chore: bump version to 0.11.4

2026-07-03 20:36:23 +08:00 · 2026-06-22 16:12:36 +00:00
52 changed files with 1823 additions and 5213 deletions
--- a/.github/ISSUE_TEMPLATE/agent_request.yml
+++ b/.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
--- a/.github/ISSUE_TEMPLATE/bug_report.yml
+++ b/.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
--- a/.github/ISSUE_TEMPLATE/feature_request.yml
+++ b/.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
--- a/.github/workflows/publish-pypi.yml
+++ b/.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
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,36 +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
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -167,7 +167,7 @@ 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
--- a/README.md
+++ b/README.md
@@ -403,7 +403,7 @@ 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
--- a/docs/community/extensions.md
+++ b/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) |
--- a/docs/community/presets.md
+++ b/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) |
--- a/docs/reference/integrations.md
+++ b/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` |
--- a/extensions/agent-context/README.md
+++ b/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.
--- a/extensions/agent-context/agent-context-config.yml
+++ b/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:
--- a/extensions/agent-context/commands/speckit.agent-context.update.md
+++ b/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

--- a/extensions/agent-context/scripts/bash/update-agent-context.sh
+++ b/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"
--- a/extensions/agent-context/scripts/powershell/update-agent-context.ps1
+++ b/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"
--- a/extensions/catalog.community.json
+++ b/extensions/catalog.community.json
@@ -1,6 +1,6 @@
 {
  "schema_version": "1.0",
-  "updated_at": "2026-06-23T00:00:00Z",
+  "updated_at": "2026-06-22T00:00:00Z",
  "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",
@@ -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",
--- a/integrations/catalog.json
+++ b/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"]
    }
  }
 }
--- a/presets/catalog.community.json
+++ b/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",
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,8 +1,7 @@
 [project]
 name = "specify-cli"
-version = "0.11.6"
+version = "0.11.4"
 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",
--- a/spec-driven.md
+++ b/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:
--- a/src/specify_cli/init.py
+++ b/src/specify_cli/init.py
--- a/src/specify_cli/_invocation_style.py
+++ b/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.

--- a/src/specify_cli/agents.py
+++ b/src/specify_cli/agents.py
@@ -427,34 +427,14 @@ 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)
--- a/src/specify_cli/commands/init.py
+++ b/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}"
--- a/src/specify_cli/extensions/init.py
+++ b/src/specify_cli/extensions/init.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, relative_extension_path_violation
+from .catalogs import CatalogEntry as BaseCatalogEntry
+from .catalogs import CatalogStackBase

 _FALLBACK_CORE_COMMAND_NAMES = frozenset(
    {
@@ -905,7 +905,7 @@ 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 +948,7 @@ 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 +985,9 @@ 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)
@@ -1201,7 +1201,7 @@ 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 +1616,7 @@ 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 +1678,21 @@ 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 +1744,38 @@ 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 +1882,31 @@ 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 +2857,7 @@ 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 +2886,17 @@ 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)}"

--- a/src/specify_cli/extensions/_commands.py
+++ b/src/specify_cli/extensions/_commands.py
--- a/src/specify_cli/integrations/init.py
+++ b/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())


--- a/src/specify_cli/integrations/_helpers.py
+++ b/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)
 # ---------------------------------------------------------------------------
--- a/src/specify_cli/integrations/_migrate_commands.py
+++ b/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")
--- a/src/specify_cli/integrations/_query_commands.py
+++ b/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].")


--- a/src/specify_cli/integrations/base.py
+++ b/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.
--- a/src/specify_cli/integrations/copilot/init.py
+++ b/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(
--- a/src/specify_cli/integrations/firebender/init.py
+++ b/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"
--- a/src/specify_cli/integrations/forge/init.py
+++ b/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,
            )

