fix: limit catalog.community.json changes to wiki entry + timestamps only

Reverts the unintended reordering and reformatting of existing extensions (aide, checkpoint, critique, threatmodel, etc.) and companion's tools array. Only the new wiki entry and updated_at timestamps are now changed. Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)
Add LLM Wiki extension to community catalog
2026-07-08 15:06:10 +08:00 · 2026-07-07 14:54:51 +00:00 · 2026-07-06 13:57:57 +00:00
47 changed files with 250 additions and 3087 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,51 +2,6 @@

 <!-- insert new changelog below this comment -->

-## [0.12.7] - 2026-07-07
-
-### Changed
-
- fix(bundler): bundle update uninstalls components dropped by new version (#3353)
- fix(workflows): route run/resume errors to stderr under --json (#3352)
- fix(workflows): fan-in validate() rejects non-mapping output (#3349)
- fix(workflows): shell step validate() rejects non-string run (#3348)
- fix(integrations): agy honors SPECKIT_INTEGRATION_AGY_EXTRA_ARGS (#3347)
- Add Orchestration Task Context Management extension to community catalog (#3372)
- Update DocGuard — CDD Enforcement extension to v0.30.0 (#3371)
- Update Ripple extension to v1.1.0 (#3370)
- feat(integrations): generalize post-processing to all format types (#3311)
- chore: release 0.12.6, begin 0.12.7.dev0 development (#3393)
-
-## [0.12.6] - 2026-07-07
-
-### Changed
-
- fix(bundler): validate catalog URLs in `catalog add` (HTTPS-only, require host) (#3367)
- Update Ralph Loop extension to v1.2.1 (#3365)
- fix extension-local script path rewriting (#3364)
- Add Charter extension to community catalog (#3363)
- feat(scripts): add Python check-prerequisites PoC (#3302)
- test: reduce registry manifest test repetition (#3146)
- fix(integrations): hermes honors SPECKIT_INTEGRATION_HERMES_EXTRA_ARGS (#3346)
- fix(extensions): coerce non-mapping YAML config roots to {} in ConfigManager (#3345)
- fix(yaml): pin goose recipe prompt block-scalar indentation (#3343)
- chore: release 0.12.5, begin 0.12.6.dev0 development (#3381)
-
-## [0.12.5] - 2026-07-06
-
-### Changed
-
- fix(workflows): match gate reject option case-insensitively (#3335)
- fix(bundler): reject host-less catalog URLs in adapters (use hostname, not netloc) (#3333)
- fix(bundler): resolve catalog search at highest-precedence source before filtering (#3331)
- fix(workflows): compare non-numeric strings lexicographically instead of returning False (#3323)
- fix(workflows): quote-aware interpolation so a literal }} in a filter arg doesn't break multi-expression templates (#3307)
- Support namespaced git feature branch templates (#3293)
- chore(deps): bump actions/setup-dotnet from 5.3.0 to 5.4.0 (#3315)
- fix(integrations): cursor-agent honors executable/extra-args env overrides (#3265)
- docs: drop stale kimi KIMI.md->AGENTS.md migration note (#3291)
- chore: release 0.12.4, begin 0.12.5.dev0 development (#3305)
-
 ## [0.12.4] - 2026-07-02

