tmp_path)
-
-        assert not (tmp_path / "AGENTS.md").exists()
-        assert not (tmp_path.parent / "outside.md").exists()
-
-    @pytest.mark.parametrize(
-        "bad_path",
-        [
-            "../outside.md",
-            "nested\\outside.md",
-            str(Path("/tmp/outside.md")),
-            "C:/tmp/outside.md",
-            "C:tmp/outside.md",
-        ],
-    )
-    def test_remove_rejects_context_files_outside_project(self, tmp_path, bad_path):
-        _write_ext_config(
-            tmp_path,
-            context_file="CLAUDE.md",
-            context_files=["AGENTS.md", bad_path],
-        )
-        outside = tmp_path.parent / "outside.md"
-        outside.write_text(
-            f"{IntegrationBase.CONTEXT_MARKER_START}\nbody\n"
-            f"{IntegrationBase.CONTEXT_MARKER_END}\n",
-            encoding="utf-8",
-        )
-        i = _CtxIntegration()
-        with pytest.raises(ValueError, match="project-relative|must not contain"):
-            i.remove_context_section(tmp_path)
-
-        assert "body" in outside.read_text(encoding="utf-8")
-
     def test_remove_uses_custom_markers(self, tmp_path):
         i = self._setup(
             tmp_path, {"start": "<!-- BEGIN -->", "end": "<!-- END -->"}
@@ -604,17 +270,6 @@ class TestExtensionEnabledGate:
         assert result is None
         assert not (tmp_path / "CLAUDE.md").exists()
 
-    def test_upsert_disabled_ignores_bad_context_files_config(self, tmp_path):
-        _write_registry(tmp_path, enabled=False)
-        _write_ext_config(
-            tmp_path,
-            context_file="CLAUDE.md",
-            context_files=["../disabled-upsert-outside.md"],
-        )
-        i = _CtxIntegration()
-        assert i.upsert_context_section(tmp_path) is None
-        assert not (tmp_path.parent / "disabled-upsert-outside.md").exists()
-
     def test_remove_skipped_when_disabled(self, tmp_path):
         _write_registry(tmp_path, enabled=False)
         i = _CtxIntegration()
@@ -628,382 +283,6 @@ class TestExtensionEnabledGate:
         # File must be unchanged when extension is disabled
         assert ctx.read_text(encoding="utf-8") == original
 
-    def test_remove_disabled_ignores_bad_context_files_config(self, tmp_path):
-        _write_registry(tmp_path, enabled=False)
-        _write_ext_config(
-            tmp_path,
-            context_file="CLAUDE.md",
-            context_files=["../disabled-remove-outside.md"],
-        )
-        outside = tmp_path.parent / "disabled-remove-outside.md"
-        outside.write_text(
-            f"{IntegrationBase.CONTEXT_MARKER_START}\nbody\n"
-            f"{IntegrationBase.CONTEXT_MARKER_END}\n",
-            encoding="utf-8",
-        )
-        i = _CtxIntegration()
-        assert i.remove_context_section(tmp_path) is False
-        assert "body" in outside.read_text(encoding="utf-8")
-
-    def test_context_file_display_disabled_uses_config_context_file(
-        self, tmp_path
-    ):
-        _write_registry(tmp_path, enabled=False)
-        _write_ext_config(
-            tmp_path,
-            context_file="AGENTS.md",
-            context_files=["../outside.md"],
-        )
-        i = _CtxIntegration()
-        assert i._context_file_display(tmp_path) == "AGENTS.md"
-
-    def test_context_file_display_disabled_without_context_file_returns_string(
-        self, tmp_path
-    ):
-        _write_registry(tmp_path, enabled=False)
-        i = _NoContextIntegration()
-        assert i._context_file_display(tmp_path) == ""
-
-
-class TestSkillPlaceholderContextValidation:
-    @pytest.mark.parametrize(
-        "bad_path",
-        [
-            "../outside.md",
-            "nested/../../outside.md",
-            "nested\\outside.md",
-            str(Path("/tmp/outside.md")),
-            "C:/tmp/outside.md",
-            "C:tmp/outside.md",
-        ],
-    )
-    def test_context_files_reject_invalid_config_paths(self, tmp_path, bad_path):
-        _write_ext_config(
-            tmp_path,
-            context_file="AGENTS.md",
-            context_files=["AGENTS.md", bad_path],
-        )
-
-        with pytest.raises(ValueError, match="project-relative|must not contain"):
-            CommandRegistrar.resolve_skill_placeholders(
-                "codex",
-                {},
-                "Read __CONTEXT_FILE__",
-                tmp_path,
-            )
-
-    @pytest.mark.parametrize(
-        "bad_path",
-        [
-            "../outside.md",
-            "C:tmp/outside.md",
-        ],
-    )
-    def test_context_file_rejects_invalid_config_path(self, tmp_path, bad_path):
-        _write_ext_config(
-            tmp_path,
-            context_file=bad_path,
-            context_files=[],
-        )
-
-        with pytest.raises(ValueError, match="project-relative|must not contain"):
-            CommandRegistrar.resolve_skill_placeholders(
-                "codex",
-                {},
-                "Read __CONTEXT_FILE__",
-                tmp_path,
-            )
-
-    def test_enabled_extension_rejects_invalid_legacy_init_options_path(
-        self, tmp_path
-    ):
-        save_init_options(tmp_path, {"context_file": "../outside.md"})
-
-        with pytest.raises(ValueError, match="must not contain"):
-            CommandRegistrar.resolve_skill_placeholders(
-                "codex",
-                {},
-                "Read __CONTEXT_FILE__",
-                tmp_path,
-            )
-
-    def test_disabled_extension_ignores_invalid_context_files(self, tmp_path):
-        _write_registry(tmp_path, enabled=False)
-        _write_ext_config(
-            tmp_path,
-            context_file="AGENTS.md",
-            context_files=["../outside.md"],
-        )
-        save_init_options(tmp_path, {"context_file": "AGENTS.md"})
-
-        content = CommandRegistrar.resolve_skill_placeholders(
-            "codex",
-            {},
-            "Read __CONTEXT_FILE__",
-            tmp_path,
-        )
-
-        assert content == "Read AGENTS.md"
-
-    def test_disabled_extension_uses_extension_context_file_before_init_options(
-        self, tmp_path
-    ):
-        _write_registry(tmp_path, enabled=False)
-        _write_ext_config(
-            tmp_path,
-            context_file="AGENTS.md",
-            context_files=["CLAUDE.md"],
-        )
-        save_init_options(tmp_path, {"context_file": "LEGACY.md"})
-
-        content = CommandRegistrar.resolve_skill_placeholders(
-            "codex",
-            {},
-            "Read __CONTEXT_FILE__",
-            tmp_path,
-        )
-
-        assert content == "Read AGENTS.md"
-
-    def test_context_files_deduplicate_with_platform_semantics(self, tmp_path):
-        duplicate = "agents.md" if os.name == "nt" else "AGENTS.md"
-        _write_ext_config(
-            tmp_path,
-            context_file="AGENTS.md",
-            context_files=["AGENTS.md", "CLAUDE.md", duplicate],
-        )
-
-        content = CommandRegistrar.resolve_skill_placeholders(
-            "codex",
-            {},
-            "Read __CONTEXT_FILE__",
-            tmp_path,
-        )
-
-        assert content == "Read AGENTS.md, CLAUDE.md"
-
-
-class TestBundledUpdaterPathValidation:
-    def test_bundled_script_env_makes_yaml_importable(self, tmp_path):
-        env = _bundled_script_env(tmp_path)
-
-        result = subprocess.run(
-            [env["SPECKIT_PYTHON"], "-c", "import yaml"],
-            env=env,
-            capture_output=True,
-            text=True,
-            timeout=30,
-        )
-
-        assert result.returncode == 0, result.stderr + result.stdout
-
-    @requires_bash
-    def test_bash_script_trims_context_file_fallback(self, tmp_path):
-        project = tmp_path / "project"
-        project.mkdir()
-        _install_agent_context_config(
-            project,
-            context_file="  AGENTS.md  ",
-            context_files=[],
-        )
-
-        result = _run_bash_agent_context_script(project)
-
-        assert result.returncode == 0, result.stderr + result.stdout
-        assert "agent-context: updated AGENTS.md" in (result.stderr + result.stdout)
-        assert (project / "AGENTS.md").exists()
-        assert not (project / "  AGENTS.md  ").exists()
-
-    @requires_bash
-    def test_bash_script_rejects_symlink_escape(self, tmp_path):
-        project = tmp_path / "project"
-        outside = tmp_path / "outside"
-        project.mkdir()
-        outside.mkdir()
-        _install_agent_context_config(
-            project,
-            context_file="AGENTS.md",
-            context_files=["link/out.md"],
-        )
-
-        if os.name == "nt":
-            root = _bash_posix_path(tmp_path)
-            create_link = subprocess.run(
-                [
-                    BASH,
-                    "-lc",
-                    f"ln -s {shlex_quote(root + '/outside')} "
-                    f"{shlex_quote(root + '/project/link')}",
-                ],
-                capture_output=True,
-                text=True,
-                timeout=30,
-            )
-            if create_link.returncode != 0:
-                pytest.skip(f"symlink unavailable: {create_link.stderr}")
-        else:
-            try:
-                (project / "link").symlink_to(outside, target_is_directory=True)
-            except OSError as exc:
-                pytest.skip(f"symlink unavailable: {exc}")
-
-        result = _run_bash_agent_context_script(project)
-
-        assert result.returncode == 1
-        assert "resolves outside the project root" in result.stderr
-        assert not (outside / "out.md").exists()
-
-    @requires_bash
-    def test_bash_script_deduplicates_context_files_in_order(self, tmp_path):
-        project = tmp_path / "project"
-        project.mkdir()
-        duplicate = "agents.md" if os.name == "nt" else "AGENTS.md"
-        _install_agent_context_config(
-            project,
-            context_file="AGENTS.md",
-            context_files=["AGENTS.md", "CLAUDE.md", duplicate],
-        )
-
-        result = _run_bash_agent_context_script(project)
-
-        assert result.returncode == 0, result.stderr + result.stdout
-        output = result.stderr + result.stdout
-        assert output.count("agent-context: updated AGENTS.md") == 1
-        assert output.count("agent-context: updated CLAUDE.md") == 1
-        assert "agent-context: updated agents.md" not in output
-
-    @requires_bash
-    def test_bash_script_falls_back_from_invalid_speckit_python(self, tmp_path):
-        project = tmp_path / "project"
-        project.mkdir()
-        _install_agent_context_config(
-            project,
-            context_file="AGENTS.md",
-            context_files=["AGENTS.md"],
-        )
-
-        result = _run_bash_agent_context_script(
-            project,
-            speckit_python="/definitely/missing/python",
-        )
-
-        assert result.returncode == 0, result.stderr + result.stdout
-        assert "agent-context: updated AGENTS.md" in (result.stderr + result.stdout)
-        assert (project / "AGENTS.md").exists()
-
-    @pytest.mark.skipif(POWERSHELL is None, reason="PowerShell not available")
-    def test_powershell_script_rejects_backslash_context_files(self, tmp_path):
-        project = tmp_path / "project"
-        project.mkdir()
-        _install_agent_context_config(
-            project,
-            context_file="AGENTS.md",
-            context_files=["nested\\AGENTS.md"],
-        )
-
-        result = _run_powershell_agent_context_script(project)
-
-        assert result.returncode == 1
-        assert "must not contain backslash separators" in (
-            result.stderr + result.stdout
-        )
-        assert not (project / "nested" / "AGENTS.md").exists()
-
-    @pytest.mark.skipif(POWERSHELL is None, reason="PowerShell not available")
-    def test_powershell_script_rejects_drive_qualified_context_files(self, tmp_path):
-        project = tmp_path / "project"
-        project.mkdir()
-        _install_agent_context_config(
-            project,
-            context_file="AGENTS.md",
-            context_files=["C:tmp/outside.md"],
-        )
-
-        result = _run_powershell_agent_context_script(project)
-
-        assert result.returncode == 1
-        assert "must be project-relative paths" in (result.stderr + result.stdout)
-        assert not (project / "tmp" / "outside.md").exists()
-
-    @pytest.mark.skipif(POWERSHELL is None, reason="PowerShell not available")
-    def test_powershell_script_deduplicates_context_files_in_order(self, tmp_path):
-        project = tmp_path / "project"
-        project.mkdir()
-        duplicate = "agents.md" if os.name == "nt" else "AGENTS.md"
-        _install_agent_context_config(
-            project,
-            context_file="AGENTS.md",
-            context_files=["AGENTS.md", "CLAUDE.md", duplicate],
-        )
-
-        result = _run_powershell_agent_context_script(project)
-
-        assert result.returncode == 0, result.stderr + result.stdout
-        output = result.stderr + result.stdout
-        assert output.count("agent-context: updated AGENTS.md") == 1
-        assert output.count("agent-context: updated CLAUDE.md") == 1
-        assert "agent-context: updated agents.md" not in output
-
-    @pytest.mark.skipif(POWERSHELL is None, reason="PowerShell not available")
-    def test_powershell_script_falls_back_from_invalid_speckit_python(self, tmp_path):
-        project = tmp_path / "project"
-        project.mkdir()
-        _install_agent_context_config(
-            project,
-            context_file="AGENTS.md",
-            context_files=["AGENTS.md"],
-        )
-
-        result = _run_powershell_agent_context_script_with_env(
-            project,
-            speckit_python=str(project / "missing-python"),
-        )
-
-        assert result.returncode == 0, result.stderr + result.stdout
-        assert "agent-context: updated AGENTS.md" in (result.stderr + result.stdout)
-        assert (project / "AGENTS.md").exists()
-
-    @pytest.mark.skipif(
-        POWERSHELL is None or os.name != "nt",
-        reason="Windows PowerShell junction test requires Windows",
-    )
-    def test_powershell_script_rejects_junction_escape(self, tmp_path):
-        project = tmp_path / "project"
-        outside = tmp_path / "outside"
-        project.mkdir()
-        outside.mkdir()
-        _install_agent_context_config(
-            project,
-            context_file="AGENTS.md",
-            context_files=["link/out.md"],
-        )
-
-        create_link = subprocess.run(
-            [
-                POWERSHELL,
-                "-NoProfile",
-                "-ExecutionPolicy",
-                "Bypass",
-                "-Command",
-                (
-                    "New-Item -ItemType Junction "
-                    f"-Path {str(project / 'link')!r} "
-                    f"-Target {str(outside)!r} | Out-Null"
-                ),
-            ],
-            capture_output=True,
-            text=True,
-            timeout=30,
-        )
-        if create_link.returncode != 0:
-            pytest.skip(f"junction unavailable: {create_link.stderr}")
-
-        result = _run_powershell_agent_context_script(project)
-
-        assert result.returncode == 1
-        assert "resolves outside the project root" in (result.stderr + result.stdout)
-        assert not (outside / "out.md").exists()
-
 