--- a/src/specify_cli/integrations/generic/init.py
+++ b/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(
--- a/src/specify_cli/integrations/hermes/init.py
+++ b/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.
--- a/src/specify_cli/integrations/manifest.py
+++ b/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
--- a/src/specify_cli/integrations/zcode/init.py
+++ b/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)",
-            ),
-        ]
--- a/src/specify_cli/presets/init.py
+++ b/src/specify_cli/presets/init.py
@@ -2707,7 +2707,7 @@ 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 +2727,7 @@ 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 +3079,7 @@ 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 +3102,7 @@ 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"
--- a/src/specify_cli/shared_infra.py
+++ b/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
--- a/tests/extensions/test_extension_agent_context.py
+++ b/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

--- a/tests/integrations/test_cli.py
+++ b/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):
--- a/tests/integrations/test_integration_codex.py
+++ b/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.
--- a/tests/integrations/test_integration_firebender.py
+++ b/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)
-        )
--- a/tests/integrations/test_integration_subcommand.py
+++ b/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 ───────────────────────────────────────────────────

--- a/tests/integrations/test_integration_zcode.py
+++ b/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
--- a/tests/integrations/test_manifest.py
+++ b/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):
--- a/tests/integrations/test_registry.py
+++ b/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
--- a/tests/test_agent_config_consistency.py
+++ b/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."""
--- a/tests/test_extension_update_hardening.py
+++ b/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"
--- a/tests/test_extensions.py
+++ b/tests/test_extensions.py
@@ -4670,177 +4670,6 @@ class TestExtensionIgnore:
 class TestExtensionAddCLI:
    """CLI integration tests for extension add command."""