 ### Changed
--- a/docs/community/extensions.md
+++ b/docs/community/extensions.md
@@ -42,7 +42,6 @@ The following community-contributed extensions are available in [`catalog.commun
 | Bugfix Workflow | Structured bugfix workflow — capture bugs, trace to spec artifacts, and patch specs surgically | `process` | Read+Write | [spec-kit-bugfix](https://github.com/Quratulain-bilal/spec-kit-bugfix) |
 | Canon | Adds canon-driven (baseline-driven) workflows: spec-first, code-first, spec-drift. Requires Canon Core preset installation. | `process` | Read+Write | [spec-kit-canon](https://github.com/maximiliamus/spec-kit-canon/tree/master/extension) |
 | Catalog CI | Automated validation for spec-kit community catalog entries — structure, URLs, diffs, and linting | `process` | Read-only | [spec-kit-catalog-ci](https://github.com/Quratulain-bilal/spec-kit-catalog-ci) |
-| Charter | Compose modular project constitutions from shared fragment registries. Centralize governance rules, select per-project fragments, track upstream changes, and keep multi-project setups consistent. | `process` | Read+Write | [spec-kit-charter](https://github.com/Fyloss/spec-kit-charter) |
 | CI Guard | Spec compliance gates for CI/CD — verify specs exist, check drift, and block merges on gaps | `process` | Read-only | [spec-kit-ci-guard](https://github.com/Quratulain-bilal/spec-kit-ci-guard) |
 | Checkpoint Extension | Commit the changes made during the middle of the implementation, so you don't end up with just one very large commit at the end | `code` | Read+Write | [spec-kit-checkpoint](https://github.com/aaronrsun/spec-kit-checkpoint) |
 | Cleanup Extension | Post-implementation quality gate that reviews changes, fixes small issues (scout rule), creates tasks for medium issues, and generates analysis for large issues | `code` | Read+Write | [spec-kit-cleanup](https://github.com/dsrednicki/spec-kit-cleanup) |
@@ -51,7 +50,7 @@ The following community-contributed extensions are available in [`catalog.commun
 | Confluence Extension | Create a doc in Confluence summarizing the specifications and planning files | `integration` | Read+Write | [spec-kit-confluence](https://github.com/aaronrsun/spec-kit-confluence) |
 | Cost Tracker | Track real LLM dollar cost across SDD workflows — per-feature budgets, per-integration comparison, and finance-ready exports | `visibility` | Read+Write | [spec-kit-cost](https://github.com/Quratulain-bilal/spec-kit-cost) |
 | Data Model Diagram | Generates Mermaid ER diagrams from Spec Kit data models after planning | `docs` | Read+Write | [spec-kit-data-model-diagram](https://github.com/benizzio/spec-kit-data-model-diagram) |
-| DocGuard — CDD Enforcement | The only doc-integrity engine with an MCP server, SARIF output, and a deterministic zero-LLM core. Validates, scores, and traces documentation against code — 24 validators, stable finding codes, GitHub Action with PR annotations, spec-kit hooks. Pure Node.js, one pinned dep. | `docs` | Read+Write | [spec-kit-docguard](https://github.com/raccioly/docguard) |
+| DocGuard — CDD Enforcement | 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. | `docs` | Read+Write | [spec-kit-docguard](https://github.com/raccioly/docguard) |
 | Extensify | Create and validate extensions and extension catalogs | `process` | Read+Write | [extensify](https://github.com/mnriem/spec-kit-extensions/tree/main/extensify) |
 | Fix Findings | Automated analyze-fix-reanalyze loop that resolves spec findings until clean | `code` | Read+Write | [spec-kit-fix-findings](https://github.com/Quratulain-bilal/spec-kit-fix-findings) |
 | FixIt Extension | Spec-aware bug fixing — maps bugs to spec artifacts, proposes a plan, applies minimal changes | `code` | Read+Write | [spec-kit-fixit](https://github.com/speckit-community/spec-kit-fixit) |
@@ -67,6 +66,7 @@ The following community-contributed extensions are available in [`catalog.commun
 | Jira Integration (Sync Engine) | Idempotent, drift-aware, fail-closed reconcile engine mirroring spec-kit specs into Jira (Epic per repo, Story per spec, Subtask per phase) | `integration` | Read+Write | [spec-kit-jira-sync](https://github.com/ashbrener/spec-kit-jira-sync) |
 | Learning Extension | Generate educational guides from implementations and enhance clarifications with mentoring context | `docs` | Read+Write | [spec-kit-learn](https://github.com/imviancagrace/spec-kit-learn) |
 | Linear Integration | Mirror spec-kit feature directories into Linear (filesystem → Linear, reconcile-based, unidirectional). | `integration` | Read+Write | [spec-kit-linear-sync](https://github.com/ashbrener/spec-kit-linear-sync) |
+| LLM Wiki | LLM-maintained compounding project wiki: source ingestion, cited answers, and consistency linting | `docs` | Read+Write | [spec-kit-wiki](https://github.com/formin/spec-kit-wiki) |
 | Loop Engineering | Engineer safe autonomous agent loops for spec-driven development: a maker/checker split, externalized loop state, and stay-the-engineer guardrails against comprehension debt and cognitive surrender | `process` | Read+Write | [spec-kit-loop](https://github.com/formin/spec-kit-loop) |
 | MAQA — Multi-Agent & Quality Assurance | Coordinator → feature → QA agent workflow with parallel worktree-based implementation. Language-agnostic. Auto-detects installed board plugins. Optional CI gate. | `process` | Read+Write | [spec-kit-maqa-ext](https://github.com/GenieRobot/spec-kit-maqa-ext) |
 | MAQA Azure DevOps Integration | Azure DevOps Boards integration for MAQA — syncs User Stories and Task children as features progress | `integration` | Read+Write | [spec-kit-maqa-azure-devops](https://github.com/GenieRobot/spec-kit-maqa-azure-devops) |
@@ -86,7 +86,6 @@ The following community-contributed extensions are available in [`catalog.commun
 | .NET Framework to Modern .NET Migration | Orchestrate end-to-end .NET Framework to modern .NET migration across 7 phases, with SDD lifecycle integration | `process` | Read+Write | [spec-kit-fx-to-net](https://github.com/RogerBestMsft/spec-kit-FxToNet) |
 | Onboard | Contextual onboarding and progressive growth for developers new to spec-kit projects. Explains specs, maps dependencies, validates understanding, and guides the next step | `process` | Read+Write | [spec-kit-onboard](https://github.com/dmux/spec-kit-onboard) |
 | Optimize | Audit and optimize AI governance for context efficiency — token budgets, rule health, interpretability, compression, coherence, and echo detection | `process` | Read+Write | [spec-kit-optimize](https://github.com/sakitA/spec-kit-optimize) |
-| Orchestration Task Context Management | Adds subagent work-unit orchestration to generated Spec Kit task files | `process` | Read+Write | [spec-kit-orchestration-task-context-management](https://github.com/benizzio/spec-kit-orchestration-task-context-management) |
 | OWASP LLM Threat Model | OWASP Top 10 for LLM Applications 2025 threat analysis on agent artifacts | `code` | Read-only | [spec-kit-threatmodel](https://github.com/NaviaSamal/spec-kit-threatmodel) |
 | Plan Review Gate | Require spec.md and plan.md to be merged via MR/PR before allowing task generation | `process` | Read-only | [spec-kit-plan-review-gate](https://github.com/luno/spec-kit-plan-review-gate) |
 | PR Bridge | Auto-generate pull request descriptions, checklists, and summaries from spec artifacts | `process` | Read-only | [spec-kit-pr-bridge-](https://github.com/Quratulain-bilal/spec-kit-pr-bridge-) |
@@ -107,7 +106,7 @@ The following community-contributed extensions are available in [`catalog.commun
 | Retro Extension | Sprint retrospective analysis with metrics, spec accuracy assessment, and improvement suggestions | `process` | Read+Write | [spec-kit-retro](https://github.com/arunt14/spec-kit-retro) |
 | Retrospective Extension | Post-implementation retrospective with spec adherence scoring, drift analysis, and human-gated spec updates | `docs` | Read+Write | [spec-kit-retrospective](https://github.com/emi-dm/spec-kit-retrospective) |
 | Review Extension | Post-implementation comprehensive code review with specialized agents for code quality, comments, tests, error handling, type design, and simplification | `code` | Read-only | [spec-kit-review](https://github.com/ismaelJimenez/spec-kit-review) |
-| Ripple | Detect side effects that tests can't catch after implementation — surface hidden ripple effects across 9 analysis categories | `code` | Read+Write | [spec-kit-ripple](https://github.com/chordpli/spec-kit-ripple) |
+| Ripple | Detect side effects that tests can't catch after implementation — delta-anchored analysis across 9 domain-agnostic categories | `code` | Read+Write | [spec-kit-ripple](https://github.com/chordpli/spec-kit-ripple) |
 | SDD Utilities | Resume interrupted workflows, validate project health, and verify spec-to-task traceability | `process` | Read+Write | [speckit-utils](https://github.com/mvanhorn/speckit-utils) |
 | Security Review | Full-project secure-by-design security audits plus staged, branch/PR, plan, task, follow-up, and apply reviews | `code` | Read+Write | [spec-kit-security-review](https://github.com/DyanGalih/spec-kit-security-review) |
 | SFSpeckit | Enterprise Salesforce SDLC with 18 commands for the full SDD lifecycle. | `process` | Read+Write | [spec-kit-sf](https://github.com/ysumanth06/spec-kit-sf) |
--- a/extensions/catalog.community.json
+++ b/extensions/catalog.community.json
@@ -670,40 +670,6 @@
      "created_at": "2026-04-11T18:00:00Z",
      "updated_at": "2026-04-11T18:00:00Z"
    },
-    "charter": {
-      "name": "Charter",
-      "id": "charter",
-      "description": "Compose modular project constitutions from shared fragment registries. Centralize governance rules, select per-project fragments, track upstream changes, and keep multi-project setups consistent.",
-      "author": "Fyloss",
-      "version": "0.3.1",
-      "download_url": "https://github.com/Fyloss/spec-kit-charter/archive/refs/tags/v0.3.1.zip",
-      "repository": "https://github.com/Fyloss/spec-kit-charter",
-      "homepage": "https://github.com/Fyloss/spec-kit-charter",
-      "documentation": "https://github.com/Fyloss/spec-kit-charter/tree/master/docs",
-      "changelog": "https://github.com/Fyloss/spec-kit-charter/blob/master/CHANGELOG.md",
-      "license": "MIT",
-      "category": "process",
-      "effect": "read-write",
-      "requires": {
-        "speckit_version": ">=0.11.9"
-      },
-      "provides": {
-        "commands": 5,
-        "hooks": 1
-      },
-      "tags": [
-        "constitution",
-        "governance",
-        "modular",
-        "fragments",
-        "registry"
-      ],
-      "verified": false,
-      "downloads": 0,
-      "stars": 0,
-      "created_at": "2026-07-06T00:00:00Z",
-      "updated_at": "2026-07-06T00:00:00Z"
-    },
    "ci-guard": {
      "name": "CI Guard",
      "id": "ci-guard",
@@ -1106,10 +1072,10 @@
    "docguard": {
      "name": "DocGuard — CDD Enforcement",
      "id": "docguard",
-      "description": "The only doc-integrity engine with an MCP server, SARIF output, and a deterministic zero-LLM core. Validates, scores, and traces documentation against code — 24 validators, stable finding codes, GitHub Action with PR annotations, spec-kit hooks. Pure Node.js, one pinned dep.",
+      "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": "0.30.0",
-      "download_url": "https://github.com/raccioly/docguard/releases/download/v0.30.0/spec-kit-docguard-v0.30.0.zip",
+      "version": "0.28.0",
+      "download_url": "https://github.com/raccioly/docguard/releases/download/v0.28.0/spec-kit-docguard-v0.28.0.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",
@@ -1145,7 +1111,7 @@
      "downloads": 0,
      "stars": 0,
      "created_at": "2026-03-13T00:00:00Z",
-      "updated_at": "2026-07-06T00:00:00Z"
+      "updated_at": "2026-06-23T00:00:00Z"
    },
    "doctor": {
      "name": "Project Health Check",
@@ -2396,39 +2362,6 @@
      "created_at": "2026-04-03T00:00:00Z",
      "updated_at": "2026-04-03T00:00:00Z"
    },
-    "orchestration-task-context-management": {
-      "name": "Orchestration Task Context Management",
-      "id": "orchestration-task-context-management",
-      "description": "Adds subagent work-unit orchestration to generated Spec Kit task files",
-      "author": "Igor Benicio de Mesquita",
-      "version": "0.0.0",
-      "download_url": "https://github.com/benizzio/spec-kit-orchestration-task-context-management/archive/refs/tags/v0.0.0.zip",
-      "repository": "https://github.com/benizzio/spec-kit-orchestration-task-context-management",
-      "homepage": "https://github.com/benizzio/spec-kit-orchestration-task-context-management",
-      "documentation": "https://github.com/benizzio/spec-kit-orchestration-task-context-management/blob/main/README.md",
-      "changelog": "https://github.com/benizzio/spec-kit-orchestration-task-context-management/blob/main/CHANGELOG.md",
-      "license": "MIT",
-      "category": "process",
-      "effect": "read-write",
-      "requires": {
-        "speckit_version": ">=0.7.2"
-      },
-      "provides": {
-        "commands": 2,
-        "hooks": 2
-      },
-      "tags": [
-        "agent",
-        "orchestration",
-        "tasks",
-        "context"
-      ],
-      "verified": false,
-      "downloads": 0,
-      "stars": 0,
-      "created_at": "2026-07-06T00:00:00Z",
-      "updated_at": "2026-07-06T00:00:00Z"
-    },
    "orchestrator": {
      "name": "Spec Orchestrator",
      "id": "orchestrator",
@@ -2746,8 +2679,8 @@
      "id": "ralph",
      "description": "Autonomous implementation loop using AI agent CLI",
      "author": "Rubiss",
-      "version": "1.2.1",
-      "download_url": "https://github.com/Rubiss-Projects/spec-kit-ralph/archive/refs/tags/v1.2.1.zip",
+      "version": "1.1.1",
+      "download_url": "https://github.com/Rubiss-Projects/spec-kit-ralph/archive/refs/tags/v1.1.1.zip",
      "repository": "https://github.com/Rubiss-Projects/spec-kit-ralph",
      "homepage": "https://github.com/Rubiss-Projects/spec-kit-ralph",
      "documentation": "https://github.com/Rubiss-Projects/spec-kit-ralph/blob/main/README.md",
@@ -2756,7 +2689,7 @@
      "category": "code",
      "effect": "read-write",
      "requires": {
-        "speckit_version": ">=0.8.5",
+        "speckit_version": ">=0.1.0",
        "tools": [
          {
            "name": "copilot",
@@ -2766,10 +2699,6 @@
            "name": "codex",
            "required": false
          },
-          {
-            "name": "claude",
-            "required": false
-          },
          {
            "name": "git",
            "required": true
@@ -2785,14 +2714,13 @@
        "automation",
        "loop",
        "copilot",
-        "codex",
-        "claude"
+        "codex"
      ],
      "verified": false,
      "downloads": 0,
      "stars": 0,
      "created_at": "2026-03-09T00:00:00Z",
-      "updated_at": "2026-07-06T00:00:00Z"
+      "updated_at": "2026-06-05T03:11:06Z"
    },
    "reconcile": {
      "name": "Reconcile Extension",
@@ -3119,10 +3047,10 @@
    "ripple": {
      "name": "Ripple",
      "id": "ripple",
-      "description": "Detect side effects that tests can't catch after implementation — surface hidden ripple effects across 9 analysis categories",
+      "description": "Detect side effects that tests can't catch after implementation — delta-anchored analysis across 9 domain-agnostic categories with fix-induced side effect detection",
      "author": "chordpli",
-      "version": "1.1.0",
-      "download_url": "https://github.com/chordpli/spec-kit-ripple/archive/refs/tags/v1.1.0.zip",
+      "version": "1.0.0",
+      "download_url": "https://github.com/chordpli/spec-kit-ripple/archive/refs/tags/v1.0.0.zip",
      "repository": "https://github.com/chordpli/spec-kit-ripple",
      "homepage": "https://github.com/chordpli/spec-kit-ripple",
      "documentation": "https://github.com/chordpli/spec-kit-ripple/blob/main/README.md",
@@ -3131,13 +3059,7 @@
      "category": "code",
      "effect": "read-write",
      "requires": {
-        "speckit_version": ">=0.2.0",
-        "tools": [
-          {
-            "name": "git",
-            "required": true
-          }
-        ]
+        "speckit_version": ">=0.2.0"
      },
      "provides": {
        "commands": 3,
@@ -3154,7 +3076,7 @@
      "downloads": 0,
      "stars": 0,
      "created_at": "2026-04-20T00:00:00Z",
-      "updated_at": "2026-07-06T00:00:00Z"
+      "updated_at": "2026-04-20T00:00:00Z"
    },
    "roadmap": {
      "name": "Spec Roadmap",
@@ -4375,6 +4297,40 @@
      "created_at": "2026-04-13T00:00:00Z",
      "updated_at": "2026-04-13T00:00:00Z"
    },
+    "wiki": {
+      "name": "LLM Wiki",
+      "id": "wiki",
+      "description": "LLM-maintained compounding project wiki: source ingestion, cited answers, and consistency linting",
+      "author": "formin",
+      "version": "1.0.0",
+      "download_url": "https://github.com/formin/spec-kit-wiki/archive/refs/tags/v1.0.0.zip",
+      "repository": "https://github.com/formin/spec-kit-wiki",
+      "homepage": "https://github.com/formin/spec-kit-wiki",
+      "documentation": "https://github.com/formin/spec-kit-wiki/blob/main/README.md",
+      "changelog": "https://github.com/formin/spec-kit-wiki/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "category": "docs",
+      "effect": "read-write",
+      "requires": {
+        "speckit_version": ">=0.2.0"
+      },
+      "provides": {
+        "commands": 5,
+        "hooks": 2
+      },
+      "tags": [
+        "wiki",
+        "knowledge-base",
+        "docs",
+        "memory",
+        "context-management"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-07-06T00:00:00Z",
+      "updated_at": "2026-07-06T00:00:00Z"
+    },
    "wireframe": {
      "name": "Wireframe Visual Feedback Loop",
      "id": "wireframe",
--- a/extensions/git/README.md
+++ b/extensions/git/README.md
@@ -7,7 +7,7 @@ Git repository initialization, feature branch creation, numbering (sequential/ti
 This extension provides Git operations as an optional, self-contained module. It manages:

 - **Repository initialization** with configurable commit messages
- **Feature branch creation** with sequential (`001-feature-name`) or timestamp (`20260319-143022-feature-name`) numbering and optional templates for branch namespaces
+- **Feature branch creation** with sequential (`001-feature-name`) or timestamp (`20260319-143022-feature-name`) numbering
 - **Branch validation** to ensure branches follow naming conventions
 - **Git remote detection** for GitHub integration (e.g., issue creation)
 - **Auto-commit** after core commands (configurable per-command with custom messages)
@@ -53,16 +53,6 @@ Configuration is stored in `.specify/extensions/git/git-config.yml`:
 # Branch numbering strategy: "sequential" or "timestamp"
 branch_numbering: sequential

-# Optional branch name template. Leave empty for the default "{number}-{slug}".
-# Supported tokens: {author}, {app}, {number}, {slug}; {slug} must not appear
-# before {number}, and the final path segment must start with {number}-.
-# Example for monorepos: "{author}/{app}/{number}-{slug}"
-branch_template: ""
-
-# Optional shorthand namespace. Leave empty to use branch_template/default behavior.
-# Example: "features/{app}" expands to "features/{app}/{number}-{slug}"
-branch_prefix: ""
-
 # Custom commit message for git init
 init_commit_message: "[Spec Kit] Initial commit"

@@ -75,10 +65,6 @@ auto_commit:
    message: "[Spec Kit] Add specification"
 ```

-`{author}` is derived from Git config and sanitized for branch names. `{app}` is derived from the Spec Kit init directory name. Custom templates must not put `{slug}` before `{number}`, and must put `{number}-` at the start of the final path segment so generated names remain valid feature branches. For a monorepo project at `apps/web/.specify/`, a template such as `{author}/{app}/{number}-{slug}` produces branches like `jdoe/web/008-guided-tour`.
-
-For simple namespace-only customization, `branch_prefix` is also accepted as a shorthand and expands to `<branch_prefix>/{number}-{slug}`.
-
 ## Installation

 ```bash
--- a/extensions/git/commands/speckit.git.feature.md
+++ b/extensions/git/commands/speckit.git.feature.md
@@ -19,7 +19,7 @@ You **MUST** consider the user input before proceeding (if not empty).
 If the user explicitly provided `GIT_BRANCH_NAME` (e.g., via environment variable, argument, or in their request), pass it through to the script by setting the `GIT_BRANCH_NAME` environment variable before invoking the script. When `GIT_BRANCH_NAME` is set:
 - The script uses the exact value as the branch name, bypassing all prefix/suffix generation
 - `--short-name`, `--number`, and `--timestamp` flags are ignored
- `FEATURE_NUM` is extracted when the final path segment starts with a numeric or timestamp feature marker (for example `042-name`, `feat/042-name`, or `jdoe/app/042-name`), otherwise set to the full branch name
+- `FEATURE_NUM` is extracted from the name if it starts with a numeric prefix, otherwise set to the full branch name

 ## Prerequisites

@@ -35,19 +35,6 @@ Determine the branch numbering strategy by checking configuration in this order:
 3. Check `.specify/init-options.json` for `branch_numbering` value (deprecated, backward compatibility — will be removed in a future release)
 4. Default to `sequential` if none of the above exist

-## Branch Name Template
-
-Check `.specify/extensions/git/git-config.yml` for an optional `branch_template` value. If it is empty or missing, use the default branch shape `{number}-{slug}`. If it is set, `{slug}` must not appear before `{number}`, its final path segment must start with `{number}-`, and the script expands these tokens:
-
- `{author}`: sanitized Git config author (`user.name`, falling back to the email local part)
- `{app}`: sanitized Spec Kit init directory name
- `{number}`: sequential number or timestamp
- `{slug}`: generated short branch slug
-
-For monorepos, a template such as `{author}/{app}/{number}-{slug}` creates names like `jdoe/web/008-guided-tour` while preserving per-project feature numbering.
-
-The script also accepts `branch_prefix` as a shorthand for simple namespaces; it expands to `<branch_prefix>/{number}-{slug}`.
-
 ## Execution

 Generate a concise short name (2-4 words) for the branch:
@@ -67,7 +54,6 @@ Run the appropriate script based on your platform:
 - Always include the JSON flag (`--json` for Bash, `-Json` for PowerShell) so the output can be parsed reliably
 - You must only ever run this script once per feature
 - The JSON output will contain `BRANCH_NAME` and `FEATURE_NUM`
- Do not manually expand `branch_template`; the script reads the git extension config and applies it consistently

 ## Graceful Degradation

@@ -78,5 +64,5 @@ If Git is not installed or the current directory is not a Git repository:
 ## Output