 # ── Extension config writers ─────────────────────────────────────────────────
 
@@ -1070,65 +349,6 @@ class TestExtensionConfigWriters:
         assert cfg["context_file"] == i.context_file
         assert "context_markers" in cfg
 
-    def test_update_init_options_preserves_context_files(self, tmp_path):
-        from specify_cli import _update_init_options_for_integration
-
-        _write_ext_config(
-            tmp_path,
-            context_file="AGENTS.md",
-            context_files=["AGENTS.md", "CLAUDE.md"],
-        )
-        i = _CtxIntegration()
-        _update_init_options_for_integration(tmp_path, i, script_type="sh")
-        cfg = _load_agent_context_config(tmp_path)
-        assert cfg["context_file"] == i.context_file
-        assert cfg["context_files"] == ["AGENTS.md", "CLAUDE.md"]
-
-    def test_update_init_options_preserves_empty_context_files(self, tmp_path):
-        from specify_cli import _update_init_options_for_integration
-
-        _write_ext_config(
-            tmp_path,
-            context_file="AGENTS.md",
-            context_files=[],
-        )
-        i = _CtxIntegration()
-        _update_init_options_for_integration(tmp_path, i, script_type="sh")
-        cfg = _load_agent_context_config(tmp_path)
-        assert cfg["context_file"] == i.context_file
-        assert cfg["context_files"] == []
-
-    def test_update_init_options_normalizes_invalid_context_files(self, tmp_path):
-        from specify_cli import _update_init_options_for_integration
-
-        _write_ext_config(tmp_path, context_file="AGENTS.md")
-        cfg = _load_agent_context_config(tmp_path)
-        cfg["context_files"] = "AGENTS.md"
-        _save_agent_context_config(tmp_path, cfg)
-
-        i = _CtxIntegration()
-        _update_init_options_for_integration(tmp_path, i, script_type="sh")
-        cfg = _load_agent_context_config(tmp_path)
-        assert cfg["context_file"] == i.context_file
-        assert cfg["context_files"] == []
-
-    def test_clear_init_options_clears_context_files(self, tmp_path):
-        from specify_cli import _clear_init_options_for_integration
-
-        save_init_options(
-            tmp_path,
-            {"integration": "claude", "ai": "claude"},
-        )
-        _write_ext_config(
-            tmp_path,
-            context_file="CLAUDE.md",
-            context_files=["AGENTS.md", "CLAUDE.md"],
-        )
-        _clear_init_options_for_integration(tmp_path, "claude")
-        cfg = _load_agent_context_config(tmp_path)
-        assert cfg.get("context_file") == ""
-        assert "context_files" not in cfg
-
     def test_update_init_options_preserves_custom_markers(self, tmp_path):
         from specify_cli import _update_init_options_for_integration
 

tests/integration/test_bundler_catalog_stack.py

@@ -1,79 +0,0 @@
-"""Integration tests for the catalog stack: precedence, policy gating, search."""
-from __future__ import annotations
-
-
-import pytest
-
-from specify_cli.bundler import BundlerError
-from specify_cli.bundler.models.catalog import CatalogSource, InstallPolicy, Scope
-from specify_cli.bundler.services.catalog_stack import CatalogStack
-from tests.bundler_helpers import catalog_entry_dict, catalog_payload
-
-
-def _source(source_id, priority, policy, url="builtin://x"):
-    return CatalogSource(
-        id=source_id, url=url, priority=priority,
-        install_policy=InstallPolicy(policy), scope=Scope.PROJECT,
-    )
-
-
-def _stack(sources, payloads):
-    def fetcher(src):
-        return payloads[src.id]
-    return CatalogStack(sources, fetcher)
-
-
-def test_resolve_prefers_highest_precedence_source():
-    sources = [
-        _source("low", 2, "install-allowed"),
-        _source("high", 1, "discovery-only"),
-    ]
-    payloads = {
-        "high": catalog_payload({"b": catalog_entry_dict("b", version="9.0.0")}),
-        "low": catalog_payload({"b": catalog_entry_dict("b", version="1.0.0")}),
-    }
-    resolved = _stack(sources, payloads).resolve("b")
-    assert resolved.source.id == "high"
-    assert resolved.entry.version == "9.0.0"
-    assert resolved.install_allowed is False
-
-
-def test_resolve_unknown_bundle_errors():
-    stack = _stack(
-        [_source("only", 1, "install-allowed")],
-        {"only": catalog_payload({})},
-    )
-    with pytest.raises(BundlerError, match="not found"):
-        stack.resolve("missing")
-
-
-def test_search_dedupes_by_precedence_and_filters():
-    sources = [_source("a", 1, "install-allowed"), _source("b", 2, "install-allowed")]
-    payloads = {
-        "a": catalog_payload({
-            "alpha": catalog_entry_dict("alpha", role="developer"),
-        }),
-        "b": catalog_payload({
-            "alpha": catalog_entry_dict("alpha", version="0.0.1"),
-            "beta": catalog_entry_dict("beta", role="qa"),
-        }),
-    }
-    stack = _stack(sources, payloads)
-
-    all_results = stack.search()
-    ids = [r.entry.id for r in all_results]
-    assert ids == ["alpha", "beta"]
-    # alpha resolved from the higher-precedence source 'a'.
-    alpha = next(r for r in all_results if r.entry.id == "alpha")
-    assert alpha.source.id == "a"
-
-    qa_only = stack.search("qa")
-    assert [r.entry.id for r in qa_only] == ["beta"]
-
-
-def test_unreachable_source_raises_named_error():
-    def fetcher(src):
-        raise RuntimeError("boom")
-    stack = CatalogStack([_source("bad", 1, "install-allowed")], fetcher)
-    with pytest.raises(BundlerError, match="bad"):
-        stack.resolve("anything")

tests/integration/test_bundler_init_install.py

@@ -1,92 +0,0 @@
-"""Install-time initialization and integration precedence (T049, T050).
-
-``specify bundle install`` into an uninitialized directory must scaffold a Spec
-Kit project first (FR-012), choosing the integration by precedence (FR-013):
-explicit ``--integration`` override → bundle-declared integration → default.
-The end-to-end test runs fully offline against bundled assets.
-"""
-from __future__ import annotations
-
-import json
-import os
-from pathlib import Path
-
-import yaml
-from typer.testing import CliRunner
-
-from specify_cli import app
-from specify_cli.bundler.models.manifest import BundleManifest
-from specify_cli.commands.bundle import _resolve_init_integration
-from specify_cli.bundler.services.packager import build_bundle
-from tests.bundler_helpers import valid_manifest_dict
-
-runner = CliRunner()
-
-
-def _manifest(**overrides):
-    data = valid_manifest_dict(**overrides)
-    return BundleManifest.from_dict(data)
-
-
-def test_precedence_override_wins():
-    manifest = _manifest(integration={"id": "claude"})
-    assert _resolve_init_integration("gemini", manifest) == "gemini"
-
-
-def test_precedence_bundle_declared_when_no_override():
-    manifest = _manifest(integration={"id": "claude"})
-    assert _resolve_init_integration(None, manifest) == "claude"
-
-
-def test_precedence_default_when_unspecified():
-    manifest = _manifest()
-    assert _resolve_init_integration(None, manifest) == "copilot"
-    assert _resolve_init_integration(None, None) == "copilot"
-
-
-def _build_mini(tmp_path: Path) -> Path:
-    bundle = tmp_path / "mini"
-    bundle.mkdir()
-    (bundle / "bundle.yml").write_text(
-        yaml.safe_dump(
-            {
-                "schema_version": "1.0",
-                "bundle": {
-                    "id": "mini",
-                    "name": "Mini",
-                    "version": "1.0.0",
-                    "role": "developer",
-                    "description": "minimal",
-                    "author": "tests",
-                    "license": "MIT",
-                },
-                "requires": {"speckit_version": ">=0.1.0"},
-                "provides": {"extensions": [{"id": "agent-context", "version": "1.0.0"}]},
-            }
-        ),
-        encoding="utf-8",
-    )
-    (bundle / "README.md").write_text("# Mini\n", encoding="utf-8")
-    return build_bundle(bundle).artifact_path
-
-
-def test_install_initializes_uninitialized_project(tmp_path: Path):
-    project = tmp_path / "proj"
-    project.mkdir()
-    artifact = _build_mini(tmp_path)
-
-    previous = Path.cwd()
-    os.chdir(project)
-    try:
-        result = runner.invoke(
-            app, ["bundle", "install", str(artifact), "--offline"]
-        )
-        assert result.exit_code == 0, result.output
-    finally:
-        os.chdir(previous)
-
-    assert (project / ".specify").is_dir()
-    marker = project / ".specify" / "integration.json"
-    assert marker.exists()
-    data = json.loads(marker.read_text(encoding="utf-8"))
-    assert "copilot" in json.dumps(data)