-    def test_catalog_add_escapes_url_markup(self, tmp_path):
-        """Catalog add should render user-supplied URLs literally."""
-        from typer.testing import CliRunner
-        from unittest.mock import patch
-        from specify_cli import app
-
-        project_dir = tmp_path / "test-project"
-        project_dir.mkdir()
-        (project_dir / ".specify").mkdir()
-
-        url = "https://example.com/[red]catalog[/red].json"
-
-        runner = CliRunner()
-        with patch.object(Path, "cwd", return_value=project_dir):
-            result = runner.invoke(
-                app,
-                [
-                    "extension",
-                    "catalog",
-                    "add",
-                    url,
-                    "--name",
-                    "community",
-                ],
-                catch_exceptions=True,
-            )
-
-        assert result.exit_code == 0, result.output
-        assert f"URL: {url}" in result.output
-
-    def test_catalog_add_escapes_config_saved_path_markup(self, tmp_path):
-        """Catalog add's saved-path label should render literally under Rich."""
-        from typer.testing import CliRunner
-        from unittest.mock import patch
-        from specify_cli import app
-
-        project_dir = tmp_path / "test-project"
-        project_dir.mkdir()
-        (project_dir / ".specify").mkdir()
-
-        display_path = "project[red]/.specify/extension-catalogs.yml"
-
-        runner = CliRunner()
-        with patch.object(Path, "cwd", return_value=project_dir), \
-             patch("specify_cli.extensions._commands._display_project_path", return_value=display_path):
-            result = runner.invoke(
-                app,
-                [
-                    "extension",
-                    "catalog",
-                    "add",
-                    "https://example.com/catalog.json",
-                    "--name",
-                    "community",
-                ],
-                catch_exceptions=True,
-            )
-
-        assert result.exit_code == 0, result.output
-        assert f"Config saved to {display_path}" in result.output
-
-    def test_catalog_list_escapes_config_path_markup(self, tmp_path):
-        """Catalog list's config-path label should render literally under Rich."""
-        from typer.testing import CliRunner
-        from unittest.mock import patch
-        from specify_cli import app
-        import yaml
-
-        project_dir = tmp_path / "test-project"
-        project_dir.mkdir()
-        specify_dir = project_dir / ".specify"
-        specify_dir.mkdir()
-        (specify_dir / "extension-catalogs.yml").write_text(
-            yaml.safe_dump(
-                {
-                    "catalogs": [
-                        {
-                            "name": "community",
-                            "url": "https://example.com/catalog.json",
-                            "priority": 10,
-                            "install_allowed": False,
-                        }
-                    ]
-                }
-            ),
-            encoding="utf-8",
-        )
-
-        display_path = "project[red]/.specify/extension-catalogs.yml"
-
-        runner = CliRunner()
-        with patch.object(Path, "cwd", return_value=project_dir), \
-             patch("specify_cli.extensions._commands._display_project_path", return_value=display_path):
-            result = runner.invoke(
-                app,
-                ["extension", "catalog", "list"],
-                catch_exceptions=True,
-            )
-
-        assert result.exit_code == 0, result.output
-        assert f"Config: {display_path}" in result.output
-
-    def test_catalog_add_escapes_config_read_exception_markup(self, tmp_path):
-        """Catalog config parse errors can include user-controlled file content."""
-        import yaml
-        from typer.testing import CliRunner
-        from unittest.mock import patch
-        from specify_cli import app
-
-        project_dir = tmp_path / "test-project"
-        project_dir.mkdir()
-        specify_dir = project_dir / ".specify"
-        specify_dir.mkdir()
-        (specify_dir / "extension-catalogs.yml").write_text("[red]bad[/red]", encoding="utf-8")
-
-        runner = CliRunner()
-        with patch.object(Path, "cwd", return_value=project_dir), \
-             patch(
-                 "specify_cli.extensions._commands.yaml.safe_load",
-                 side_effect=yaml.YAMLError("bad [red]catalog[/red] yaml"),
-             ):
-            result = runner.invoke(
-                app,
-                [
-                    "extension",
-                    "catalog",
-                    "add",
-                    "https://example.com/catalog.json",
-                    "--name",
-                    "community",
-                ],
-                catch_exceptions=True,
-            )
-
-        assert result.exit_code == 1, result.output
-        assert "bad [red]catalog[/red]" in result.output
-        assert "yaml" in result.output
-
-    def test_catalog_add_escapes_url_validation_exception_markup(self, tmp_path):
-        """URL validation errors may include user-controlled URL text."""
-        from typer.testing import CliRunner
-        from unittest.mock import patch
-        from specify_cli import app
-
-        project_dir = tmp_path / "test-project"
-        project_dir.mkdir()
-        (project_dir / ".specify").mkdir()
-
-        runner = CliRunner()
-        with patch.object(Path, "cwd", return_value=project_dir), \
-             patch.object(
-                 ExtensionCatalog,
-                 "_validate_catalog_url",
-                 side_effect=ValidationError("bad [red]url[/red]"),
-             ):
-            result = runner.invoke(
-                app,
-                [
-                    "extension",
-                    "catalog",
-                    "add",
-                    "https://example.com/[red]catalog[/red].json",
-                    "--name",
-                    "community",
-                ],
-                catch_exceptions=True,
-            )
-
-        assert result.exit_code == 1, result.output
-        assert "bad [red]url[/red]" in result.output
-
    def test_add_dev_links_copilot_agent_when_supported(
        self, extension_dir, project_dir, temp_dir
    ):
@@ -5054,85 +4883,6 @@ class TestExtensionAddCLI:
                f"confirm must precede spinner, got: {call_order}"
        assert result.exit_code == 0  # user declined → clean exit