 The script outputs JSON with:
- `BRANCH_NAME`: The branch name (e.g., `003-user-auth`, `20260319-143022-user-auth`, or `jdoe/web/003-user-auth`)
+- `BRANCH_NAME`: The branch name (e.g., `003-user-auth` or `20260319-143022-user-auth`)
 - `FEATURE_NUM`: The numeric or timestamp prefix used
--- a/extensions/git/commands/speckit.git.validate.md
+++ b/extensions/git/commands/speckit.git.validate.md
@@ -22,24 +22,24 @@ Get the current branch name:
 git rev-parse --abbrev-ref HEAD
 ```

-The branch name's final path segment must start with one of these feature markers:
+The branch name must match one of these patterns:

-1. **Sequential**: `[0-9]{3,}-` (e.g., `001-feature-name`, `042-fix-bug`, `1000-big-feature`, `jdoe/web/008-guided-tour`)
-2. **Timestamp**: `[0-9]{8}-[0-9]{6}-` (e.g., `20260319-143022-feature-name`, `jdoe/web/20260319-143022-feature-name`)
+1. **Sequential**: `^[0-9]{3,}-` (e.g., `001-feature-name`, `042-fix-bug`, `1000-big-feature`)
+2. **Timestamp**: `^[0-9]{8}-[0-9]{6}-` (e.g., `20260319-143022-feature-name`)

 ## Execution

 If on a feature branch (matches either pattern):
 - Output: `✓ On feature branch: <branch-name>`
 - Check if the corresponding spec directory exists under `specs/`:
-  - For sequential branches, look for `specs/<prefix>-*` where prefix matches the numeric portion, regardless of branch namespace prefixes
-  - For timestamp branches, look for `specs/<prefix>-*` where prefix matches the `YYYYMMDD-HHMMSS` portion, regardless of branch namespace prefixes
+  - For sequential branches, look for `specs/<prefix>-*` where prefix matches the numeric portion
+  - For timestamp branches, look for `specs/<prefix>-*` where prefix matches the `YYYYMMDD-HHMMSS` portion
 - If spec directory exists: `✓ Spec directory found: <path>`
 - If spec directory missing: `⚠ No spec directory found for prefix <prefix>`

 If NOT on a feature branch:
 - Output: `✗ Not on a feature branch. Current branch: <branch-name>`
- Output: `Feature branches should be named like: 001-feature-name, 20260319-143022-feature-name, or <namespace>/001-feature-name`
+- Output: `Feature branches should be named like: 001-feature-name or 20260319-143022-feature-name`

 ## Graceful Degradation

--- a/extensions/git/config-template.yml
+++ b/extensions/git/config-template.yml
@@ -4,16 +4,6 @@
 # Branch numbering strategy: "sequential" (001, 002, ...) or "timestamp" (YYYYMMDD-HHMMSS)
 branch_numbering: sequential

-# Optional branch name template. Leave empty for the default "{number}-{slug}".
-# Supported tokens: {author}, {app}, {number}, {slug}
-# {slug} must not appear before {number}; final path segment must start with {number}-.
-# Example for monorepos: "{author}/{app}/{number}-{slug}"
-branch_template: ""
-
-# Optional shorthand namespace. Leave empty to use branch_template/default behavior.
-# Example: "features/{app}" expands to "features/{app}/{number}-{slug}"
-branch_prefix: ""
-
 # Commit message used by `git commit` during repository initialization
 init_commit_message: "[Spec Kit] Initial commit"

--- a/extensions/git/extension.yml
+++ b/extensions/git/extension.yml
@@ -4,7 +4,7 @@ extension:
  id: git
  name: "Git Branching Workflow"
  version: "1.0.0"
-  description: "Feature branch creation, numbering (sequential/timestamp), templating, validation, and Git remote detection"
+  description: "Feature branch creation, numbering (sequential/timestamp), validation, and Git remote detection"
  author: spec-kit-core
  repository: https://github.com/github/spec-kit
  license: MIT
@@ -19,7 +19,7 @@ provides:
  commands:
    - name: speckit.git.feature
      file: commands/speckit.git.feature.md
-      description: "Create a feature branch with sequential or timestamp numbering and optional templates"
+      description: "Create a feature branch with sequential or timestamp numbering"
    - name: speckit.git.validate
      file: commands/speckit.git.validate.md
      description: "Validate current branch follows feature branch naming conventions"
@@ -137,6 +137,4 @@ tags:
 config:
  defaults:
    branch_numbering: sequential
-    branch_template: ""
-    branch_prefix: ""
    init_commit_message: "[Spec Kit] Initial commit"
--- a/extensions/git/git-config.yml
+++ b/extensions/git/git-config.yml
@@ -4,16 +4,6 @@
 # Branch numbering strategy: "sequential" (001, 002, ...) or "timestamp" (YYYYMMDD-HHMMSS)
 branch_numbering: sequential

-# Optional branch name template. Leave empty for the default "{number}-{slug}".
-# Supported tokens: {author}, {app}, {number}, {slug}
-# {slug} must not appear before {number}; final path segment must start with {number}-.
-# Example for monorepos: "{author}/{app}/{number}-{slug}"
-branch_template: ""
-
-# Optional shorthand namespace. Leave empty to use branch_template/default behavior.
-# Example: "features/{app}" expands to "features/{app}/{number}-{slug}"
-branch_prefix: ""
-
 # Commit message used by `git commit` during repository initialization
 init_commit_message: "[Spec Kit] Initial commit"

--- a/extensions/git/scripts/bash/create-new-feature-branch.sh
+++ b/extensions/git/scripts/bash/create-new-feature-branch.sh
@@ -75,10 +75,6 @@ while [ $i -le $# ]; do
            echo "Environment variables:"
            echo "  GIT_BRANCH_NAME     Use this exact branch name, bypassing all prefix/suffix generation"
            echo ""
-            echo "Configuration:"
-            echo "  branch_template     Optional git-config.yml template with {author}, {app}, {number}, {slug}"
-            echo "  branch_prefix       Optional shorthand namespace expanded before {number}-{slug}"
-            echo ""
            echo "Examples:"
            echo "  $0 'Add user authentication system' --short-name 'user-auth'"
            echo "  $0 'Implement OAuth2 integration for API' --number 5"
@@ -131,28 +127,16 @@ get_highest_from_specs() {

 # Function to get highest number from git branches
 get_highest_from_branches() {
-    local scope_prefix="${1:-}"
-    git branch -a 2>/dev/null | sed -E 's/^[+*][[:space:]]+//; s/^[[:space:]]+//; s|^remotes/[^/]*/||' | _extract_highest_number "$scope_prefix"
+    git branch -a 2>/dev/null | sed -E 's/^[+*][[:space:]]+//; s/^[[:space:]]+//; s|^remotes/[^/]*/||' | _extract_highest_number
 }

 # Extract the highest sequential feature number from a list of ref names (one per line).
 _extract_highest_number() {
-    local scope_prefix="${1:-}"
    local highest=0
    while IFS= read -r name; do
        [ -z "$name" ] && continue
-        if [ -n "$scope_prefix" ]; then
-            case "$name" in
-                "$scope_prefix"*) name="${name#"$scope_prefix"}" ;;
-                *) continue ;;
-            esac
-        fi
-        name="${name##*/}"
-        if echo "$name" | grep -Eq '^[0-9]{3,}-' \
-            && ! echo "$name" | grep -Eq '^[0-9]{8}-[0-9]{6}-' \
-            && ! echo "$name" | grep -Eq '^[0-9]{7}-[0-9]{6}-' \
-            && ! echo "$name" | grep -Eq '^[0-9]{7,8}-[0-9]{6}$'; then
-            number=$(echo "$name" | grep -Eo '^[0-9]{3,}-' | sed -E 's/-$//' || echo "0")
+        if echo "$name" | grep -Eq '^[0-9]{3,}-' && ! echo "$name" | grep -Eq '^[0-9]{8}-[0-9]{6}-'; then
+            number=$(echo "$name" | grep -Eo '^[0-9]+' || echo "0")
            number=$((10#$number))
            if [ "$number" -gt "$highest" ]; then
                highest=$number
@@ -164,12 +148,11 @@ _extract_highest_number() {

 # Function to get highest number from remote branches without fetching (side-effect-free)
 get_highest_from_remote_refs() {
-    local scope_prefix="${1:-}"
    local highest=0

    for remote in $(git remote 2>/dev/null); do
        local remote_highest
-        remote_highest=$(GIT_TERMINAL_PROMPT=0 git ls-remote --heads "$remote" 2>/dev/null | sed 's|.*refs/heads/||' | _extract_highest_number "$scope_prefix")
+        remote_highest=$(GIT_TERMINAL_PROMPT=0 git ls-remote --heads "$remote" 2>/dev/null | sed 's|.*refs/heads/||' | _extract_highest_number)
        if [ "$remote_highest" -gt "$highest" ]; then
            highest=$remote_highest
        fi
@@ -182,17 +165,16 @@ get_highest_from_remote_refs() {
 check_existing_branches() {
    local specs_dir="$1"
    local skip_fetch="${2:-false}"
-    local scope_prefix="${3:-}"

    if [ "$skip_fetch" = true ]; then
-        local highest_remote=$(get_highest_from_remote_refs "$scope_prefix")
-        local highest_branch=$(get_highest_from_branches "$scope_prefix")
+        local highest_remote=$(get_highest_from_remote_refs)
+        local highest_branch=$(get_highest_from_branches)
        if [ "$highest_remote" -gt "$highest_branch" ]; then
            highest_branch=$highest_remote
        fi
    else
        git fetch --all --prune >/dev/null 2>&1 || true
-        local highest_branch=$(get_highest_from_branches "$scope_prefix")
+        local highest_branch=$(get_highest_from_branches)
    fi

    local highest_spec=$(get_highest_from_specs "$specs_dir")
@@ -291,152 +273,6 @@ fi
 cd "$REPO_ROOT"

 SPECS_DIR="$REPO_ROOT/specs"
-CONFIG_FILE="$REPO_ROOT/.specify/extensions/git/git-config.yml"
-
-read_git_config_value() {
-    local key="$1"
-    [ -f "$CONFIG_FILE" ] || return 0
-    grep -E "^[[:space:]]*${key}:" "$CONFIG_FILE" 2>/dev/null \
-        | head -n 1 \
-        | sed -E "s/^[[:space:]]*${key}:[[:space:]]*//" \
-        | sed -E 's/[[:space:]]+#.*$//' \
-        | sed -E 's/^[[:space:]]+|[[:space:]]+$//g' \
-        | sed -E 's/^"//; s/"$//' \
-        | sed -E "s/^'//; s/'$//"
-}
-
-branch_token() {
-    local value="$1"
-    local fallback="$2"
-    local cleaned
-    cleaned=$(clean_branch_name "$value")
-    if [ -n "$cleaned" ]; then
-        printf '%s\n' "$cleaned"
-    else
-        printf '%s\n' "$fallback"
-    fi
-}
-
-get_author_token() {
-    local author=""
-    if command -v git >/dev/null 2>&1; then
-        author=$(git config user.name 2>/dev/null || true)
-        if [ -z "$author" ]; then
-            author=$(git config user.email 2>/dev/null | sed 's/@.*$//' || true)
-        fi
-    fi
-    if [ -z "$author" ]; then
-        author="${USER:-unknown}"
-    fi
-    branch_token "$author" "unknown"
-}
-
-get_app_token() {
-    branch_token "$(basename "$REPO_ROOT")" "app"
-}
-
-resolve_branch_template() {
-    local template
-    local prefix
-    template=$(read_git_config_value "branch_template")
-    if [ -n "$template" ]; then
-        printf '%s\n' "$template"
-        return
-    fi
-
-    prefix=$(read_git_config_value "branch_prefix")
-    if [ -z "$prefix" ]; then
-        printf '%s\n' ""
-        return
-    fi
-    case "$prefix" in
-        */) printf '%s%s\n' "$prefix" "{number}-{slug}" ;;
-        *) printf '%s/%s\n' "$prefix" "{number}-{slug}" ;;
-    esac
-}
-
-render_branch_template() {
-    local template="$1"
-    local feature_num="$2"
-    local branch_suffix="$3"
-    local rendered="$template"
-    rendered=${rendered//\{author\}/$AUTHOR_TOKEN}
-    rendered=${rendered//\{app\}/$APP_TOKEN}
-    rendered=${rendered//\{number\}/$feature_num}