tests/integration/test_bundler_install_flow.py

@@ -1,222 +0,0 @@
-"""Integration tests for the install → record → remove lifecycle (offline, fake installer).
-
-Uses :class:`FakeInstaller` so no network or real primitive machinery is touched
-(Constitution Principle II network-mocking, Principle IV offline-first).
-"""
-from __future__ import annotations
-
-from pathlib import Path
-
-import pytest
-
-from specify_cli.bundler import BundlerError
-from specify_cli.bundler.models.manifest import BundleManifest
-from specify_cli.bundler.models.records import load_records
-from specify_cli.bundler.services.installer import install_bundle, remove_bundle
-from specify_cli.bundler.services.resolver import resolve_install_plan
-from tests.bundler_helpers import FakeInstaller, make_project, valid_manifest_dict
-
-
-def _plan(manifest):
-    return resolve_install_plan(
-        manifest, speckit_version="0.11.2", active_integration="copilot"
-    )
-
-
-def test_install_records_and_invokes_primitives(tmp_path: Path):
-    make_project(tmp_path)
-    manifest = BundleManifest.from_dict(valid_manifest_dict())
-    installer = FakeInstaller()
-
-    result = install_bundle(tmp_path, _plan(manifest), installer, manifest=manifest)
-
-    assert len(result.installed) == 4
-    assert len(installer.install_calls) == 4
-    records = load_records(tmp_path)
-    assert len(records) == 1
-    assert records[0].bundle_id == "demo-bundle"
-
-
-def test_install_is_idempotent(tmp_path: Path):
-    make_project(tmp_path)
-    manifest = BundleManifest.from_dict(valid_manifest_dict())
-    installer = FakeInstaller()
-
-    install_bundle(tmp_path, _plan(manifest), installer, manifest=manifest)
-    second = install_bundle(tmp_path, _plan(manifest), installer, manifest=manifest)
-
-    # Second install adds nothing and does not duplicate the record.
-    assert second.installed == []
-    assert len(second.skipped) == 4
-    assert len(load_records(tmp_path)) == 1
-
-
-def test_partial_failure_rolls_back_and_records_nothing(tmp_path: Path):
-    make_project(tmp_path)
-    manifest = BundleManifest.from_dict(valid_manifest_dict())
-    installer = FakeInstaller(fail_on="preset-a")
-
-    with pytest.raises(BundlerError):
-        install_bundle(tmp_path, _plan(manifest), installer, manifest=manifest)
-
-    # ext-a was installed first, then rolled back; no record persisted.
-    assert installer.installed == set()
-    assert load_records(tmp_path) == []
-
-
-def test_remove_is_non_collateral(tmp_path: Path):
-    make_project(tmp_path)
-    installer = FakeInstaller()
-
-    # Bundle A provides a shared preset; Bundle B also provides it.
-    data_a = valid_manifest_dict()
-    data_a["bundle"]["id"] = "a"
-    data_b = valid_manifest_dict()
-    data_b["bundle"]["id"] = "b"
-    data_b["provides"] = {"presets": [
-        {"id": "preset-a", "version": "2.0.0", "priority": 10, "strategy": "append"}
-    ]}
-
-    man_a = BundleManifest.from_dict(data_a)
-    man_b = BundleManifest.from_dict(data_b)
-    install_bundle(tmp_path, _plan(man_a), installer, manifest=man_a)
-    install_bundle(tmp_path, _plan(man_b), installer, manifest=man_b)
-
-    # Removing B must NOT uninstall preset-a (still needed by A).
-    result = remove_bundle(tmp_path, "b", installer)
-    assert ("presets", "preset-a") in {(c.kind, c.id) for c in result.skipped}
-    assert installer.is_installed(tmp_path, man_a.presets[0]) is True
-
-    remaining = {r.bundle_id for r in load_records(tmp_path)}
-    assert remaining == {"a"}
-
-
-def test_remove_unknown_bundle_errors(tmp_path: Path):
-    make_project(tmp_path)
-    with pytest.raises(BundlerError, match="not installed"):
-        remove_bundle(tmp_path, "ghost", FakeInstaller())
-
-
-def test_remove_reports_uninstalled_not_installed(tmp_path: Path):
-    make_project(tmp_path)
-    manifest = BundleManifest.from_dict(valid_manifest_dict())
-    installer = FakeInstaller()
-    install_bundle(tmp_path, _plan(manifest), installer, manifest=manifest)
-
-    result = remove_bundle(tmp_path, "demo-bundle", installer)
-
-    # Removal flows populate the dedicated ``uninstalled`` list; ``installed``
-    # stays empty so the result type is never ambiguous for callers.
-    assert result.installed == []
-    assert len(result.uninstalled) == 4
-    assert installer.installed == set()
-
-
-def test_remove_counts_only_components_actually_removed(tmp_path: Path):
-    make_project(tmp_path)
-    manifest = BundleManifest.from_dict(valid_manifest_dict())
-    installer = FakeInstaller()
-    install_bundle(tmp_path, _plan(manifest), installer, manifest=manifest)
-
-    # Simulate one contributed component already gone from disk (e.g. removed
-    # out of band). It must not be reported as uninstalled and remove() must
-    # not be called for it.
-    gone = manifest.components[0]
-    installer.installed.discard((gone.kind, gone.id))
-
-    result = remove_bundle(tmp_path, "demo-bundle", installer)
-
-    assert len(result.uninstalled) == 3
-    assert (gone.kind, gone.id) not in installer.remove_calls
-    assert gone in result.skipped
-    make_project(tmp_path)
-    manifest = BundleManifest.from_dict(valid_manifest_dict())
-    installer = FakeInstaller()
-
-    install_bundle(tmp_path, _plan(manifest), installer, manifest=manifest)
-    result = install_bundle(
-        tmp_path, _plan(manifest), installer, manifest=manifest, refresh=True
-    )
-
-    # With refresh, already-installed components are re-applied, not skipped.
-    assert result.skipped == []
-    assert len(result.refreshed) == 4
-    assert len(installer.refresh_calls) == 4
-    assert result.changed is True
-
-
-def test_refresh_falls_back_to_install_without_hook(tmp_path: Path):
-    make_project(tmp_path)
-    manifest = BundleManifest.from_dict(valid_manifest_dict())
-
-    class NoRefreshInstaller(FakeInstaller):
-        refresh = None  # type: ignore[assignment]
-
-    installer = NoRefreshInstaller()
-    install_bundle(tmp_path, _plan(manifest), installer, manifest=manifest)
-    before = len(installer.install_calls)
-    result = install_bundle(
-        tmp_path, _plan(manifest), installer, manifest=manifest, refresh=True
-    )
-
-    # No refresh hook → re-install path keeps components current.
-    assert len(result.refreshed) == 4
-    assert len(installer.install_calls) == before + 4
-
-
-def test_update_preserves_original_installed_at(tmp_path: Path):
-    make_project(tmp_path)
-    manifest = BundleManifest.from_dict(valid_manifest_dict())
-    installer = FakeInstaller()
-    install_bundle(tmp_path, _plan(manifest), installer, manifest=manifest)
-
-    original = load_records(tmp_path)[0].installed_at
-
-    # A refresh (bundle update) must not rewrite the original install timestamp.
-    install_bundle(tmp_path, _plan(manifest), installer, manifest=manifest, refresh=True)
-
-    assert load_records(tmp_path)[0].installed_at == original
-
-
-def test_refresh_does_not_touch_independently_installed_component(tmp_path: Path):
-    # bundle update (refresh) must not re-apply a component installed
-    # independently and tracked by no bundle — refreshing it would be a
-    # collateral change to something the bundle does not own (FR-022).
-    make_project(tmp_path)
-    manifest = BundleManifest.from_dict(valid_manifest_dict())
-    installer = FakeInstaller()
-    installer.installed.add(("extensions", "ext-a"))
-
-    result = install_bundle(
-        tmp_path, _plan(manifest), installer, manifest=manifest, refresh=True
-    )
-
-    # ext-a is skipped (not refreshed) and never attributed to the bundle.
-    assert ("extensions", "ext-a") not in installer.refresh_calls
-    assert ("extensions", "ext-a") in {(c.kind, c.id) for c in result.skipped}
-    assert ("extensions", "ext-a") not in {(c.kind, c.id) for c in result.refreshed}
-    contributed = {
-        (c.kind, c.id) for c in load_records(tmp_path)[0].contributed_components
-    }
-    assert ("extensions", "ext-a") not in contributed
-
-
-def test_pre_existing_component_is_not_attributed_or_removed(tmp_path: Path):
-    # A component installed independently (before any bundle) must not be
-    # attributed to the bundle, so removing the bundle never uninstalls it
-    # (FR-022, no collateral removal).
-    make_project(tmp_path)
-    manifest = BundleManifest.from_dict(valid_manifest_dict())
-    installer = FakeInstaller()
-    # Pre-install ext-a independently — no bundle record references it yet.
-    installer.installed.add(("extensions", "ext-a"))
-
-    install_bundle(tmp_path, _plan(manifest), installer, manifest=manifest)
-
-    contributed = {
-        (c.kind, c.id) for c in load_records(tmp_path)[0].contributed_components
-    }
-    assert ("extensions", "ext-a") not in contributed
-
-    remove_bundle(tmp_path, "demo-bundle", installer)
-    assert ("extensions", "ext-a") in installer.installed