-    def test_add_status_escapes_extension_markup(self, tmp_path):
-        """User-controlled extension names must not be parsed as Rich markup."""
-        from rich.markup import escape as escape_markup
-        from typer.testing import CliRunner
-        from unittest.mock import MagicMock, patch
-        from specify_cli import app
-
-        project_dir = tmp_path / "test-project"
-        project_dir.mkdir()
-        (project_dir / ".specify").mkdir()
-
-        status_messages: list[str] = []
-
-        def record_status(message, *args, **kwargs):
-            status_messages.append(message)
-            return MagicMock()
-
-        extension_name = "[red]bad[/red]"
-        runner = CliRunner()
-        with patch.object(Path, "cwd", return_value=project_dir), \
-             patch("specify_cli.console.status", side_effect=record_status):
-            result = runner.invoke(
-                app,
-                ["extension", "add", extension_name, "--dev"],
-                catch_exceptions=True,
-            )
-
-        assert result.exit_code == 1
-        assert status_messages == [
-            f"[cyan]Installing extension: {escape_markup(extension_name)}[/cyan]"
-        ]
-
-    def test_add_post_install_hint_escapes_manifest_id_markup(self, tmp_path):
-        """Extension IDs printed in Rich-rendered hints must stay literal."""
-        import io
-        from types import SimpleNamespace
-        from typer.testing import CliRunner
-        from unittest.mock import patch
-        from specify_cli import app
-
-        class FakeResponse(io.BytesIO):
-            def __enter__(self):
-                return self
-
-            def __exit__(self, exc_type, exc, tb):
-                return False
-
-        project_dir = tmp_path / "test-project"
-        project_dir.mkdir()
-        (project_dir / ".specify").mkdir()
-
-        manifest_id = "[red]bad[/red]"
-
-        def fake_install_from_zip(self_obj, zip_path, speckit_version, priority=10, force=False):
-            return SimpleNamespace(
-                id=manifest_id,
-                name="Bad Extension",
-                version="1.0.0",
-                description="Test extension",
-                warnings=[],
-                commands=[],
-                hooks=[],
-            )
-
-        runner = CliRunner()
-        with patch.object(Path, "cwd", return_value=project_dir), \
-             patch("typer.confirm", return_value=True), \
-             patch("specify_cli.authentication.http.open_url", return_value=FakeResponse(b"zip-bytes")), \
-             patch.object(ExtensionManager, "install_from_zip", fake_install_from_zip), \
-             patch.object(ExtensionRegistry, "get", return_value={}):
-            result = runner.invoke(
-                app,
-                ["extension", "add", "bad", "--from", "https://example.com/ext.zip"],
-                catch_exceptions=True,
-            )
-
-        assert result.exit_code == 0, result.output
-        assert ".specify/extensions/[red]bad[/red]/" in result.output
-
    def test_add_from_url_cancel_exits_cleanly(self, tmp_path):
        """Declining the --from <url> confirmation should exit with code 0."""
        from typer.testing import CliRunner
@@ -5155,131 +4905,6 @@ class TestExtensionAddCLI:
        assert result.exit_code == 0
        assert "Cancelled" in result.output