-    rendered=${rendered//\{slug\}/$branch_suffix}
-    printf '%s\n' "$rendered"
-}
-
-validate_branch_template() {
-    local template="$1"
-    [ -n "$template" ] || return 0
-    local feature_segment
-    feature_segment="${template##*/}"
-    case "$template" in
-        *"{number}"*) ;;
-        *)
-            >&2 echo "Error: branch_template must include the {number} token so generated branches remain valid feature branches."
-            exit 1
-            ;;
-    esac
-    case "$template" in
-        *"{slug}"*"{number}"*)
-            >&2 echo "Error: branch_template must not place {slug} before {number}; use {slug} only in the final feature segment."
-            exit 1
-            ;;
-    esac
-    case "$feature_segment" in
-        "{number}-"*) ;;
-        *)
-            >&2 echo "Error: branch_template must put {number}- at the start of the final path segment so generated branches remain valid feature branches."
-            exit 1
-            ;;
-    esac
-}
-
-build_branch_name() {
-    local feature_num="$1"
-    local branch_suffix="$2"
-    if [ -n "$BRANCH_TEMPLATE" ]; then
-        render_branch_template "$BRANCH_TEMPLATE" "$feature_num" "$branch_suffix"
-    else
-        printf '%s-%s\n' "$feature_num" "$branch_suffix"
-    fi
-}
-
-branch_scope_prefix() {
-    local template="$1"
-    local prefix="$template"
-    [ -n "$prefix" ] || return 0
-    case "$prefix" in
-        *"{number}"*) prefix="${prefix%%\{number\}*}" ;;
-        *"{slug}"*) prefix="${prefix%%\{slug\}*}" ;;
-        *) return 0 ;;
-    esac
-    render_branch_template "$prefix" "" "$BRANCH_SUFFIX"
-}
-
-extract_feature_num_from_branch() {
-    local branch_name="$1"
-    local feature_segment="${branch_name##*/}"
-    local match
-    match=$(printf '%s\n' "$feature_segment" | grep -Eo '^[0-9]{8}-[0-9]{6}-' | head -n 1 || true)
-    if [ -n "$match" ]; then
-        printf '%s\n' "$match" | sed -E 's/-$//'
-        return
-    fi
-    match=$(printf '%s\n' "$feature_segment" | grep -Eo '^[0-9]+-' | head -n 1 || true)
-    if [ -n "$match" ]; then
-        printf '%s\n' "$match" | sed -E 's/-$//'
-        return
-    fi
-    printf '%s\n' "$branch_name"
-}
-
-AUTHOR_TOKEN=$(get_author_token)
-APP_TOKEN=$(get_app_token)
-BRANCH_TEMPLATE=$(resolve_branch_template)
-validate_branch_template "$BRANCH_TEMPLATE"

 # Function to generate branch name with stop word filtering
 generate_branch_name() {
@@ -482,8 +318,18 @@ generate_branch_name() {
 # Check for GIT_BRANCH_NAME env var override (exact branch name, no prefix/suffix)
 if [ -n "${GIT_BRANCH_NAME:-}" ]; then
    BRANCH_NAME="$GIT_BRANCH_NAME"
-    FEATURE_NUM=$(extract_feature_num_from_branch "$BRANCH_NAME")
-    BRANCH_SUFFIX="$BRANCH_NAME"
+    # Extract FEATURE_NUM from the branch name if it starts with a numeric prefix
+    # Check timestamp pattern first (YYYYMMDD-HHMMSS-) since it also matches the simpler ^[0-9]+ pattern
+    if echo "$BRANCH_NAME" | grep -Eq '^[0-9]{8}-[0-9]{6}-'; then
+        FEATURE_NUM=$(echo "$BRANCH_NAME" | grep -Eo '^[0-9]{8}-[0-9]{6}')
+        BRANCH_SUFFIX="${BRANCH_NAME#${FEATURE_NUM}-}"
+    elif echo "$BRANCH_NAME" | grep -Eq '^[0-9]+-'; then
+        FEATURE_NUM=$(echo "$BRANCH_NAME" | grep -Eo '^[0-9]+')
+        BRANCH_SUFFIX="${BRANCH_NAME#${FEATURE_NUM}-}"
+    else
+        FEATURE_NUM="$BRANCH_NAME"
+        BRANCH_SUFFIX="$BRANCH_NAME"
+    fi
 else
    # Generate branch name
    if [ -n "$SHORT_NAME" ]; then
@@ -501,17 +347,16 @@ else
    # Determine branch prefix
    if [ "$USE_TIMESTAMP" = true ]; then
        FEATURE_NUM=$(date +%Y%m%d-%H%M%S)
-        BRANCH_NAME=$(build_branch_name "$FEATURE_NUM" "$BRANCH_SUFFIX")
+        BRANCH_NAME="${FEATURE_NUM}-${BRANCH_SUFFIX}"
    else
-        BRANCH_SCOPE_PREFIX=$(branch_scope_prefix "$BRANCH_TEMPLATE")
        if [ -z "$BRANCH_NUMBER" ]; then
            if [ "$DRY_RUN" = true ] && [ "$HAS_GIT" = true ]; then
-                BRANCH_NUMBER=$(check_existing_branches "$SPECS_DIR" true "$BRANCH_SCOPE_PREFIX")
+                BRANCH_NUMBER=$(check_existing_branches "$SPECS_DIR" true)
            elif [ "$DRY_RUN" = true ]; then
                HIGHEST=$(get_highest_from_specs "$SPECS_DIR")
                BRANCH_NUMBER=$((HIGHEST + 1))
            elif [ "$HAS_GIT" = true ]; then
-                BRANCH_NUMBER=$(check_existing_branches "$SPECS_DIR" false "$BRANCH_SCOPE_PREFIX")
+                BRANCH_NUMBER=$(check_existing_branches "$SPECS_DIR")
            else
                HIGHEST=$(get_highest_from_specs "$SPECS_DIR")
                BRANCH_NUMBER=$((HIGHEST + 1))
@@ -519,7 +364,7 @@ else
        fi

        FEATURE_NUM=$(printf "%03d" "$((10#$BRANCH_NUMBER))")
-        BRANCH_NAME=$(build_branch_name "$FEATURE_NUM" "$BRANCH_SUFFIX")
+        BRANCH_NAME="${FEATURE_NUM}-${BRANCH_SUFFIX}"
    fi
 fi

@@ -531,23 +376,18 @@ if [ -n "${GIT_BRANCH_NAME:-}" ] && [ "$BRANCH_BYTE_LEN" -gt $MAX_BRANCH_LENGTH
    >&2 echo "Error: GIT_BRANCH_NAME must be 244 bytes or fewer in UTF-8. Provided value is ${BRANCH_BYTE_LEN} bytes."
    exit 1
 elif [ "$BRANCH_BYTE_LEN" -gt $MAX_BRANCH_LENGTH ]; then
+    PREFIX_LENGTH=$(( ${#FEATURE_NUM} + 1 ))
+    MAX_SUFFIX_LENGTH=$((MAX_BRANCH_LENGTH - PREFIX_LENGTH))
+
+    TRUNCATED_SUFFIX=$(echo "$BRANCH_SUFFIX" | cut -c1-$MAX_SUFFIX_LENGTH)
+    TRUNCATED_SUFFIX=$(echo "$TRUNCATED_SUFFIX" | sed 's/-$//')
+
    ORIGINAL_BRANCH_NAME="$BRANCH_NAME"
-    TRUNCATED_SUFFIX="$BRANCH_SUFFIX"
-    while [ "$(_byte_length "$BRANCH_NAME")" -gt "$MAX_BRANCH_LENGTH" ] && [ -n "$TRUNCATED_SUFFIX" ]; do
-        TRUNCATED_SUFFIX="${TRUNCATED_SUFFIX%?}"
-        TRUNCATED_SUFFIX="${TRUNCATED_SUFFIX%-}"
-        BRANCH_NAME=$(build_branch_name "$FEATURE_NUM" "$TRUNCATED_SUFFIX")
-    done
-    if [ "$(_byte_length "$BRANCH_NAME")" -gt "$MAX_BRANCH_LENGTH" ]; then
-        >&2 echo "Error: Branch template prefix exceeds GitHub's 244-byte branch name limit."
-        exit 1
-    fi
+    BRANCH_NAME="${FEATURE_NUM}-${TRUNCATED_SUFFIX}"

    >&2 echo "[specify] Warning: Branch name exceeded GitHub's 244-byte limit"
-    ORIGINAL_BRANCH_BYTE_LEN=$(_byte_length "$ORIGINAL_BRANCH_NAME")
-    TRUNCATED_BRANCH_BYTE_LEN=$(_byte_length "$BRANCH_NAME")
-    >&2 echo "[specify] Original: $ORIGINAL_BRANCH_NAME (${ORIGINAL_BRANCH_BYTE_LEN} bytes)"
-    >&2 echo "[specify] Truncated to: $BRANCH_NAME (${TRUNCATED_BRANCH_BYTE_LEN} bytes)"
+    >&2 echo "[specify] Original: $ORIGINAL_BRANCH_NAME (${#ORIGINAL_BRANCH_NAME} bytes)"
+    >&2 echo "[specify] Truncated to: $BRANCH_NAME (${#BRANCH_NAME} bytes)"
 fi

 if [ "$DRY_RUN" != true ]; then
--- a/extensions/git/scripts/bash/git-common.sh
+++ b/extensions/git/scripts/bash/git-common.sh
@@ -23,9 +23,8 @@ spec_kit_effective_branch_name() {
 }

 # Validate that a branch name matches the expected feature branch pattern.
-# Accepts sequential (###-* with >=3 digits) or timestamp (YYYYMMDD-HHMMSS-*) formats,
-# either at the start of the branch or after path-style namespace prefixes.
-# Logic aligned with the git extension's PowerShell Test-FeatureBranch twin.
+# Accepts sequential (###-* with >=3 digits) or timestamp (YYYYMMDD-HHMMSS-*) formats.
+# Logic aligned with scripts/bash/common.sh check_feature_branch after effective-name normalization.
 check_feature_branch() {
    local raw="$1"
    local has_git_repo="$2"
@@ -38,17 +37,16 @@ check_feature_branch() {

    local branch
    branch=$(spec_kit_effective_branch_name "$raw")
-    local feature_segment="${branch##*/}"

    # Accept sequential prefix (3+ digits) but exclude malformed timestamps
    # Malformed: 7-or-8 digit date + 6-digit time with no trailing slug (e.g. "2026031-143022" or "20260319-143022")
    local is_sequential=false
-    if [[ "$feature_segment" =~ ^[0-9]{3,}- ]] && [[ ! "$feature_segment" =~ ^[0-9]{7}-[0-9]{6}- ]] && [[ ! "$feature_segment" =~ ^[0-9]{7,8}-[0-9]{6}$ ]]; then
+    if [[ "$branch" =~ ^[0-9]{3,}- ]] && [[ ! "$branch" =~ ^[0-9]{7}-[0-9]{6}- ]] && [[ ! "$branch" =~ ^[0-9]{7,8}-[0-9]{6}$ ]]; then
        is_sequential=true
    fi
-    if [[ "$is_sequential" != "true" ]] && [[ ! "$feature_segment" =~ ^[0-9]{8}-[0-9]{6}- ]]; then
+    if [[ "$is_sequential" != "true" ]] && [[ ! "$branch" =~ ^[0-9]{8}-[0-9]{6}- ]]; then
        echo "ERROR: Not on a feature branch. Current branch: $raw" >&2
-        echo "Feature branches should be named like: 001-feature-name, 1234-feature-name, 20260319-143022-feature-name, or <prefix>/001-feature-name" >&2
+        echo "Feature branches should be named like: 001-feature-name, 1234-feature-name, or 20260319-143022-feature-name" >&2
        return 1
    fi

--- a/extensions/git/scripts/powershell/create-new-feature-branch.ps1
+++ b/extensions/git/scripts/powershell/create-new-feature-branch.ps1
@@ -34,10 +34,6 @@ if ($Help) {
    Write-Host "Environment variables:"
    Write-Host "  GIT_BRANCH_NAME     Use this exact branch name, bypassing all prefix/suffix generation"
    Write-Host ""
-    Write-Host "Configuration:"
-    Write-Host "  branch_template     Optional git-config.yml template with {author}, {app}, {number}, {slug}"
-    Write-Host "  branch_prefix       Optional shorthand namespace expanded before {number}-{slug}"
-    Write-Host ""
    exit 0
 }

@@ -71,23 +67,11 @@ function Get-HighestNumberFromSpecs {
 }

 function Get-HighestNumberFromNames {
-    param(
-        [string[]]$Names,
-        [string]$ScopePrefix = ''
-    )
+    param([string[]]$Names)

    [long]$highest = 0
    foreach ($name in $Names) {
-        if ($ScopePrefix -and -not $name.StartsWith($ScopePrefix, [System.StringComparison]::Ordinal)) {
-            continue
-        }
-        if ($ScopePrefix) {
-            $name = $name.Substring($ScopePrefix.Length)
-        }
-        $name = ($name -split '/')[-1]
-        $hasTimestampPrefix = $name -match '^\d{8}-\d{6}-'
-        $hasMalformedTimestamp = ($name -match '^\d{7}-\d{6}-') -or ($name -match '^(?:\d{7}|\d{8})-\d{6}$')
-        if ($name -match '^(\d{3,})-' -and -not $hasTimestampPrefix -and -not $hasMalformedTimestamp) {
+        if ($name -match '^(\d{3,})-' -and $name -notmatch '^\d{8}-\d{6}-') {
            [long]$num = 0
            if ([long]::TryParse($matches[1], [ref]$num) -and $num -gt $highest) {
                $highest = $num
@@ -98,7 +82,7 @@ function Get-HighestNumberFromNames {
 }

 function Get-HighestNumberFromBranches {
-    param([string]$ScopePrefix = '')
+    param()

    try {
        $branches = git branch -a 2>$null
@@ -106,7 +90,7 @@ function Get-HighestNumberFromBranches {
            $cleanNames = $branches | ForEach-Object {
                $_.Trim() -replace '^[+*]?\s+', '' -replace '^remotes/[^/]+/', ''
            }
-            return Get-HighestNumberFromNames -Names $cleanNames -ScopePrefix $ScopePrefix
+            return Get-HighestNumberFromNames -Names $cleanNames
        }
    } catch {
        Write-Verbose "Could not check Git branches: $_"
@@ -115,8 +99,6 @@ function Get-HighestNumberFromBranches {
 }

 function Get-HighestNumberFromRemoteRefs {