tests/integration/test_bundler_local_install.py

@@ -1,114 +0,0 @@
-"""Tests for installing a bundle from a local artifact/path (T045).
-
-The resolution-level tests are pure; the end-to-end test installs the bundled
-``agent-context`` extension fully offline from a built ``.zip`` artifact,
-proving the real in-process primitive dispatch (T044) works without a network.
-"""
-from __future__ import annotations
-
-import os
-from pathlib import Path
-
-import pytest
-import yaml
-from typer.testing import CliRunner
-
-from specify_cli import app
-from specify_cli.bundler import BundlerError
-from specify_cli.commands.bundle import _local_manifest_source
-from tests.bundler_helpers import make_project, valid_manifest_dict, write_manifest
-
-
-def test_local_source_none_for_non_path():
-    assert _local_manifest_source("some-catalog-bundle-id") is None
-
-
-def test_local_source_from_directory(tmp_path: Path):
-    write_manifest(tmp_path, valid_manifest_dict())
-    manifest = _local_manifest_source(str(tmp_path))
-    assert manifest is not None
-    assert manifest.bundle.id == "demo-bundle"
-
-
-def test_local_source_from_bundle_yml(tmp_path: Path):
-    path = write_manifest(tmp_path, valid_manifest_dict())
-    manifest = _local_manifest_source(str(path))
-    assert manifest is not None
-    assert manifest.bundle.id == "demo-bundle"
-
-
-def test_local_source_from_zip_artifact(tmp_path: Path):
-    bundle_dir = tmp_path / "bundle"
-    bundle_dir.mkdir()
-    write_manifest(bundle_dir, valid_manifest_dict())
-    (bundle_dir / "README.md").write_text("# demo\n", encoding="utf-8")
-
-    runner = CliRunner()
-    result = runner.invoke(app, ["bundle", "build", "--path", str(bundle_dir)])
-    assert result.exit_code == 0, result.output
-    artifact = next(bundle_dir.glob("*.zip"))
-
-    manifest = _local_manifest_source(str(artifact))
-    assert manifest is not None
-    assert manifest.bundle.id == "demo-bundle"
-
-
-def test_local_source_rejects_unknown_file(tmp_path: Path):
-    weird = tmp_path / "thing.txt"
-    weird.write_text("nope", encoding="utf-8")
-    with pytest.raises(BundlerError, match="not a recognised bundle source"):
-        _local_manifest_source(str(weird))
-
-
-def test_install_bundled_extension_from_zip_offline(tmp_path: Path):
-    """End-to-end: build → install (offline, local .zip) → list → remove."""
-    project = make_project(tmp_path / "proj")
-
-    bundle_dir = tmp_path / "mini"
-    bundle_dir.mkdir()
-    (bundle_dir / "bundle.yml").write_text(
-        yaml.safe_dump(
-            {
-                "schema_version": "1.0",
-                "bundle": {
-                    "id": "mini",
-                    "name": "Mini",
-                    "version": "1.0.0",
-                    "role": "developer",
-                    "description": "minimal",
-                    "author": "tests",
-                    "license": "MIT",
-                },
-                "requires": {"speckit_version": ">=0.1.0"},
-                "provides": {
-                    "extensions": [{"id": "agent-context", "version": "1.0.0"}]
-                },
-            }
-        ),
-        encoding="utf-8",
-    )
-    (bundle_dir / "README.md").write_text("# Mini\n", encoding="utf-8")
-
-    runner = CliRunner()
-    previous = Path.cwd()
-    os.chdir(project)
-    try:
-        build = runner.invoke(app, ["bundle", "build", "--path", str(bundle_dir)])
-        assert build.exit_code == 0, build.output
-        artifact = next(bundle_dir.glob("*.zip"))
-
-        install = runner.invoke(app, ["bundle", "install", str(artifact), "--offline"])
-        assert install.exit_code == 0, install.output
-
-        from specify_cli.extensions import ExtensionManager
-
-        assert ExtensionManager(project).registry.is_installed("agent-context")
-
-        listing = runner.invoke(app, ["bundle", "list"])
-        assert "mini" in listing.output
-
-        remove = runner.invoke(app, ["bundle", "remove", "mini"])
-        assert remove.exit_code == 0, remove.output
-        assert not ExtensionManager(project).registry.is_installed("agent-context")
-    finally:
-        os.chdir(previous)

tests/integration/test_bundler_offline.py

@@ -1,78 +0,0 @@
-"""Offline-first tests (Constitution Principle IV).
-
-Assert that consume/author flows work with no network access: built-in catalogs
-resolve offline, file:// catalogs resolve offline, and http(s) sources are
-refused (never silently attempted) when network is disabled.
-"""
-from __future__ import annotations
-
-from pathlib import Path
-
-import pytest
-
-from specify_cli.bundler import BundlerError
-from specify_cli.bundler.models.catalog import CatalogSource, InstallPolicy, Scope
-from specify_cli.bundler.services.adapters import make_catalog_fetcher
-from specify_cli.bundler.services.catalog_stack import CatalogStack
-from tests.bundler_helpers import catalog_entry_dict, write_catalog_file
-
-
-def _src(source_id, url, priority=1, policy="install-allowed"):
-    return CatalogSource(
-        id=source_id, url=url, priority=priority,
-        install_policy=InstallPolicy(policy), scope=Scope.PROJECT,
-    )
-
-
-def test_builtin_catalog_resolves_offline():
-    fetcher = make_catalog_fetcher(allow_network=False)
-    stack = CatalogStack([_src("default", "builtin://default")], fetcher)
-    # Built-in default ships empty; search works without network and returns [].
-    assert stack.search() == []
-
-
-def test_file_catalog_resolves_offline(tmp_path: Path):
-    catalog_path = tmp_path / "catalog.json"
-    write_catalog_file(catalog_path, {"demo": catalog_entry_dict("demo")})
-    fetcher = make_catalog_fetcher(allow_network=False)
-    stack = CatalogStack([_src("local", str(catalog_path))], fetcher)
-    resolved = stack.resolve("demo")
-    assert resolved.entry.id == "demo"
-
-
-def test_http_source_refused_when_offline():
-    fetcher = make_catalog_fetcher(allow_network=False)
-    stack = CatalogStack([_src("remote", "https://example.com/catalog.json")], fetcher)
-    with pytest.raises(BundlerError, match="Network access disabled"):
-        stack.resolve("anything")
-
-
-def test_missing_file_catalog_errors_offline(tmp_path: Path):
-    fetcher = make_catalog_fetcher(allow_network=False)
-    stack = CatalogStack([_src("local", str(tmp_path / "nope.json"))], fetcher)
-    with pytest.raises(BundlerError):
-        stack.resolve("anything")
-
-
-def test_file_url_catalog_resolves_offline(tmp_path: Path):
-    catalog_path = tmp_path / "catalog.json"
-    write_catalog_file(catalog_path, {"demo": catalog_entry_dict("demo")})
-    fetcher = make_catalog_fetcher(allow_network=False)
-    stack = CatalogStack([_src("local", catalog_path.as_uri())], fetcher)
-    resolved = stack.resolve("demo")
-    assert resolved.entry.id == "demo"
-
-
-def test_plain_http_remote_rejected_before_network():
-    # HTTPS is required for non-localhost catalogs; reject http:// up front.
-    fetcher = make_catalog_fetcher(allow_network=True)
-    stack = CatalogStack([_src("remote", "http://example.com/catalog.json")], fetcher)
-    with pytest.raises(BundlerError, match="must use HTTPS"):
-        stack.resolve("anything")
-
-
-def test_remote_url_without_host_rejected():
-    fetcher = make_catalog_fetcher(allow_network=True)
-    stack = CatalogStack([_src("remote", "https:///catalog.json")], fetcher)
-    with pytest.raises(BundlerError, match="valid URL with a host"):
-        stack.resolve("anything")

tests/integration/test_bundler_security_paths.py

@@ -1,173 +0,0 @@
-"""Security tests: path-traversal / symlink confinement (Constitution Principle V).
-
-These assert the bundler refuses to read or write outside an allowed root, so a
-malicious manifest or artifact path cannot escape the project/bundle directory.
-"""
-from __future__ import annotations
-
-import os
-from pathlib import Path
-
-import pytest
-
-from specify_cli.bundler import BundlerError
-from specify_cli.bundler.lib.yamlio import ensure_within, is_safe_relpath
-
-
-def test_ensure_within_allows_child(tmp_path: Path):
-    root = tmp_path / "bundle"
-    root.mkdir()
-    child = root / "sub" / "file.txt"
-    assert ensure_within(root, child) == child.resolve()
-
-
-def test_ensure_within_rejects_parent_traversal(tmp_path: Path):
-    root = tmp_path / "bundle"
-    root.mkdir()
-    escape = root / ".." / "secret.txt"
-    with pytest.raises(BundlerError, match="escapes"):
-        ensure_within(root, escape)
-
-
-def test_ensure_within_rejects_absolute_outside(tmp_path: Path):
-    root = tmp_path / "bundle"
-    root.mkdir()
-    with pytest.raises(BundlerError):
-        ensure_within(root, Path("/etc/passwd"))
-
-
-@pytest.mark.skipif(os.name == "nt", reason="symlink semantics differ on Windows")
-def test_ensure_within_rejects_symlink_escape(tmp_path: Path):
-    root = tmp_path / "bundle"
-    root.mkdir()
-    outside = tmp_path / "outside.txt"
-    outside.write_text("secret", encoding="utf-8")
-    link = root / "link.txt"
-    link.symlink_to(outside)
-    with pytest.raises(BundlerError, match="escapes"):
-        ensure_within(root, link)
-
-
-@pytest.mark.parametrize("rel,safe", [
-    ("a/b.txt", True),
-    ("./a.txt", True),
-    ("../escape", False),
-    ("a/../../escape", False),
-    ("/abs", False),
-    ("C:/abs", False),
-    ("C:\\abs", False),
-    ("\\\\server\\share", False),
-    ("", False),
-])
-def test_is_safe_relpath(rel, safe):
-    assert is_safe_relpath(rel) is safe
-
-
-def test_build_skips_symlinks(tmp_path: Path):
-    """Packager must not follow symlinks out of the bundle dir."""
-    import yaml
-
-    from specify_cli.bundler.services.packager import build_bundle
-    from tests.bundler_helpers import valid_manifest_dict
-
-    bundle = tmp_path / "bundle"
-    bundle.mkdir()
-    (bundle / "bundle.yml").write_text(
-        yaml.safe_dump(valid_manifest_dict()), encoding="utf-8"
-    )
-    (bundle / "README.md").write_text("# Demo", encoding="utf-8")
-
-    if os.name != "nt":
-        secret = tmp_path / "secret.txt"
-        secret.write_text("top secret", encoding="utf-8")
-        (bundle / "leak.txt").symlink_to(secret)
-
-    result = build_bundle(bundle, output_dir=tmp_path / "out")
-    import zipfile
-
-    with zipfile.ZipFile(result.artifact_path) as archive:
-        names = archive.namelist()
-    assert "leak.txt" not in names
-    assert "bundle.yml" in names
-
-
-def test_load_records_refuses_symlinked_specify_escape(tmp_path: Path):
-    # Reading bundle-records.json must honour the same confinement as writes:
-    # a symlinked .specify pointing outside project_root is refused.
-    from specify_cli.bundler.models.records import load_records
-
-    project = tmp_path / "proj"
-    project.mkdir()
-    outside = tmp_path / "outside"
-    outside.mkdir()
-    (outside / "bundle-records.json").write_text(
-        '{"schema_version": "1.0", "bundles": []}', encoding="utf-8"
-    )
-    (project / ".specify").symlink_to(outside, target_is_directory=True)
-
-    with pytest.raises(BundlerError, match="escapes the allowed root"):
-        load_records(project)
-
-
-def test_active_integration_refuses_symlinked_specify_escape(tmp_path: Path):
-    # Reading the integration marker must not follow a .specify symlink that
-    # resolves outside project_root; an escape is treated as "not determinable".
-    from specify_cli.bundler.lib.project import active_integration
-
-    project = tmp_path / "proj"
-    project.mkdir()
-    outside = tmp_path / "outside"
-    outside.mkdir()
-    (outside / "integration.json").write_text(
-        '{"integration": "leaked"}', encoding="utf-8"
-    )
-    (project / ".specify").symlink_to(outside, target_is_directory=True)
-
-    assert active_integration(project) is None
-
-
-def test_read_catalog_config_refuses_symlinked_specify_escape(tmp_path: Path):
-    from specify_cli.bundler.commands_impl import catalog_config as cc
-
-    project = tmp_path / "proj"
-    project.mkdir()
-    outside = tmp_path / "outside"
-    outside.mkdir()
-    (outside / "bundle-catalogs.yml").write_text(
-        "schema_version: '1.0'\ncatalogs: []\n", encoding="utf-8"
-    )
-    (project / ".specify").symlink_to(outside, target_is_directory=True)
-
-    with pytest.raises(BundlerError, match="escapes the allowed root"):
-        cc._read(project)
-
-
-def test_load_source_stack_refuses_symlinked_specify_dir(tmp_path: Path):
-    from specify_cli.bundler.models.catalog import load_source_stack
-
-    project = tmp_path / "project"
-    project.mkdir()
-    outside = tmp_path / "outside"
-    outside.mkdir()
-    (outside / "bundle-catalogs.yml").write_text("catalogs: []\n", encoding="utf-8")
-    try:
-        (project / ".specify").symlink_to(outside, target_is_directory=True)
-    except (OSError, NotImplementedError):
-        pytest.skip("symlinks not supported on this platform")
-    with pytest.raises(BundlerError, match="escapes the allowed root"):
-        load_source_stack(project)
-
-
-def test_find_project_root_ignores_symlinked_specify(tmp_path: Path):
-    from specify_cli.bundler.lib.project import find_project_root
-
-    real = tmp_path / "real-specify"
-    real.mkdir()
-    project = tmp_path / "project"
-    project.mkdir()
-    try:
-        (project / ".specify").symlink_to(real, target_is_directory=True)
-    except (OSError, NotImplementedError):
-        pytest.skip("symlinks not supported on this platform")
-    # A symlinked .specify must not be accepted as a project root.
-    assert find_project_root(project) is None