-    def test_add_from_url_escapes_download_exception_markup(self, tmp_path):
-        """Download errors can include user-controlled URL text."""
-        import urllib.error
-        from typer.testing import CliRunner
-        from unittest.mock import patch
-        from specify_cli import app
-
-        project_dir = tmp_path / "test-project"
-        project_dir.mkdir()
-        (project_dir / ".specify").mkdir()
-
-        runner = CliRunner()
-        with patch.object(Path, "cwd", return_value=project_dir), \
-             patch("typer.confirm", return_value=True), \
-             patch(
-                 "specify_cli.authentication.http.open_url",
-                 side_effect=urllib.error.URLError("bad [red]download[/red]"),
-             ):
-            result = runner.invoke(
-                app,
-                [
-                    "extension",
-                    "add",
-                    "my-ext",
-                    "--from",
-                    "https://example.com/[red]ext[/red].zip",
-                ],
-                catch_exceptions=True,
-            )
-
-        assert result.exit_code == 1, result.output
-        assert "https://example.com/[red]ext[/red].zip" in result.output
-        assert "bad [red]download[/red]" in result.output
-
-    @pytest.mark.parametrize(
-        ("exc_type", "label"),
-        [
-            (ValidationError, "Validation Error"),
-            (CompatibilityError, "Compatibility Error"),
-            (ExtensionError, "Error"),
-        ],
-    )
-    def test_add_exception_handlers_escape_markup(self, tmp_path, exc_type, label):
-        """Extension install exceptions can include manifest-controlled values."""
-        from typer.testing import CliRunner
-        from unittest.mock import patch
-        from specify_cli import app
-
-        project_dir = tmp_path / "test-project"
-        project_dir.mkdir()
-        (project_dir / ".specify").mkdir()
-
-        ext_dir = tmp_path / "ext"
-        ext_dir.mkdir()
-        (ext_dir / "extension.yml").write_text("extension:\n  id: test\n", encoding="utf-8")
-
-        runner = CliRunner()
-        with patch.object(Path, "cwd", return_value=project_dir), \
-             patch.object(
-                 ExtensionManager,
-                 "install_from_directory",
-                 side_effect=exc_type("bad [red]extension[/red]"),
-             ):
-            result = runner.invoke(
-                app,
-                ["extension", "add", str(ext_dir), "--dev"],
-                catch_exceptions=True,
-            )
-
-        assert result.exit_code == 1, result.output
-        assert f"{label}:" in result.output
-        assert "bad [red]extension[/red]" in result.output
-
-    def test_add_from_url_uses_cache_tempfile_for_untrusted_extension_name(self, tmp_path):
-        """The extension argument must not control the downloaded ZIP path."""
-        import io
-        from types import SimpleNamespace
-        from typer.testing import CliRunner
-        from unittest.mock import patch
-        from specify_cli import app
-
-        class FakeResponse(io.BytesIO):
-            def __enter__(self):
-                return self
-
-            def __exit__(self, exc_type, exc, tb):
-                return False
-
-        project_dir = tmp_path / "test-project"
-        project_dir.mkdir()
-        (project_dir / ".specify").mkdir()
-        downloads_dir = project_dir / ".specify" / "extensions" / ".cache" / "downloads"
-        installed = {}
-
-        def fake_install_from_zip(self_obj, zip_path, speckit_version, priority=10, force=False):
-            captured_path = Path(zip_path)
-            installed["zip_path"] = captured_path
-            installed["zip_bytes"] = captured_path.read_bytes()
-            return SimpleNamespace(
-                id="escape",
-                name="Escape Test",
-                version="1.0.0",
-                description="Test extension",
-                warnings=[],
-                commands=[],
-                hooks=[],
-            )
-
-        runner = CliRunner()
-        with patch.object(Path, "cwd", return_value=project_dir), \
-             patch("typer.confirm", return_value=True), \
-             patch("specify_cli.authentication.http.open_url", return_value=FakeResponse(b"zip-bytes")), \
-             patch.object(ExtensionManager, "install_from_zip", fake_install_from_zip):
-            result = runner.invoke(
-                app,
-                ["extension", "add", "../outside", "--from", "https://example.com/ext.zip"],
-                catch_exceptions=True,
-            )
-
-        assert result.exit_code == 0
-        assert installed["zip_bytes"] == b"zip-bytes"
-        assert installed["zip_path"].resolve().is_relative_to(downloads_dir.resolve())
-        assert installed["zip_path"].name.startswith("extension-url-download-")
-        assert not installed["zip_path"].exists()
-

 class TestDownloadExtensionBundled:
    """Tests for download_extension handling of bundled extensions."""
@@ -5544,62 +5169,6 @@ class TestExtensionUpdateCLI:
        for cmd_file in command_files:
            assert cmd_file.exists(), f"Expected command file to be restored after rollback: {cmd_file}"

-    @pytest.mark.parametrize(
-        ("manifest_text", "expected_detail"),
-        [
-            ("- not\n- a\n- mapping\n", "YAML mapping"),
-            ("extension: []\n", "'extension' mapping"),
-        ],
-    )
-    def test_update_rejects_malformed_zip_manifest(
-        self, tmp_path, monkeypatch, manifest_text, expected_detail
-    ):
-        """Downloaded extension.yml shape must be valid before ID validation."""
-        from typer.testing import CliRunner
-        from unittest.mock import patch
-        from specify_cli import app
-        import zipfile
-
-        fake_home = tmp_path / "home"
-        fake_home.mkdir()
-        monkeypatch.setattr(Path, "home", lambda: fake_home)
-
-        runner = CliRunner()
-        project_dir = tmp_path / "project"
-        project_dir.mkdir()
-        (project_dir / ".specify").mkdir()
-        (project_dir / ".claude" / "skills").mkdir(parents=True)
-
-        manager = ExtensionManager(project_dir)
-        v1_dir = self._create_extension_source(tmp_path, "1.0.0")
-        manager.install_from_directory(v1_dir, "0.1.0")
-        original_registry_entry = manager.registry.get("test-ext")
-
-        zip_path = tmp_path / "bad-manifest.zip"
-        with zipfile.ZipFile(zip_path, "w") as zf:
-            zf.writestr("extension.yml", manifest_text)
-
-        with patch.object(Path, "cwd", return_value=project_dir), \
-             patch.object(ExtensionCatalog, "get_extension_info", return_value={
-                 "id": "test-ext",
-                 "name": "Test Extension",
-                 "version": "2.0.0",
-                 "_install_allowed": True,
-             }), \
-             patch.object(ExtensionCatalog, "download_extension", return_value=zip_path):
-            result = runner.invoke(
-                app,
-                ["extension", "update", "test-ext"],
-                input="y\n",
-                catch_exceptions=True,
-            )
-
-        assert result.exit_code == 1, result.output
-        assert "Invalid extension manifest in downloaded archive" in result.output
-        assert expected_detail in result.output
-        assert "AttributeError" not in result.output
-        assert ExtensionManager(project_dir).registry.get("test-ext") == original_registry_entry
-