-    param([string]$ScopePrefix = '')
-
    [long]$highest = 0
    try {
        $remotes = git remote 2>$null
@@ -129,7 +111,7 @@ function Get-HighestNumberFromRemoteRefs {
                    $refNames = $refs | ForEach-Object {
                        if ($_ -match 'refs/heads/(.+)$') { $matches[1] }
                    } | Where-Object { $_ }
-                    $remoteHighest = Get-HighestNumberFromNames -Names $refNames -ScopePrefix $ScopePrefix
+                    $remoteHighest = Get-HighestNumberFromNames -Names $refNames
                    if ($remoteHighest -gt $highest) { $highest = $remoteHighest }
                }
            }
@@ -143,19 +125,18 @@ function Get-HighestNumberFromRemoteRefs {
 function Get-NextBranchNumber {
    param(
        [string]$SpecsDir,
-        [switch]$SkipFetch,
-        [string]$ScopePrefix = ''
+        [switch]$SkipFetch
    )

    if ($SkipFetch) {
-        $highestBranch = Get-HighestNumberFromBranches -ScopePrefix $ScopePrefix
-        $highestRemote = Get-HighestNumberFromRemoteRefs -ScopePrefix $ScopePrefix
+        $highestBranch = Get-HighestNumberFromBranches
+        $highestRemote = Get-HighestNumberFromRemoteRefs
        $highestBranch = [Math]::Max($highestBranch, $highestRemote)
    } else {
        try {
            git fetch --all --prune 2>$null | Out-Null
        } catch { }
-        $highestBranch = Get-HighestNumberFromBranches -ScopePrefix $ScopePrefix
+        $highestBranch = Get-HighestNumberFromBranches
    }

    $highestSpec = Get-HighestNumberFromSpecs -SpecsDir $SpecsDir
@@ -251,145 +232,6 @@ if (Get-Command Test-HasGit -ErrorAction SilentlyContinue) {
 Set-Location $repoRoot

 $specsDir = Join-Path $repoRoot 'specs'
-$configFile = Join-Path $repoRoot ".specify/extensions/git/git-config.yml"
-
-function Read-GitConfigValue {
-    param([string]$Key)
-
-    if (-not (Test-Path -LiteralPath $configFile -PathType Leaf)) { return '' }
-    $escapedKey = [regex]::Escape($Key)
-    foreach ($line in Get-Content -LiteralPath $configFile) {
-        if ($line -match "^\s*$escapedKey\s*:\s*(.*)$") {
-            $val = ($matches[1] -replace '\s+#.*$', '').Trim()
-            $val = $val -replace '^["'']', '' -replace '["'']$', ''
-            return $val
-        }
-    }
-    return ''
-}
-
-function ConvertTo-BranchToken {
-    param(
-        [string]$Value,
-        [string]$Fallback
-    )
-
-    $cleaned = ConvertTo-CleanBranchName -Name $Value
-    if ($cleaned) { return $cleaned }
-    return $Fallback
-}
-
-function Get-GitAuthorToken {
-    $author = ''
-    if (Get-Command git -ErrorAction SilentlyContinue) {
-        try { $author = (git config user.name 2>$null | Out-String).Trim() } catch {}
-        if (-not $author) {
-            try {
-                $email = (git config user.email 2>$null | Out-String).Trim()
-                if ($email) { $author = ($email -split '@')[0] }
-            } catch {}
-        }
-    }
-    if (-not $author) { $author = if ($env:USER) { $env:USER } elseif ($env:USERNAME) { $env:USERNAME } else { 'unknown' } }
-    return ConvertTo-BranchToken -Value $author -Fallback 'unknown'
-}
-
-function Get-AppToken {
-    return ConvertTo-BranchToken -Value (Split-Path $repoRoot -Leaf) -Fallback 'app'
-}
-
-function Resolve-BranchTemplate {
-    $template = Read-GitConfigValue -Key 'branch_template'
-    if ($template) { return $template }
-
-    $prefix = Read-GitConfigValue -Key 'branch_prefix'
-    if (-not $prefix) { return '' }
-    if ($prefix.EndsWith('/')) { return "${prefix}{number}-{slug}" }
-    return "$prefix/{number}-{slug}"
-}
-
-function Expand-BranchTemplate {
-    param(
-        [string]$Template,
-        [string]$FeatureNum,
-        [string]$BranchSuffix
-    )
-
-    $rendered = $Template.Replace('{author}', $authorToken)
-    $rendered = $rendered.Replace('{app}', $appToken)
-    $rendered = $rendered.Replace('{number}', $FeatureNum)
-    $rendered = $rendered.Replace('{slug}', $BranchSuffix)
-    return $rendered
-}
-
-function Assert-BranchTemplateValid {
-    param([string]$Template)
-
-    if ($Template -and -not $Template.Contains('{number}')) {
-        throw "branch_template must include the {number} token so generated branches remain valid feature branches."
-    }
-    if ($Template) {
-        $numberIndex = $Template.IndexOf('{number}', [System.StringComparison]::Ordinal)
-        $slugIndex = $Template.IndexOf('{slug}', [System.StringComparison]::Ordinal)
-        if ($slugIndex -ge 0 -and $slugIndex -lt $numberIndex) {
-            throw "branch_template must not place {slug} before {number}; use {slug} only in the final feature segment."
-        }
-        $featureSegment = ($Template -split '/')[-1]
-        if (-not $featureSegment.StartsWith('{number}-', [System.StringComparison]::Ordinal)) {
-            throw "branch_template must put {number}- at the start of the final path segment so generated branches remain valid feature branches."
-        }
-    }
-}
-
-function New-BranchName {
-    param(
-        [string]$FeatureNum,
-        [string]$BranchSuffix
-    )
-
-    if ($branchTemplate) {
-        return Expand-BranchTemplate -Template $branchTemplate -FeatureNum $FeatureNum -BranchSuffix $BranchSuffix
-    }
-    return "$FeatureNum-$BranchSuffix"
-}
-
-function Get-BranchScopePrefix {
-    param(
-        [string]$Template,
-        [string]$BranchSuffix
-    )
-
-    if (-not $Template) { return '' }
-    $numberIndex = $Template.IndexOf('{number}', [System.StringComparison]::Ordinal)
-    $slugIndex = $Template.IndexOf('{slug}', [System.StringComparison]::Ordinal)
-    $indexes = @($numberIndex, $slugIndex) | Where-Object { $_ -ge 0 } | Sort-Object
-    if (-not $indexes) { return '' }
-    $prefix = $Template.Substring(0, $indexes[0])
-    return Expand-BranchTemplate -Template $prefix -FeatureNum '' -BranchSuffix $BranchSuffix
-}
-
-function Get-FeatureNumberFromBranchName {
-    param([string]$BranchName)
-
-    $featureSegment = ($BranchName -split '/')[-1]
-    if ($featureSegment -match '^(\d{8}-\d{6})-') {
-        return $matches[1]
-    }
-    if ($featureSegment -match '^(\d+)-') {
-        return $matches[1]
-    }
-    return $BranchName
-}
-
-function Get-Utf8ByteCount {
-    param([string]$Value)
-    return [System.Text.Encoding]::UTF8.GetByteCount($Value)
-}
-
-$authorToken = Get-GitAuthorToken
-$appToken = Get-AppToken
-$branchTemplate = Resolve-BranchTemplate
-Assert-BranchTemplateValid -Template $branchTemplate

 function Get-BranchName {
    param([string]$Description)
@@ -434,11 +276,19 @@ function Get-BranchName {
 if ($env:GIT_BRANCH_NAME) {
    $branchName = $env:GIT_BRANCH_NAME
    # Check 244-byte limit (UTF-8) for override names
-    $branchNameUtf8ByteCount = Get-Utf8ByteCount -Value $branchName
+    $branchNameUtf8ByteCount = [System.Text.Encoding]::UTF8.GetByteCount($branchName)
    if ($branchNameUtf8ByteCount -gt 244) {
        throw "GIT_BRANCH_NAME must be 244 bytes or fewer in UTF-8. Provided value is $branchNameUtf8ByteCount bytes; please supply a shorter override branch name."
    }
-    $featureNum = Get-FeatureNumberFromBranchName -BranchName $branchName
+    # Extract FEATURE_NUM from the branch name if it starts with a numeric prefix
+    # Check timestamp pattern first (YYYYMMDD-HHMMSS-) since it also matches the simpler ^\d+ pattern
+    if ($branchName -match '^(\d{8}-\d{6})-') {
+        $featureNum = $matches[1]
+    } elseif ($branchName -match '^(\d+)-') {
+        $featureNum = $matches[1]
+    } else {
+        $featureNum = $branchName
+    }
 } else {
    if ($ShortName) {
        $branchSuffix = ConvertTo-CleanBranchName -Name $ShortName
@@ -453,41 +303,39 @@ if ($env:GIT_BRANCH_NAME) {

    if ($Timestamp) {
        $featureNum = Get-Date -Format 'yyyyMMdd-HHmmss'
-        $branchName = New-BranchName -FeatureNum $featureNum -BranchSuffix $branchSuffix
+        $branchName = "$featureNum-$branchSuffix"
    } else {
-        $branchScopePrefix = Get-BranchScopePrefix -Template $branchTemplate -BranchSuffix $branchSuffix
        if ($Number -eq 0) {
            if ($DryRun -and $hasGit) {
-                $Number = Get-NextBranchNumber -SpecsDir $specsDir -SkipFetch -ScopePrefix $branchScopePrefix
+                $Number = Get-NextBranchNumber -SpecsDir $specsDir -SkipFetch
            } elseif ($DryRun) {
                $Number = (Get-HighestNumberFromSpecs -SpecsDir $specsDir) + 1
            } elseif ($hasGit) {
-                $Number = Get-NextBranchNumber -SpecsDir $specsDir -ScopePrefix $branchScopePrefix
+                $Number = Get-NextBranchNumber -SpecsDir $specsDir
            } else {
                $Number = (Get-HighestNumberFromSpecs -SpecsDir $specsDir) + 1
            }
        }

        $featureNum = ('{0:000}' -f $Number)
-        $branchName = New-BranchName -FeatureNum $featureNum -BranchSuffix $branchSuffix
+        $branchName = "$featureNum-$branchSuffix"
    }
 }

 $maxBranchLength = 244
-if ((Get-Utf8ByteCount -Value $branchName) -gt $maxBranchLength) {
+if ($branchName.Length -gt $maxBranchLength) {
+    $prefixLength = $featureNum.Length + 1
+    $maxSuffixLength = $maxBranchLength - $prefixLength
+
+    $truncatedSuffix = $branchSuffix.Substring(0, [Math]::Min($branchSuffix.Length, $maxSuffixLength))
+    $truncatedSuffix = $truncatedSuffix -replace '-$', ''
+
    $originalBranchName = $branchName
-    $truncatedSuffix = $branchSuffix
-    while ((Get-Utf8ByteCount -Value $branchName) -gt $maxBranchLength -and $truncatedSuffix.Length -gt 0) {
-        $truncatedSuffix = $truncatedSuffix.Substring(0, $truncatedSuffix.Length - 1) -replace '-$', ''
-        $branchName = New-BranchName -FeatureNum $featureNum -BranchSuffix $truncatedSuffix
-    }
-    if ((Get-Utf8ByteCount -Value $branchName) -gt $maxBranchLength) {
-        throw "Branch template prefix exceeds GitHub's 244-byte branch name limit."
-    }
+    $branchName = "$featureNum-$truncatedSuffix"

    Write-Warning "[specify] Branch name exceeded GitHub's 244-byte limit"
-    Write-Warning "[specify] Original: $originalBranchName ($(Get-Utf8ByteCount -Value $originalBranchName) bytes)"
-    Write-Warning "[specify] Truncated to: $branchName ($(Get-Utf8ByteCount -Value $branchName) bytes)"
+    Write-Warning "[specify] Original: $originalBranchName ($($originalBranchName.Length) bytes)"
+    Write-Warning "[specify] Truncated to: $branchName ($($branchName.Length) bytes)"
 }

 if (-not $DryRun) {
--- a/extensions/git/scripts/powershell/git-common.ps1
+++ b/extensions/git/scripts/powershell/git-common.ps1
@@ -37,15 +37,14 @@ function Test-FeatureBranch {

    $raw = $Branch
    $Branch = Get-SpecKitEffectiveBranchName $raw
-    $featureSegment = ($Branch -split '/')[-1]

-    # Accept sequential prefix (3+ digits), at the start or after namespace
-    # segments, but exclude malformed timestamps.
-    $hasMalformedTimestamp = ($featureSegment -match '^[0-9]{7}-[0-9]{6}-') -or ($featureSegment -match '^(?:\d{7}|\d{8})-\d{6}$')