tests/integrations/test_cli.py

@@ -263,206 +263,6 @@ class TestInitIntegrationFlag:
         assert (scripts_dir / "setup-plan.sh").exists()
         assert (templates_dir / "plan-template.md").exists()
 
-    def test_shared_infra_removes_stale_managed_script(self, tmp_path):
-        """A managed script the core no longer ships (e.g. the legacy
-        update-agent-context.sh, superseded by the agent-context extension) is
-        removed, and the manifest stops tracking it (#3076)."""
-        from specify_cli import _install_shared_infra
-        from specify_cli.integrations.manifest import IntegrationManifest
-
-        project = tmp_path / "stale-test"
-        project.mkdir()
-        (project / ".specify").mkdir()
-        scripts_dir = project / ".specify" / "scripts" / "bash"
-        scripts_dir.mkdir(parents=True)
-
-        # Legacy orphan the current bundle no longer ships, recorded in the
-        # manifest as a managed file (hash matches on disk) — a pre-refactor install.
-        stale_rel = ".specify/scripts/bash/update-agent-context.sh"
-        (scripts_dir / "update-agent-context.sh").write_text("# legacy orphan\n", encoding="utf-8")
-        manifest = IntegrationManifest("speckit", project, version="test")
-        manifest.record_existing(stale_rel)
-        manifest.save()
-
-        _install_shared_infra(project, "sh", force=False)
-
-        # The orphan is gone and the manifest no longer tracks it.
-        assert not (scripts_dir / "update-agent-context.sh").exists()
-        refreshed = IntegrationManifest.load("speckit", project)
-        assert stale_rel not in refreshed.files
-        # Scripts the core DOES ship are installed and tracked.
-        assert (scripts_dir / "common.sh").exists()
-        assert ".specify/scripts/bash/common.sh" in refreshed.files
-
-    def test_shared_infra_preserves_modified_stale_script(self, tmp_path):
-        """A user-modified stale script is preserved (hash diverges from the
-        managed baseline), never silently deleted (#3076)."""
-        from specify_cli import _install_shared_infra
-        from specify_cli.integrations.manifest import IntegrationManifest
-
-        project = tmp_path / "stale-modified"
-        project.mkdir()
-        (project / ".specify").mkdir()
-        scripts_dir = project / ".specify" / "scripts" / "bash"
-        scripts_dir.mkdir(parents=True)
-
-        stale = scripts_dir / "update-agent-context.sh"
-        stale.write_text("# original managed\n", encoding="utf-8")
-        manifest = IntegrationManifest("speckit", project, version="test")
-        manifest.record_existing(".specify/scripts/bash/update-agent-context.sh")
-        manifest.save()
-
-        # User customizes it after install → on-disk hash now diverges.
-        stale.write_text("# user customization\n", encoding="utf-8")
-
-        _install_shared_infra(project, "sh", force=False)
-
-        # Preserved: it is no longer a managed (hash-matching) copy.
-        assert stale.exists()
-        assert stale.read_text(encoding="utf-8") == "# user customization\n"
-
-    def test_shared_infra_prunes_orphan_manifest_entry_when_file_absent(self, tmp_path):
-        """A stale manifest entry whose file is already gone from disk is pruned
-        so the manifest stays consistent, not left tracked forever (#3076 review)."""
-        from specify_cli import _install_shared_infra
-        from specify_cli.integrations.manifest import IntegrationManifest
-
-        project = tmp_path / "orphan-entry"
-        project.mkdir()
-        (project / ".specify").mkdir()
-        scripts_dir = project / ".specify" / "scripts" / "bash"
-        scripts_dir.mkdir(parents=True)
-
-        stale_rel = ".specify/scripts/bash/update-agent-context.sh"
-        stale = scripts_dir / "update-agent-context.sh"
-        stale.write_text("# legacy orphan\n", encoding="utf-8")
-        manifest = IntegrationManifest("speckit", project, version="test")
-        manifest.record_existing(stale_rel)
-        manifest.save()
-        # File removed out of band, but the manifest still tracks it.
-        stale.unlink()
-
-        _install_shared_infra(project, "sh", force=False)
-
-        refreshed = IntegrationManifest.load("speckit", project)
-        assert stale_rel not in refreshed.files
-
-    def test_shared_infra_empty_script_source_keeps_tracked_scripts(self, tmp_path, monkeypatch):
-        """If the bundle's script source dir exists but is empty, stale-cleanup
-        must NOT run (no source files seen → can't tell what's obsolete): a
-        previously-tracked script is preserved, never mass-deleted (#3076 review)."""
-        from specify_cli import _install_shared_infra, shared_infra
-        from specify_cli.integrations.manifest import IntegrationManifest
-
-        # Point the script source at an empty ``bash/`` directory.
-        empty_src = tmp_path / "empty-bundle" / "scripts"
-        (empty_src / "bash").mkdir(parents=True)
-        monkeypatch.setattr(shared_infra, "shared_scripts_source", lambda **kw: empty_src)
-
-        project = tmp_path / "empty-source"
-        project.mkdir()
-        (project / ".specify").mkdir()
-        scripts_dir = project / ".specify" / "scripts" / "bash"
-        scripts_dir.mkdir(parents=True)
-        tracked_rel = ".specify/scripts/bash/common.sh"
-        (scripts_dir / "common.sh").write_text("# tracked\n", encoding="utf-8")
-        manifest = IntegrationManifest("speckit", project, version="test")
-        manifest.record_existing(tracked_rel)
-        manifest.save()
-
-        _install_shared_infra(project, "sh", force=False)
-
-        # Empty source → scripts_scanned stays False → nothing deleted.
-        assert (scripts_dir / "common.sh").exists()
-        refreshed = IntegrationManifest.load("speckit", project)
-        assert tracked_rel in refreshed.files
-
-    def test_shared_infra_stale_cleanup_ignores_unsafe_manifest_keys(self, tmp_path):
-        """A corrupted/hand-edited manifest key with a ``..`` segment is skipped
-        before any filesystem access — its traversal target is never deleted
-        (#3076 review, containment guard)."""
-        import hashlib
-        import json
-        from specify_cli import _install_shared_infra
-
-        project = tmp_path / "unsafe-key"
-        project.mkdir()
-        scripts_dir = project / ".specify" / "scripts" / "bash"
-        scripts_dir.mkdir(parents=True)
-        manifest_dir = project / ".specify" / "integrations"
-        manifest_dir.mkdir(parents=True)
-
-        # A file the traversal key would resolve to (outside scripts/bash/).
-        victim = project / ".specify" / "scripts" / "keep-me.sh"
-        victim_bytes = b"# do not touch\n"
-        victim.write_bytes(victim_bytes)
-
-        # Hand-crafted manifest: a key under the script prefix but with a ``..``
-        # segment, with the *matching* hash so that — absent the containment guard
-        # — stale-cleanup would consider it managed and unlink the target.
-        traversal_key = ".specify/scripts/bash/../keep-me.sh"
-        (manifest_dir / "speckit.manifest.json").write_text(
-            json.dumps({
-                "integration": "speckit",
-                "version": "test",
-                "files": {traversal_key: hashlib.sha256(victim_bytes).hexdigest()},
-            }),
-            encoding="utf-8",
-        )
-
-        _install_shared_infra(project, "sh", force=False)
-
-        # The unsafe key was skipped; its target file is untouched.
-        assert victim.exists()
-        assert victim.read_bytes() == victim_bytes
-
-    def test_shared_infra_stale_cleanup_skips_escaping_key_without_failing(
-        self, tmp_path, monkeypatch
-    ):
-        """A key that passes the lexical guard but escapes containment — e.g. a
-        Windows drive-relative ``C:tmp`` that is not ``is_absolute()`` yet discards
-        the project root when joined — is skipped via ``_validate_rel_path``, never
-        unlinked, and never turned into an install-time hard failure (#3076 review
-        round 4). Simulated portably by forcing ``_validate_rel_path`` to reject the
-        managed key, since real drive-relative paths only escape on Windows."""
-        from specify_cli import _install_shared_infra
-        from specify_cli.integrations import manifest as manifest_mod
-        from specify_cli.integrations.manifest import IntegrationManifest
-
-        project = tmp_path / "escaping-key"
-        project.mkdir()
-        (project / ".specify").mkdir()
-        scripts_dir = project / ".specify" / "scripts" / "bash"
-        scripts_dir.mkdir(parents=True)
-
-        # A managed stale orphan that would normally be removed.
-        stale_rel = ".specify/scripts/bash/update-agent-context.sh"
-        stale = scripts_dir / "update-agent-context.sh"
-        stale.write_text("# legacy orphan\n", encoding="utf-8")
-        manifest = IntegrationManifest("speckit", project, version="test")
-        manifest.record_existing(stale_rel)
-        manifest.save()
-
-        # Force the containment check to reject this key, as it would for a
-        # drive-relative escape on Windows. The cleanup must skip it gracefully.
-        real_validate = manifest_mod._validate_rel_path
-
-        def fake_validate(rel, root):
-            if str(rel).endswith("update-agent-context.sh"):
-                raise ValueError("simulated drive-relative escape")
-            return real_validate(rel, root)
-
-        monkeypatch.setattr(manifest_mod, "_validate_rel_path", fake_validate)
-
-        # Must not raise (no install-time hard failure from a corrupted key).
-        _install_shared_infra(project, "sh", force=False)
-
-        # The escaping key was skipped, so its file is left untouched...
-        assert stale.exists()
-        assert stale.read_text(encoding="utf-8") == "# legacy orphan\n"
-        # ...yet the install otherwise completed: real scripts are installed.
-        assert (scripts_dir / "common.sh").exists()
-
     def test_shared_infra_skip_warning_displayed(self, tmp_path, capsys):
         """Console warning is displayed when files are skipped."""
         from specify_cli import _install_shared_infra
@@ -1515,78 +1315,6 @@ class TestIntegrationCatalogDiscoveryCLI:
         assert extension_list.exit_code == 0, extension_list.output
         assert "Config: .specify/extension-catalogs.yml" in extension_list.output
 