 class TestExtensionListCLI:
    """Test extension list CLI output format."""
@@ -6483,24 +6052,6 @@ class TestHookInvocationRendering:
        assert execution["command"] == "speckit.tasks"
        assert execution["invocation"] == "$speckit-tasks"

-    def test_zcode_hooks_render_dollar_skill_invocation(self, project_dir):
-        """ZCode projects with skills mode should render $speckit-* invocations."""
-        init_options = project_dir / ".specify" / "init-options.json"
-        init_options.parent.mkdir(parents=True, exist_ok=True)
-        init_options.write_text(json.dumps({"ai": "zcode", "ai_skills": True}))
-
-        hook_executor = HookExecutor(project_dir)
-        execution = hook_executor.execute_hook(
-            {
-                "extension": "test-ext",
-                "command": "speckit.tasks",
-                "optional": False,
-            }
-        )
-
-        assert execution["command"] == "speckit.tasks"
-        assert execution["invocation"] == "$speckit-tasks"
-
    def test_non_boolean_ai_skills_keeps_default_hook_invocation(self, project_dir):
        """Corrupted truthy ai_skills values should not enable skill invocation."""
        init_options = project_dir / ".specify" / "init-options.json"
@@ -6694,118 +6245,6 @@ class TestExtensionRemoveCLI:

        assert "2 commands" in result.output

-    def test_remove_output_escapes_extension_id_markup(self, tmp_path):
-        """Removal paths and reinstall hints must not parse extension IDs as markup."""
-        from types import SimpleNamespace
-        from typer.testing import CliRunner
-        from unittest.mock import patch
-        from specify_cli import app
-
-        project_dir = tmp_path / "project"
-        project_dir.mkdir()
-        (project_dir / ".specify").mkdir()
-
-        extension_id = "[red]bad[/red]"
-        installed = [
-            {
-                "id": extension_id,
-                "name": "Bad Extension",
-                "version": "1.0.0",
-                "description": "Test extension",
-                "enabled": True,
-            }
-        ]
-
-        runner = CliRunner()
-        with patch.object(Path, "cwd", return_value=project_dir), \
-             patch.object(ExtensionManager, "list_installed", return_value=installed), \
-             patch.object(ExtensionManager, "get_extension", return_value=SimpleNamespace(commands=[])), \
-             patch.object(ExtensionRegistry, "get", return_value={"registered_commands": {}, "registered_skills": []}), \
-             patch.object(ExtensionManager, "remove", return_value=True):
-            result = runner.invoke(
-                app,
-                ["extension", "remove", extension_id, "--force"],
-                catch_exceptions=True,
-            )
-
-        assert result.exit_code == 0, result.output
-        assert ".specify/extensions/.backup/[red]bad[/red]/" in result.output
-        assert "specify extension add [red]bad[/red]" in result.output
-
-
-class TestExtensionStateCLI:
-    """CLI tests for installed extension state commands."""
-
-    def test_enable_registry_error_escapes_extension_id_markup(self, tmp_path):
-        """Registry-corruption errors should render extension IDs literally."""
-        from typer.testing import CliRunner
-        from unittest.mock import patch
-        from specify_cli import app
-
-        project_dir = tmp_path / "project"
-        project_dir.mkdir()
-        (project_dir / ".specify").mkdir()
-
-        extension_id = "[red]bad[/red]"
-        installed = [
-            {
-                "id": extension_id,
-                "name": "Bad Extension",
-                "version": "1.0.0",
-                "description": "Test extension",
-                "enabled": False,
-            }
-        ]
-
-        runner = CliRunner()
-        with patch.object(Path, "cwd", return_value=project_dir), \
-             patch.object(ExtensionManager, "list_installed", return_value=installed), \
-             patch.object(ExtensionRegistry, "get", return_value=None):
-            result = runner.invoke(
-                app,
-                ["extension", "enable", extension_id],
-                catch_exceptions=True,
-            )
-
-        assert result.exit_code == 1, result.output
-        assert "Extension '[red]bad[/red]' not found in registry" in result.output
-
-    def test_disable_reenable_hint_escapes_extension_id_markup(self, tmp_path):
-        """Disable success hints should not parse extension IDs as markup."""
-        from typer.testing import CliRunner
-        from unittest.mock import patch
-        from specify_cli import app
-
-        project_dir = tmp_path / "project"
-        project_dir.mkdir()
-        (project_dir / ".specify").mkdir()
-
-        extension_id = "[red]bad[/red]"
-        installed = [
-            {
-                "id": extension_id,
-                "name": "Bad Extension",
-                "version": "1.0.0",
-                "description": "Test extension",
-                "enabled": True,
-            }
-        ]
-
-        runner = CliRunner()
-        with patch.object(Path, "cwd", return_value=project_dir), \
-             patch.object(ExtensionManager, "list_installed", return_value=installed), \
-             patch.object(ExtensionRegistry, "get", return_value={"enabled": True}), \
-             patch.object(ExtensionRegistry, "update", return_value=None), \
-             patch.object(HookExecutor, "get_project_config", return_value={}):
-            result = runner.invoke(
-                app,
-                ["extension", "disable", extension_id],
-                catch_exceptions=True,
-            )
-
-        assert result.exit_code == 0, result.output
-        assert "specify extension enable [red]bad[/red]" in result.output
-

 class TestClineExtensionHyphenation:
    """Test that Cline integration uses hyphenated commands and frontmatter references."""
--- a/tests/test_presets.py
+++ b/tests/test_presets.py
@@ -1033,32 +1033,6 @@ class TestPresetResolver:
        result = resolver.resolve("hidden-template")
        assert result is None

-    def test_collect_all_layers_finds_bundled_core_without_specify_commands(
-        self, project_dir
-    ):
-        """Tier-5 fallback locates the bundled core command when
-        .specify/templates/commands/ has no matching file.
-
-        Regression test for #3086: a stale ``.parent`` chain made the
-        source-checkout fallback resolve to ``src/templates/...`` (which does
-        not exist), so ``wrap`` presets found no base layer. The fallback must
-        resolve against the real repo-root ``templates/commands`` tree.
-        """
-        # project_dir's commands dir is empty, so tier-4 cannot satisfy this.
-        resolver = PresetResolver(project_dir)
-        layers = resolver.collect_all_layers("speckit.implement", "command")
-        assert layers, "expected a bundled core base layer to be found"
-        assert layers[-1]["source"] == "core (bundled)"
-        assert layers[-1]["path"].parts[-2:] == ("commands", "implement.md")
-
-    def test_resolve_command_falls_back_to_bundled_core(self, project_dir):
-        """resolve() tier-5 returns the bundled core command when
-        .specify/templates/commands/ lacks it (regression for #3086)."""
-        resolver = PresetResolver(project_dir)
-        result = resolver.resolve("speckit.implement", "command")
-        assert result is not None
-        assert result.parts[-2:] == ("commands", "implement.md")
-

 class TestResolveCore:
    """Test PresetResolver.resolve_core() skips the installed-presets tier."""