-    def test_extension_catalog_add_rejects_non_mapping_config_root(self, tmp_path):
-        project = self._make_project(tmp_path)
-        cfg_path = project / ".specify" / "extension-catalogs.yml"
-        cfg_path.write_text("- not\n- a\n- mapping\n", encoding="utf-8")
-
-        result = self._invoke([
-            "extension", "catalog", "add",
-            "https://example.com/extension-catalog.yml",
-            "--name", "demo-extensions",
-        ], project)
-
-        assert result.exit_code == 1, result.output
-        output = _normalize_cli_output(result.output)
-        assert "Invalid catalog config .specify/extension-catalogs.yml" in output
-        assert "expected a YAML mapping at the root" in output
-        assert "AttributeError" not in output
-
-    def test_extension_catalog_remove_rejects_non_mapping_config_root(self, tmp_path):
-        project = self._make_project(tmp_path)
-        cfg_path = project / ".specify" / "extension-catalogs.yml"
-        cfg_path.write_text("- not\n- a\n- mapping\n", encoding="utf-8")
-
-        result = self._invoke(["extension", "catalog", "remove", "demo"], project)
-
-        assert result.exit_code == 1, result.output
-        output = _normalize_cli_output(result.output)
-        assert "Invalid catalog config .specify/extension-catalogs.yml" in output
-        assert "expected a YAML mapping at the root" in output
-        assert "AttributeError" not in output
-
-    def test_extension_catalog_add_escapes_catalog_name_markup(self, tmp_path):
-        project = self._make_project(tmp_path)
-        catalog_name = "[red]demo[/red]"
-
-        result = self._invoke([
-            "extension", "catalog", "add",
-            "https://example.com/extension-catalog.yml",
-            "--name", catalog_name,
-        ], project)
-
-        assert result.exit_code == 0, result.output
-        output = _normalize_cli_output(result.output)
-        assert f"Added catalog '{catalog_name}'" in output
-
-    def test_extension_catalog_remove_escapes_catalog_name_markup(self, tmp_path):
-        project = self._make_project(tmp_path)
-        catalog_name = "[red]demo[/red]"
-        cfg_path = project / ".specify" / "extension-catalogs.yml"
-        cfg_path.write_text(
-            yaml.safe_dump(
-                {
-                    "catalogs": [
-                        {
-                            "name": catalog_name,
-                            "url": "https://example.com/extension-catalog.yml",
-                            "priority": 10,
-                            "install_allowed": False,
-                            "description": "",
-                        }
-                    ]
-                },
-                sort_keys=False,
-            ),
-            encoding="utf-8",
-        )
-
-        result = self._invoke(["extension", "catalog", "remove", catalog_name], project)
-
-        assert result.exit_code == 0, result.output
-        output = _normalize_cli_output(result.output)
-        assert f"Removed catalog '{catalog_name}'" in output
-
     # -- search ------------------------------------------------------------
 
     def test_search_lists_all(self, tmp_path, monkeypatch):

tests/integrations/test_integration_codex.py

@@ -29,80 +29,6 @@ class TestCodexInitFlow:
         assert result.exit_code == 0, f"init --integration codex failed: {result.output}"
         assert (target / ".agents" / "skills" / "speckit-plan" / "SKILL.md").exists()
 
-    def test_plan_skill_references_configured_context_files(self, tmp_path):
-        """Plan skill should render all configured agent context files."""
-        from specify_cli import _save_agent_context_config
-
-        target = tmp_path / "test-proj"
-        target.mkdir()
-        _save_agent_context_config(
-            target,
-            {
-                "context_file": "AGENTS.md",
-                "context_files": ["AGENTS.md", "CLAUDE.md"],
-                "context_markers": {
-                    "start": "<!-- SPECKIT START -->",
-                    "end": "<!-- SPECKIT END -->",
-                },
-            },
-        )
-
-        integration = get_integration("codex")
-        manifest = IntegrationManifest("codex", target)
-        integration.setup(target, manifest, script_type="sh")
-
-        plan_skill = target / ".agents" / "skills" / "speckit-plan" / "SKILL.md"
-        content = plan_skill.read_text(encoding="utf-8")
-        assert "AGENTS.md, CLAUDE.md" in content
-        assert "__CONTEXT_FILE__" not in content
-
-    def test_plan_skill_ignores_context_files_when_agent_context_disabled(
-        self, tmp_path
-    ):
-        """Disabled agent-context must not leak stale context_files into commands."""
-        from specify_cli import _save_agent_context_config
-
-        target = tmp_path / "test-proj"
-        target.mkdir()
-        registry = target / ".specify" / "extensions" / ".registry"
-        registry.parent.mkdir(parents=True, exist_ok=True)
-        registry.write_text(
-            """
-{
-  "schema_version": "1.0",
-  "extensions": {
-    "agent-context": {
-      "version": "1.0.0",
-      "enabled": false
-    }
-  }
-}
-""".strip(),
-            encoding="utf-8",
-        )
-        _save_agent_context_config(
-            target,
-            {
-                "context_file": "AGENTS.md",
-                "context_files": ["../outside.md", "CLAUDE.md"],
-                "context_markers": {
-                    "start": "<!-- SPECKIT START -->",
-                    "end": "<!-- SPECKIT END -->",
-                },
-            },
-        )
-
-        integration = get_integration("codex")
-        manifest = IntegrationManifest("codex", target)
-        integration.setup(target, manifest, script_type="sh")
-
-        plan_skill = target / ".agents" / "skills" / "speckit-plan" / "SKILL.md"
-        content = plan_skill.read_text(encoding="utf-8")
-        assert "AGENTS.md, CLAUDE.md" not in content
-        assert "../outside.md" not in content
-        assert "AGENTS.md" in content
-        assert "__CONTEXT_FILE__" not in content
-
 
 class TestCodexHookCommandNote:
     """Verify dot-to-hyphen normalization note is injected in hook sections.

tests/integrations/test_integration_firebender.py

@@ -1,45 +0,0 @@
-"""Tests for FirebenderIntegration."""
-
-from specify_cli.integrations import get_integration
-from specify_cli.integrations.manifest import IntegrationManifest
-
-from .test_integration_base_markdown import MarkdownIntegrationTests
-
-
-class TestFirebenderIntegration(MarkdownIntegrationTests):
-    KEY = "firebender"
-    FOLDER = ".firebender/"
-    COMMANDS_SUBDIR = "commands"
-    REGISTRAR_DIR = ".firebender/commands"
-    CONTEXT_FILE = ".firebender/rules/specify-rules.mdc"
-
-    # Firebender reads custom slash commands from ``.firebender/commands/*.mdc``,
-    # so this integration uses the ``.mdc`` extension instead of the ``.md``
-    # default the base mixin assumes. Override the two extension-specific tests.
-    def test_registrar_config(self):
-        i = get_integration(self.KEY)
-        assert i.registrar_config["dir"] == self.REGISTRAR_DIR
-        assert i.registrar_config["format"] == "markdown"
-        assert i.registrar_config["args"] == "$ARGUMENTS"
-        assert i.registrar_config["extension"] == ".mdc"
-
-    def test_setup_creates_files(self, tmp_path):
-        i = get_integration(self.KEY)
-        m = IntegrationManifest(self.KEY, tmp_path)
-        created = i.setup(tmp_path, m)
-        assert len(created) > 0
-        cmd_files = [f for f in created if "scripts" not in f.parts]
-        for f in cmd_files:
-            assert f.exists()
-            assert f.name.startswith("speckit.")
-            assert f.name.endswith(".mdc")
-
-    def _expected_files(self, script_variant: str) -> list[str]:
-        # Firebender emits ``.mdc`` command files, so remap the base mixin's
-        # ``.md`` expectations for files under this integration's command dir.
-        cmd_dir = get_integration(self.KEY).registrar_config["dir"]
-        prefix = cmd_dir + "/"
-        return sorted(
-            f[:-3] + ".mdc" if f.startswith(prefix) and f.endswith(".md") else f
-            for f in super()._expected_files(script_variant)
-        )

tests/integrations/test_integration_subcommand.py

@@ -15,22 +15,19 @@ from tests.conftest import strip_ansi
 runner = CliRunner()
 
 
-def _init_project(tmp_path, integration="copilot", integration_options=None):
+def _init_project(tmp_path, integration="copilot"):
     """Helper: init a spec-kit project with the given integration."""
     project = tmp_path / "proj"
     project.mkdir()
-    args = [
-        "init", "--here",
-        "--integration", integration,
-        "--script", "sh",
-        "--ignore-agent-tools",
-    ]
-    if integration_options:
-        args += ["--integration-options", integration_options]
     old_cwd = os.getcwd()
     try:
         os.chdir(project)
-        result = runner.invoke(app, args, catch_exceptions=False)
+        result = runner.invoke(app, [
+            "init", "--here",
+            "--integration", integration,
+            "--script", "sh",
+            "--ignore-agent-tools",
+        ], catch_exceptions=False)
     finally:
         os.chdir(old_cwd)
     assert result.exit_code == 0, f"init failed: {result.output}"
@@ -1240,137 +1237,6 @@ class TestIntegrationInstall:
         assert "/speckit-specify" in script_content
         assert "/speckit.specify" not in script_content
 
-    def test_install_defers_extension_commands_until_use(self, tmp_path):
-        """Installing a second integration does not register enabled extensions.
-
-        Maintainer-requested behavior for #2886: extension command back-fill is
-        limited to ``integration use`` / ``switch`` / ``upgrade``. Plain
-        ``install`` only adds the integration; selecting it with ``use`` then
-        registers the enabled extensions for that agent.
-        """
-        project = _init_project(tmp_path, "claude")
-
-        result = _run_in_project(project, ["extension", "add", "git"])
-        assert result.exit_code == 0, f"extension add failed: {result.output}"
-
-        registry_path = project / ".specify" / "extensions" / ".registry"
-        registered = json.loads(registry_path.read_text(encoding="utf-8"))[
-            "extensions"
-        ]["git"]["registered_commands"]
-        assert "claude" in registered
-        assert "codex" not in registered, "precondition: codex not yet installed"
-
-        result = _run_in_project(project, [
-            "integration", "install", "codex",
-            "--script", "sh",
-        ])
-        assert result.exit_code == 0, result.output
-
-        # Install alone does not back-fill the git extension for the secondary
-        # agent.
-        registered = json.loads(registry_path.read_text(encoding="utf-8"))[
-            "extensions"
-        ]["git"]["registered_commands"]
-        assert "claude" in registered, "existing agent registration preserved"
-        assert "codex" not in registered
-        assert not (
-            project / ".agents" / "skills" / "speckit-git-feature" / "SKILL.md"
-        ).exists()
-
-        result = _run_in_project(project, ["integration", "use", "codex"])
-        assert result.exit_code == 0, result.output
-
-        registered = json.loads(registry_path.read_text(encoding="utf-8"))[
-            "extensions"
-        ]["git"]["registered_commands"]
-        assert "codex" in registered, "use should register extension commands (#2886)"
-        assert (
-            project / ".agents" / "skills" / "speckit-git-feature" / "SKILL.md"
-        ).exists()
-
-    def test_install_does_not_register_disabled_extensions(self, tmp_path):
-        """A disabled extension must not be registered for a newly installed agent."""
-        project = _init_project(tmp_path, "claude")
-
-        result = _run_in_project(project, ["extension", "add", "git"])
-        assert result.exit_code == 0, f"extension add failed: {result.output}"
-        result = _run_in_project(project, ["extension", "disable", "git"])
-        assert result.exit_code == 0, result.output
-
-        result = _run_in_project(project, [
-            "integration", "install", "codex",
-            "--script", "sh",
-        ])
-        assert result.exit_code == 0, result.output
-
-        registry_path = project / ".specify" / "extensions" / ".registry"
-        git_meta = json.loads(registry_path.read_text(encoding="utf-8"))[
-            "extensions"
-        ]["git"]
-        assert git_meta["enabled"] is False
-        assert "codex" not in git_meta["registered_commands"]
-        assert not (
-            project / ".agents" / "skills" / "speckit-git-feature" / "SKILL.md"
-        ).exists()
-
-    def test_install_skills_mode_secondary_agent_defers_extension_artifacts(self, tmp_path):
-        """A non-active skills-mode agent gets extension artifacts only on use.
-
-        Plain ``install`` has no extension side effects. Once the secondary
-        Copilot ``--skills`` integration is selected with ``use``, it becomes the
-        active agent and receives extension skills.
-        """
-        project = _init_project(tmp_path, "claude")
-
-        result = _run_in_project(project, ["extension", "add", "git"])
-        assert result.exit_code == 0, f"extension add failed: {result.output}"
-
-        # Copilot is not multi_install_safe, so --force is required to add it
-        # alongside the existing default integration.
-        result = _run_in_project(project, [
-            "integration", "install", "copilot",
-            "--script", "sh",
-            "--integration-options", "--skills",
-            "--force",
-        ])
-        assert result.exit_code == 0, result.output
-
-        # Precondition that makes --skills load-bearing: copilot IS in skills
-        # mode, so its own core commands are scaffolded as skills.
-        assert (
-            project / ".github" / "skills" / "speckit-specify" / "SKILL.md"
-        ).exists(), "precondition: copilot installed in skills mode"
-
-        # The git extension is not registered for the non-active copilot agent
-        # during install.
-        git_meta = json.loads(
-            (project / ".specify" / "extensions" / ".registry").read_text(encoding="utf-8")
-        )["extensions"]["git"]
-        assert "copilot" not in git_meta["registered_commands"]
-        assert not (
-            project / ".github" / "agents" / "speckit.git.feature.agent.md"
-        ).exists()
-        assert not (
-            project / ".github" / "skills" / "speckit-git-feature" / "SKILL.md"
-        ).exists()
-
-        result = _run_in_project(project, ["integration", "use", "copilot"])
-        assert result.exit_code == 0, result.output
-
-        git_meta = json.loads(
-            (project / ".specify" / "extensions" / ".registry").read_text(encoding="utf-8")
-        )["extensions"]["git"]
-        # `use` makes copilot active, so extension artifacts follow copilot's
-        # skills-mode layout.
-        assert "copilot" not in git_meta["registered_commands"]
-        assert "speckit-git-feature" in git_meta["registered_skills"]
-        assert not (
-            project / ".github" / "agents" / "speckit.git.feature.agent.md"
-        ).exists()
-        assert (
-            project / ".github" / "skills" / "speckit-git-feature" / "SKILL.md"
-        ).exists()
-
 
 # ── uninstall ────────────────────────────────────────────────────────
 
@@ -1858,40 +1724,6 @@ class TestIntegrationSwitch:
         assert "claude" in registered_commands
         assert "opencode" not in registered_commands
 
-    def test_switch_installed_target_backfills_extension_commands(self, tmp_path):
-        """Switching to an already-installed agent should register extensions."""
-        project = _init_project(tmp_path, "claude")
-
-        result = _run_in_project(project, ["extension", "add", "git"])
-        assert result.exit_code == 0, f"extension add failed: {result.output}"
-
-        registry_path = project / ".specify" / "extensions" / ".registry"
-        registered = json.loads(registry_path.read_text(encoding="utf-8"))[
-            "extensions"
-        ]["git"]["registered_commands"]
-        assert "claude" in registered
-        assert "codex" not in registered, "precondition: codex not yet installed"
-
-        result = _run_in_project(project, [
-            "integration", "install", "codex",
-            "--script", "sh",
-        ])
-        assert result.exit_code == 0, result.output
-
-        codex_git_feature = (
-            project / ".agents" / "skills" / "speckit-git-feature" / "SKILL.md"
-        )
-        assert not codex_git_feature.exists()
-
-        result = _run_in_project(project, ["integration", "switch", "codex"])
-        assert result.exit_code == 0, result.output
-
-        registered = json.loads(registry_path.read_text(encoding="utf-8"))[
-            "extensions"
-        ]["git"]["registered_commands"]
-        assert "codex" in registered
-        assert codex_git_feature.exists()
-
     def test_switch_migrates_copilot_skills_extension_commands(self, tmp_path):
         """Copilot --skills should receive extension skills, not .agent.md files."""
         project = _init_project(tmp_path, "opencode")
@@ -2492,93 +2324,6 @@ class TestIntegrationUpgrade:
             "shared .sh scripts must be executable after upgrade"
         )
 
-    def test_upgrade_backfills_extension_commands_for_agent(self, tmp_path):
-        """Upgrade re-registers enabled extensions for the upgraded agent.
-
-        Regression for #2886: agents installed before extension back-fill
-        existed (or whose extension artifacts went missing) should regain the
-        enabled extensions' commands on ``upgrade``, reaching parity with
-        ``switch``.
-        """
-        project = _init_project(tmp_path, "claude")
-
-        result = _run_in_project(project, ["extension", "add", "git"])
-        assert result.exit_code == 0, f"extension add failed: {result.output}"
-
-        result = _run_in_project(project, [
-            "integration", "install", "codex",
-            "--script", "sh",
-        ])
-        assert result.exit_code == 0, result.output
-
-        # Simulate a project created before the install/upgrade back-fill: drop
-        # codex's extension registration and its rendered artifacts.
-        registry_path = project / ".specify" / "extensions" / ".registry"
-        registry = json.loads(registry_path.read_text(encoding="utf-8"))
-        registry["extensions"]["git"]["registered_commands"].pop("codex", None)
-        registry_path.write_text(json.dumps(registry), encoding="utf-8")
-        agents_skills = project / ".agents" / "skills"
-        for skill_dir in agents_skills.glob("speckit-git-*"):
-            shutil.rmtree(skill_dir)
-
-        # Precondition: codex is now missing the git extension.
-        assert "codex" not in json.loads(registry_path.read_text(encoding="utf-8"))[
-            "extensions"
-        ]["git"]["registered_commands"]
-        assert not (agents_skills / "speckit-git-feature" / "SKILL.md").exists()
-
-        result = _run_in_project(project, [
-            "integration", "upgrade", "codex",
-            "--script", "sh",
-        ])
-        assert result.exit_code == 0, result.output
-
-        # Upgrade back-filled the git extension for codex.
-        registered = json.loads(registry_path.read_text(encoding="utf-8"))[
-            "extensions"
-        ]["git"]["registered_commands"]
-        assert "codex" in registered, "upgrade should re-register extension commands (#2886)"
-        assert (agents_skills / "speckit-git-feature" / "SKILL.md").exists()
-
-    def test_upgrade_non_active_agent_preserves_active_agent_skills(self, tmp_path):
-        """Upgrading a non-active agent must not touch the active agent's skills.
-
-        Regression for the #2886 wiring: extension skill rendering is
-        active-agent-scoped, so routing upgrade of a *secondary* agent through
-        ``register_enabled_extensions_for_agent`` used to re-render the
-        *active* skills-mode agent's extension skills as a side effect —
-        resurrecting skill files the user had deliberately deleted. The skills
-        pass is now gated on the target being the active agent. (Skills parity
-        for non-active agents is tracked separately in #2948.)
-        """
-        # Active agent: copilot in skills mode → git extension renders as skills.
-        project = _init_project(tmp_path, "copilot", integration_options="--skills")
-        result = _run_in_project(project, ["extension", "add", "git"])
-        assert result.exit_code == 0, f"extension add failed: {result.output}"
-
-        skill = project / ".github" / "skills" / "speckit-git-feature" / "SKILL.md"
-        assert skill.exists(), "precondition: active copilot has the git extension skill"
-
-        # Add a secondary (non-active) agent; copilot is not multi_install_safe.
-        result = _run_in_project(project, [
-            "integration", "install", "codex", "--script", "sh", "--force",
-        ])
-        assert result.exit_code == 0, result.output
-
-        # The user deliberately removes the active agent's git skill.
-        shutil.rmtree(skill.parent)
-        assert not skill.exists()
-
-        # Upgrading the *non-active* agent must not re-render copilot's skills.
-        result = _run_in_project(project, [
-            "integration", "upgrade", "codex", "--script", "sh",
-        ])
-        assert result.exit_code == 0, result.output
-        assert not skill.exists(), (
-            "upgrading a non-active agent must not resurrect the active agent's "
-            "deleted extension skill (#2886)"
-        )
-
 
 # ── Full lifecycle ───────────────────────────────────────────────────
 

tests/integrations/test_integration_zcode.py

@@ -1,38 +0,0 @@
-"""Tests for ZcodeIntegration — skills-based integration (Z.AI)."""
-
-from .test_integration_base_skills import SkillsIntegrationTests
-
-
-class TestZcodeIntegration(SkillsIntegrationTests):
-    KEY = "zcode"
-    FOLDER = ".zcode/"
-    COMMANDS_SUBDIR = "skills"
-    REGISTRAR_DIR = ".zcode/skills"
-    CONTEXT_FILE = "ZCODE.md"
-
-
-class TestZcodeInvocation:
-    """ZCode renders $speckit-* chat invocations (like Codex)."""
-
-    def test_next_steps_show_dollar_skill_invocation(self, tmp_path):
-        """ZCode next-steps guidance should display $speckit-* usage."""
-        import os
-        from typer.testing import CliRunner
-        from specify_cli import app
-
-        project = tmp_path / "zcode-next-steps"
-        project.mkdir()
-        old_cwd = os.getcwd()
-        try:
-            os.chdir(project)
-            runner = CliRunner()
-            result = runner.invoke(app, [
-                "init", "--here", "--integration", "zcode",
-                "--ignore-agent-tools", "--script", "sh",
-            ], catch_exceptions=False)
-        finally:
-            os.chdir(old_cwd)
-
-        assert result.exit_code == 0
-        assert "$speckit-constitution" in result.output
-        assert "/speckit.constitution" not in result.output

tests/integrations/test_manifest.py

@@ -116,34 +116,6 @@ class TestManifestPathTraversal:
         assert len(removed) == 1
         assert removed[0].name == "safe.txt"
 
-    def test_remove_drops_entry_and_is_noop_second_time(self, tmp_path):
-        (tmp_path / "f.txt").write_text("x", encoding="utf-8")
-        m = IntegrationManifest("test", tmp_path)
-        m.record_existing("f.txt")
-        assert "f.txt" in m.files
-        assert m.remove("f.txt") is True
-        assert "f.txt" not in m.files
-        assert m.remove("f.txt") is False  # already gone → no-op
-
-    def test_remove_rejects_absolute_path(self, tmp_path):
-        # Matches record_existing/is_recovered: an absolute key can never be a
-        # canonical manifest key, so remove() rejects it lexically and leaves
-        # the tracked entry untouched.
-        (tmp_path / "f.txt").write_text("x", encoding="utf-8")
-        m = IntegrationManifest("test", tmp_path)
-        m.record_existing("f.txt")
-        import sys
-        abs_input = "C:\\tmp\\f.txt" if sys.platform == "win32" else "/tmp/f.txt"
-        assert m.remove(abs_input) is False
-        assert "f.txt" in m.files
-
-    def test_remove_rejects_parent_traversal(self, tmp_path):
-        (tmp_path / "f.txt").write_text("x", encoding="utf-8")
-        m = IntegrationManifest("test", tmp_path)
-        m.record_existing("f.txt")
-        assert m.remove("../f.txt") is False
-        assert "f.txt" in m.files
-
 
 class TestManifestCheckModified:
     def test_unmodified_file(self, tmp_path):

tests/integrations/test_registry.py

@@ -23,7 +23,7 @@ ALL_INTEGRATION_KEYS = [
     # Stage 3 — standard markdown integrations
     "claude", "qwen", "opencode", "junie", "kilocode", "auggie",
     "roo", "rovodev", "codebuddy", "qodercli", "amp", "shai", "bob", "trae",
-    "pi", "iflow", "kiro-cli", "windsurf", "vibe", "cursor-agent", "firebender",
+    "pi", "iflow", "kiro-cli", "windsurf", "vibe", "cursor-agent",
     # Stage 4 — TOML integrations
     "gemini", "tabnine",
     # Stage 5 — skills, generic & option-driven integrations

tests/test_agent_config_consistency.py

@@ -1,158 +1,15 @@
 """Consistency checks for agent configuration across runtime surfaces."""
 
-import re
 from pathlib import Path
 
-import yaml
-
 from specify_cli import AGENT_CONFIG
 from specify_cli.extensions import CommandRegistrar
 
 REPO_ROOT = Path(__file__).resolve().parent.parent
 
-ISSUE_TEMPLATE_AGENT_KEYS = [
-    "amp",
-    "agy",
-    "auggie",
-    "claude",
-    "cline",
-    "codebuddy",
-    "codex",
-    "cursor-agent",
-    "devin",
-    "firebender",
-    "forge",
-    "gemini",
-    "copilot",
-    "goose",
-    "hermes",
-    "bob",
-    "iflow",
-    "junie",
-    "kilocode",
-    "kimi",
-    "kiro-cli",
-    "lingma",
-    "vibe",
-    "opencode",
-    "pi",
-    "qodercli",
-    "qwen",
-    "roo",
-    "rovodev",
-    "shai",
-    "tabnine",
-    "trae",
-    "windsurf",
-    "zcode",
-    "zed",
-]
-
-
-def _issue_template(path: str) -> dict:
-    return yaml.safe_load((REPO_ROOT / path).read_text(encoding="utf-8"))
-
-
-def _body_item_by_id(template: dict, item_id: str) -> dict:
-    for item in template["body"]:
-        if item.get("id") == item_id:
-            return item
-    raise AssertionError(f"Expected issue template body item {item_id!r}")
-
-
-def _dropdown_options(path: str, item_id: str) -> list[str]:
-    item = _body_item_by_id(_issue_template(path), item_id)
-    return item["attributes"]["options"]
-
-
-def _normalized_markdown(text: str) -> str:
-    return " ".join(text.split())
-
-
-def _markdown_value_containing(path: str, marker: str) -> str:
-    template = _issue_template(path)
-    normalized_marker = _normalized_markdown(marker)
-    for item in template["body"]:
-        if item.get("type") != "markdown":
-            continue
-        value = item["attributes"]["value"]
-        if normalized_marker in _normalized_markdown(value):
-            return value
-    raise AssertionError(f"Expected issue template markdown containing {marker!r}")
-
-
-def _markdown_paragraph_containing(path: str, marker: str) -> str:
-    value = _markdown_value_containing(path, marker)
-    normalized_marker = _normalized_markdown(marker)
-    for paragraph in re.split(r"\n\s*\n", value):
-        if normalized_marker in _normalized_markdown(paragraph):
-            return paragraph
-    raise AssertionError(f"Expected issue template paragraph containing {marker!r}")
-
-
-def _supported_agent_names_from_agent_request_template() -> list[str]:
-    marker = "**Currently supported agents**:"
-    paragraph = _markdown_paragraph_containing(
-        ".github/ISSUE_TEMPLATE/agent_request.yml",
-        marker,
-    )
-    supported_agents_text = _normalized_markdown(paragraph).split(marker, 1)[1].strip()
-    return [agent.strip() for agent in supported_agents_text.split(",")]
-
 
 class TestAgentConfigConsistency:
-    """Ensure agent configuration stays synchronized across key surfaces."""
-
-    def test_issue_template_agent_lists_match_runtime_integrations(self):
-        """GitHub issue templates should list all concrete built-in agents."""
-        concrete_agent_keys = set(AGENT_CONFIG) - {"generic"}
-        issue_template_agent_keys = set(ISSUE_TEMPLATE_AGENT_KEYS)
-
-        missing_agent_keys = sorted(concrete_agent_keys - issue_template_agent_keys)
-        unexpected_agent_keys = sorted(issue_template_agent_keys - concrete_agent_keys)
-        duplicate_agent_keys = sorted(
-            key
-            for key in issue_template_agent_keys
-            if ISSUE_TEMPLATE_AGENT_KEYS.count(key) > 1
-        )
-        assert not missing_agent_keys, (
-            "Issue template agent list is missing AGENT_CONFIG keys: "
-            f"{missing_agent_keys}"
-        )
-        assert not unexpected_agent_keys, (
-            "Issue template agent list includes unknown AGENT_CONFIG keys: "
-            f"{unexpected_agent_keys}"
-        )
-        assert not duplicate_agent_keys, (
-            "Issue template agent list contains duplicate keys: "
-            f"{duplicate_agent_keys}"
-        )
-
-        issue_template_agent_names = [
-            AGENT_CONFIG[key]["name"] for key in ISSUE_TEMPLATE_AGENT_KEYS
-        ]
-        assert "Generic (bring your own agent)" not in issue_template_agent_names
-
-        bug_options = _dropdown_options(
-            ".github/ISSUE_TEMPLATE/bug_report.yml",
-            "ai-agent",
-        )
-        assert bug_options == issue_template_agent_names + ["Not applicable"]
-
-        feature_options = _dropdown_options(
-            ".github/ISSUE_TEMPLATE/feature_request.yml",
-            "ai-agent",
-        )
-        assert feature_options == [
-            "All agents",
-            *issue_template_agent_names,
-            "Not applicable",
-        ]
-
-        assert (
-            _supported_agent_names_from_agent_request_template()
-            == issue_template_agent_names
-        )
+    """Ensure kiro-cli migration stays synchronized across key surfaces."""
 
     def test_runtime_config_uses_kiro_cli_and_removes_q(self):
         """AGENT_CONFIG should include kiro-cli and exclude legacy q."""

tests/test_extension_update_hardening.py

@@ -107,51 +107,3 @@ def test_extension_update_rollback_corrupted_config(project_dir, monkeypatch):
     assert isinstance(restored_config, dict)
     assert "hooks" in restored_config
     assert restored_config["hooks"] == {}
-
-
-def test_extension_update_skills_backup_no_collision(project_dir, monkeypatch):
-    """Regression: skills agents name every command file SKILL.md (one per
-    command subdirectory). Backup must keep the per-command path so rollback
-    restores each skill's own content instead of overwriting them onto a
-    single backup path."""
-    monkeypatch.chdir(project_dir)
-
-    config_path = project_dir / ".specify" / "extensions.yml"
-    config_path.write_text(yaml.dump({"installed": ["test-ext"], "hooks": {}}))
-
-    # Two skill command files with DISTINCT content, mirroring the claude
-    # skills layout (.claude/skills/<name>/SKILL.md).
-    skills_root = project_dir / ".claude" / "skills"
-    plan_file = skills_root / "speckit-plan" / "SKILL.md"
-    tasks_file = skills_root / "speckit-tasks" / "SKILL.md"
-    plan_file.parent.mkdir(parents=True)
-    tasks_file.parent.mkdir(parents=True)
-    plan_file.write_text("PLAN CONTENT")
-    tasks_file.write_text("TASKS CONTENT")
-
-    monkeypatch.setattr(ExtensionManager, "list_installed", lambda self: [{"id": "test-ext", "name": "Test Ext", "version": "1.0.0"}])
-    monkeypatch.setattr(ExtensionRegistry, "get", lambda self, ext_id: {
-        "version": "1.0.0",
-        "enabled": True,
-        "registered_commands": {"claude": ["speckit.plan", "speckit.tasks"]},
-    })
-    monkeypatch.setattr(ExtensionCatalog, "get_extension_info", lambda self, ext_id: {"id": "test-ext", "name": "Test Ext", "version": "1.1.0", "download_url": "https://example.com/ext.zip"})
-
-    # Fail at download (step 5, after the command backup in step 3). Delete the
-    # originals first to simulate an install clobbering them, forcing rollback
-    # to rely entirely on the backups.
-    def mock_download_fail(self, ext_id):
-        plan_file.unlink()
-        tasks_file.unlink()
-        raise Exception("Download failed")
-
-    monkeypatch.setattr(ExtensionCatalog, "download_extension", mock_download_fail)
-    monkeypatch.setattr("typer.confirm", lambda _: True)
-
-    result = runner.invoke(app, ["extension", "update", "test-ext"], obj={"project_root": project_dir})
-
-    assert result.exit_code == 1
-    # Rollback must restore EACH skill's own content, not a single collided copy.
-    assert plan_file.exists() and tasks_file.exists()
-    assert plan_file.read_text() == "PLAN CONTENT"
-    assert tasks_file.read_text() == "TASKS CONTENT"