-    $isSequential = ($featureSegment -match '^[0-9]{3,}-') -and (-not $hasMalformedTimestamp)
-    if (-not $isSequential -and $featureSegment -notmatch '^\d{8}-\d{6}-') {
+    # Accept sequential prefix (3+ digits) but exclude malformed timestamps
+    # Malformed: 7-or-8 digit date + 6-digit time with no trailing slug (e.g. "2026031-143022" or "20260319-143022")
+    $hasMalformedTimestamp = ($Branch -match '^[0-9]{7}-[0-9]{6}-') -or ($Branch -match '^(?:\d{7}|\d{8})-\d{6}$')
+    $isSequential = ($Branch -match '^[0-9]{3,}-') -and (-not $hasMalformedTimestamp)
+    if (-not $isSequential -and $Branch -notmatch '^\d{8}-\d{6}-') {
        [Console]::Error.WriteLine("ERROR: Not on a feature branch. Current branch: $raw")
-        [Console]::Error.WriteLine("Feature branches should be named like: 001-feature-name, 1234-feature-name, 20260319-143022-feature-name, or <prefix>/001-feature-name")
+        [Console]::Error.WriteLine("Feature branches should be named like: 001-feature-name, 1234-feature-name, or 20260319-143022-feature-name")
        return $false
    }
    return $true
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "specify-cli"
-version = "0.12.7"
+version = "0.12.5.dev0"
 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"
--- a/scripts/python/check_prerequisites.py
+++ b/scripts/python/check_prerequisites.py
@@ -1,207 +0,0 @@
-#!/usr/bin/env python3
-"""Consolidated prerequisite checking script."""
-
-from __future__ import annotations
-
-import json
-import sys
-from dataclasses import dataclass
-from pathlib import Path
-
-try:
-    from common import FeaturePaths, format_speckit_command, get_feature_paths
-except ImportError:  # pragma: no cover - direct execution from unusual cwd
-    sys.path.insert(0, str(Path(__file__).resolve().parent))
-    from common import FeaturePaths, format_speckit_command, get_feature_paths
-
-
-def _json_line(payload: object) -> str:
-    return json.dumps(payload, ensure_ascii=False, separators=(",", ":")) + "\n"
-
-
-HELP_TEXT = """Usage: check_prerequisites.py [OPTIONS]
-
-Consolidated prerequisite checking for Spec-Driven Development workflow.
-
-OPTIONS:
-  --json              Output in JSON format
-  --require-tasks     Require tasks.md to exist (for implementation phase)
-  --include-tasks     Include tasks.md in AVAILABLE_DOCS list
-  --paths-only        Only output path variables (no prerequisite validation)
-  --help, -h          Show this help message
-
-EXAMPLES:
-  # Check task prerequisites (plan.md required)
-  ./check_prerequisites.py --json
-
-  # Check implementation prerequisites (plan.md + tasks.md required)
-  ./check_prerequisites.py --json --require-tasks --include-tasks
-
-  # Get feature paths only (no validation)
-  ./check_prerequisites.py --paths-only
-
-"""
-
-
-@dataclass(frozen=True)
-class Args:
-    json_mode: bool = False
-    require_tasks: bool = False
-    include_tasks: bool = False
-    paths_only: bool = False
-
-
-def _parse_args(argv: list[str]) -> Args:
-    json_mode = False
-    require_tasks = False
-    include_tasks = False
-    paths_only = False
-
-    for arg in argv:
-        if arg == "--json":
-            json_mode = True
-        elif arg == "--require-tasks":
-            require_tasks = True
-        elif arg == "--include-tasks":
-            include_tasks = True
-        elif arg == "--paths-only":
-            paths_only = True
-        elif arg in {"--help", "-h"}:
-            sys.stdout.write(HELP_TEXT)
-            raise SystemExit(0)
-        else:
-            print(
-                f"ERROR: Unknown option '{arg}'. Use --help for usage information.",
-                file=sys.stderr,
-            )
-            raise SystemExit(1)
-
-    return Args(
-        json_mode=json_mode,
-        require_tasks=require_tasks,
-        include_tasks=include_tasks,
-        paths_only=paths_only,
-    )
-
-
-def _dir_has_entries(path: Path) -> bool:
-    try:
-        return path.is_dir() and any(path.iterdir())
-    except OSError:
-        return False
-
-
-def _available_docs(paths: FeaturePaths, include_tasks: bool) -> list[str]:
-    docs: list[str] = []
-    if paths.research.is_file():
-        docs.append("research.md")
-    if paths.data_model.is_file():
-        docs.append("data-model.md")
-    if _dir_has_entries(paths.contracts_dir):
-        docs.append("contracts/")
-    if paths.quickstart.is_file():
-        docs.append("quickstart.md")
-    if include_tasks and paths.tasks.is_file():
-        docs.append("tasks.md")
-    return docs
-
-
-def _print_paths_only(paths: FeaturePaths, json_mode: bool) -> None:
-    if json_mode:
-        sys.stdout.write(
-            _json_line(
-                {
-                    "REPO_ROOT": str(paths.repo_root),
-                    "BRANCH": paths.current_branch,
-                    "FEATURE_DIR": str(paths.feature_dir),
-                    "FEATURE_SPEC": str(paths.feature_spec),
-                    "IMPL_PLAN": str(paths.impl_plan),
-                    "TASKS": str(paths.tasks),
-                }
-            )
-        )
-        return
-
-    print(f"REPO_ROOT: {paths.repo_root}")
-    print(f"BRANCH: {paths.current_branch}")
-    print(f"FEATURE_DIR: {paths.feature_dir}")
-    print(f"FEATURE_SPEC: {paths.feature_spec}")
-    print(f"IMPL_PLAN: {paths.impl_plan}")
-    print(f"TASKS: {paths.tasks}")
-
-
-def _check_file(path: Path, description: str) -> None:
-    marker = "✓" if path.is_file() else "✗"
-    print(f"  {marker} {description}")
-
-
-def _check_dir(path: Path, description: str) -> None:
-    marker = "✓" if _dir_has_entries(path) else "✗"
-    print(f"  {marker} {description}")
-
-
-def _print_text_results(paths: FeaturePaths, include_tasks: bool) -> None:
-    print(f"FEATURE_DIR:{paths.feature_dir}")
-    print("AVAILABLE_DOCS:")
-    _check_file(paths.research, "research.md")
-    _check_file(paths.data_model, "data-model.md")
-    _check_dir(paths.contracts_dir, "contracts/")
-    _check_file(paths.quickstart, "quickstart.md")
-    if include_tasks:
-        _check_file(paths.tasks, "tasks.md")
-
-
-def main(argv: list[str] | None = None) -> int:
-    args = _parse_args(list(argv if argv is not None else sys.argv[1:]))
-
-    try:
-        paths = get_feature_paths(
-            no_persist=args.paths_only,
-            script_file=Path(__file__),
-        )
-    except SystemExit as exc:
-        if exc.code == 0:
-            return 0
-        print("ERROR: Failed to resolve feature paths", file=sys.stderr)
-        return int(exc.code) if isinstance(exc.code, int) else 1
-
-    if args.paths_only:
-        _print_paths_only(paths, args.json_mode)
-        return 0
-
-    if not paths.feature_dir.is_dir():
-        print(f"ERROR: Feature directory not found: {paths.feature_dir}", file=sys.stderr)
-        print(
-            f"Run {format_speckit_command('specify', paths.repo_root)} first to create the feature structure.",
-            file=sys.stderr,
-        )
-        return 1
-
-    if not paths.impl_plan.is_file():
-        print(f"ERROR: plan.md not found in {paths.feature_dir}", file=sys.stderr)
-        print(
-            f"Run {format_speckit_command('plan', paths.repo_root)} first to create the implementation plan.",
-            file=sys.stderr,
-        )
-        return 1
-
-    if args.require_tasks and not paths.tasks.is_file():
-        print(f"ERROR: tasks.md not found in {paths.feature_dir}", file=sys.stderr)
-        print(
-            f"Run {format_speckit_command('tasks', paths.repo_root)} first to create the task list.",
-            file=sys.stderr,
-        )
-        return 1
-
-    docs = _available_docs(paths, args.include_tasks)
-    if args.json_mode:
-        sys.stdout.write(
-            _json_line({"FEATURE_DIR": str(paths.feature_dir), "AVAILABLE_DOCS": docs})
-        )
-    else:
-        _print_text_results(paths, args.include_tasks)
-    return 0
-
-
-if __name__ == "__main__":
-    raise SystemExit(main())
--- a/scripts/python/common.py
+++ b/scripts/python/common.py
@@ -1,210 +0,0 @@
-"""Shared helpers for Spec Kit Python scripts."""
-
-from __future__ import annotations
-
-import json
-import os
-import sys
-from dataclasses import dataclass
-from pathlib import Path
-
-
-def _trim_trailing_separators(value: Path) -> str:
-    text = str(value)
-    while len(text) > 1 and text.endswith((os.sep, "/")):
-        text = text[:-1]
-    return text
-
-
-def find_specify_root(start_dir: Path | None = None) -> Path | None:
-    current = (start_dir or Path.cwd()).resolve()
-    while True:
-        if (current / ".specify").is_dir():
-            return current
-        parent = current.parent
-        if parent == current:
-            return None
-        current = parent
-
-
-def resolve_specify_init_dir() -> Path:
-    raw = os.environ.get("SPECIFY_INIT_DIR", "")
-    candidate = Path(raw)
-    if not candidate.is_absolute():
-        candidate = Path.cwd() / candidate
-    try:
-        init_root = candidate.resolve(strict=True)
-    except OSError:
-        print(
-            f"ERROR: SPECIFY_INIT_DIR does not point to an existing directory: {raw}",
-            file=sys.stderr,
-        )
-        raise SystemExit(1)
-    if not init_root.is_dir():
-        print(
-            f"ERROR: SPECIFY_INIT_DIR does not point to an existing directory: {raw}",
-            file=sys.stderr,
-        )
-        raise SystemExit(1)
-    if not (init_root / ".specify").is_dir():
-        print(
-            "ERROR: SPECIFY_INIT_DIR is not a Spec Kit project "
-            f"(no .specify/ directory): {init_root}",
-            file=sys.stderr,
-        )
-        raise SystemExit(1)
-    return init_root
-
-
-def get_repo_root(script_file: Path | None = None) -> Path:
-    if os.environ.get("SPECIFY_INIT_DIR"):
-        return resolve_specify_init_dir()
-
-    specify_root = find_specify_root()
-    if specify_root is not None:
-        return specify_root
-
-    if script_file is not None:
-        script_root = find_specify_root(script_file.resolve().parent)
-        if script_root is not None:
-            return script_root
-
-        # Installed scripts live at .specify/scripts/python/<script>.py.
-        return script_file.resolve().parents[3]
-    return Path.cwd().resolve()
-
-
-def get_current_branch() -> str:
-    return os.environ.get("SPECIFY_FEATURE", "")
-
-
-def read_feature_json_feature_directory(repo_root: Path) -> str:
-    feature_json = repo_root / ".specify" / "feature.json"
-    if not feature_json.is_file():
-        return ""
-    try:
-        data = json.loads(feature_json.read_text(encoding="utf-8"))
-    except (OSError, json.JSONDecodeError):
-        return ""
-    value = data.get("feature_directory") if isinstance(data, dict) else None
-    return value if isinstance(value, str) else ""
-
-
-def _json_dump(data: dict[str, str]) -> str:
-    return json.dumps(data, ensure_ascii=False, separators=(",", ":")) + "\n"
-
-
-def persist_feature_json(repo_root: Path, feature_dir_value: str) -> None:
-    value = feature_dir_value
-    try:
-        relative = Path(value)
-        if relative.is_absolute():
-            try:
-                value = relative.resolve().relative_to(repo_root.resolve()).as_posix()
-            except ValueError:
-                value = str(relative)
-    except OSError:
-        pass
-
-    current = read_feature_json_feature_directory(repo_root)
-    if current == value:
-        return
-
-    specify_dir = repo_root / ".specify"
-    specify_dir.mkdir(parents=True, exist_ok=True)
-    (specify_dir / "feature.json").write_text(
-        _json_dump({"feature_directory": value}),
-        encoding="utf-8",
-    )
-
-
-@dataclass(frozen=True)
-class FeaturePaths:
-    repo_root: Path
-    current_branch: str
-    feature_dir: Path
-    feature_spec: Path
-    impl_plan: Path
-    tasks: Path
-    research: Path
-    data_model: Path
-    quickstart: Path
-    contracts_dir: Path
-
-
-def get_feature_paths(
-    *, no_persist: bool = False, script_file: Path | None = None
-) -> FeaturePaths:
-    repo_root = get_repo_root(script_file)
-    current_branch = get_current_branch()
-
-    feature_dir_raw = os.environ.get("SPECIFY_FEATURE_DIRECTORY", "")
-    if feature_dir_raw:
-        feature_dir = Path(feature_dir_raw)
-        if not feature_dir.is_absolute():
-            feature_dir = repo_root / feature_dir
-        if not no_persist:
-            persist_feature_json(repo_root, feature_dir_raw)
-    elif (repo_root / ".specify" / "feature.json").is_file():
-        stored = read_feature_json_feature_directory(repo_root)
-        if not stored:
-            print(
-                "ERROR: Feature directory not found. Set SPECIFY_FEATURE_DIRECTORY "
-                "or ensure .specify/feature.json contains feature_directory.",
-                file=sys.stderr,
-            )
-            raise SystemExit(1)
-        feature_dir = Path(stored)
-        if not feature_dir.is_absolute():
-            feature_dir = repo_root / feature_dir
-    else:
-        print(
-            "ERROR: Feature directory not found. Set SPECIFY_FEATURE_DIRECTORY "
-            "or run the specify command to create .specify/feature.json.",
-            file=sys.stderr,
-        )
-        raise SystemExit(1)
-
-    if not current_branch:
-        current_branch = Path(_trim_trailing_separators(feature_dir)).name
-
-    return FeaturePaths(
-        repo_root=repo_root,
-        current_branch=current_branch,
-        feature_dir=feature_dir,
-        feature_spec=feature_dir / "spec.md",
-        impl_plan=feature_dir / "plan.md",
-        tasks=feature_dir / "tasks.md",
-        research=feature_dir / "research.md",
-        data_model=feature_dir / "data-model.md",
-        quickstart=feature_dir / "quickstart.md",
-        contracts_dir=feature_dir / "contracts",
-    )
-
-
-def get_invoke_separator(repo_root: Path) -> str:
-    integration_json = repo_root / ".specify" / "integration.json"
-    if not integration_json.is_file():
-        return "."
-    try:
-        state = json.loads(integration_json.read_text(encoding="utf-8"))
-        key = state.get("default_integration") or state.get("integration") or ""
-        settings = state.get("integration_settings")
-        if isinstance(key, str) and isinstance(settings, dict):
-            entry = settings.get(key)
-            if isinstance(entry, dict) and entry.get("invoke_separator") in {".", "-"}:
-                return entry["invoke_separator"]
-    except (OSError, json.JSONDecodeError):
-        pass
-    return "."
-
-
-def format_speckit_command(command_name: str, repo_root: Path) -> str:
-    separator = get_invoke_separator(repo_root)
-    name = command_name.lstrip("/")
-    if name.startswith("speckit."):
-        name = name[len("speckit.") :]
-    elif name.startswith("speckit-"):
-        name = name[len("speckit-") :]
-    name = name.replace(".", separator)
-    return f"/speckit{separator}{name}"
--- a/src/specify_cli/agents.py
+++ b/src/specify_cli/agents.py
@@ -148,9 +148,7 @@ class CommandRegistrar:
        )
        return f"---\n{yaml_str}---\n"

-    def _adjust_script_paths(
-        self, frontmatter: dict, extension_id: Optional[str] = None
-    ) -> dict:
+    def _adjust_script_paths(self, frontmatter: dict) -> dict:
        """Normalize script paths in frontmatter to generated project locations.

        Rewrites known repo-relative and top-level script paths under the
@@ -160,7 +158,6 @@ class CommandRegistrar:

        Args:
            frontmatter: Frontmatter dictionary
-            extension_id: Extension id when rendering extension-owned commands.

        Returns:
            Modified frontmatter with normalized project paths
@@ -171,15 +168,11 @@ class CommandRegistrar:
        if isinstance(scripts, dict):
            for key, script_path in scripts.items():
                if isinstance(script_path, str):
-                    scripts[key] = self.rewrite_project_relative_paths(
-                        script_path, extension_id=extension_id
-                    )
+                    scripts[key] = self.rewrite_project_relative_paths(script_path)
        return frontmatter

    @staticmethod
-    def rewrite_project_relative_paths(
-        text: str, extension_id: Optional[str] = None
-    ) -> str:
+    def rewrite_project_relative_paths(text: str) -> str:
        """Rewrite repo-relative paths to their generated project locations."""
        if not isinstance(text, str) or not text:
            return text
@@ -191,18 +184,10 @@ class CommandRegistrar:
        ):
            text = text.replace(old, new)

-        # Only rewrite top-level style references so existing generated paths
-        # like ".specify/extensions/<ext>/scripts/..." remain intact. When
-        # rendering extension commands, top-level "scripts/" is extension-local.
-        scripts_replacement = (
-            f".specify/extensions/{extension_id}/scripts/"
-            if extension_id
-            else ".specify/scripts/"
-        )
+        # Only rewrite top-level style references so extension-local paths like
+        # ".specify/extensions/<ext>/scripts/..." remain intact.
        text = re.sub(r'(^|[\s`"\'(])(?:\.?/)?memory/', r"\1.specify/memory/", text)
-        text = re.sub(
-            r'(^|[\s`"\'(])(?:\.?/)?scripts/', rf"\1{scripts_replacement}", text
-        )
+        text = re.sub(r'(^|[\s`"\'(])(?:\.?/)?scripts/', r"\1.specify/scripts/", text)
        text = re.sub(
            r'(^|[\s`"\'(])(?:\.?/)?templates/', r"\1.specify/templates/", text
        )
@@ -327,7 +312,6 @@ class CommandRegistrar:
        source_id: str,
        source_file: str,
        project_root: Path,
-        extension_id: Optional[str] = None,
    ) -> str:
        """Render a command override as a SKILL.md file.

@@ -347,7 +331,7 @@ class CommandRegistrar:
        agent_config = self.AGENT_CONFIGS.get(agent_name, {})
        if agent_config.get("extension") == "/SKILL.md":
            body = self.resolve_skill_placeholders(
-                agent_name, frontmatter, body, project_root, extension_id=extension_id
+                agent_name, frontmatter, body, project_root
            )

        description = frontmatter.get(
@@ -409,11 +393,7 @@ class CommandRegistrar:

    @staticmethod
    def resolve_skill_placeholders(
-        agent_name: str,
-        frontmatter: dict,
-        body: str,
-        project_root: Path,
-        extension_id: Optional[str] = None,
+        agent_name: str, frontmatter: dict, body: str, project_root: Path
    ) -> str:
        """Resolve script placeholders for skills-backed agents."""
        if not isinstance(frontmatter, dict):
@@ -453,9 +433,7 @@ class CommandRegistrar:

        body = body.replace("{ARGS}", "$ARGUMENTS").replace("__AGENT__", agent_name)

-        return CommandRegistrar.rewrite_project_relative_paths(
-            body, extension_id=extension_id
-        )
+        return CommandRegistrar.rewrite_project_relative_paths(body)

    def _convert_argument_placeholder(
        self, content: str, from_placeholder: str, to_placeholder: str
@@ -550,7 +528,6 @@ class CommandRegistrar:
        context_note: str = None,
        _resolved_dir: Path = None,
        link_outputs: bool = False,
-        extension_id: Optional[str] = None,
    ) -> List[str]:
        """Register commands for a specific agent.

@@ -568,7 +545,6 @@ class CommandRegistrar:
            link_outputs: If True, write rendered output to a source-local
                dev cache and symlink the agent command file to it. Falls back
                to a normal file write when symlinks are unavailable.
-            extension_id: Extension id when rendering extension-owned commands.

        Returns:
            List of registered command names
@@ -638,9 +614,7 @@ class CommandRegistrar:
                        frontmatter[key] = core_frontmatter[key]
                frontmatter.pop("strategy", None)

-            frontmatter = self._adjust_script_paths(
-                frontmatter, extension_id=extension_id
-            )
+            frontmatter = self._adjust_script_paths(frontmatter)

            for key in agent_config.get("strip_frontmatter_keys", []):
                frontmatter.pop(key, None)
@@ -679,11 +653,10 @@ class CommandRegistrar:
                    source_id,
                    cmd_file,
                    project_root,
-                    extension_id=extension_id,
                )
            elif agent_config["format"] == "markdown":
                body = self.resolve_skill_placeholders(
-                    agent_name, frontmatter, body, project_root, extension_id=extension_id
+                    agent_name, frontmatter, body, project_root
                )
                body = self._convert_argument_placeholder(
                    body, "$ARGUMENTS", agent_config["args"]
@@ -693,7 +666,7 @@ class CommandRegistrar:
                )
            elif agent_config["format"] == "toml":
                body = self.resolve_skill_placeholders(
-                    agent_name, frontmatter, body, project_root, extension_id=extension_id
+                    agent_name, frontmatter, body, project_root
                )
                body = self._convert_argument_placeholder(
                    body, "$ARGUMENTS", agent_config["args"]
@@ -706,17 +679,6 @@ class CommandRegistrar:
            else:
                raise ValueError(f"Unsupported format: {agent_config['format']}")

-            # -- Post-process for non-skills agents -----------------------
-            _integration = None
-            if agent_config["extension"] != "/SKILL.md":
-                from specify_cli.integrations import (  # noqa: PLC0415
-                    get_integration,
-                )
-
-                _integration = get_integration(agent_name)
-                if _integration is not None:
-                    output = _integration.post_process_command_content(output)
-
            dest_file = commands_dir / f"{output_name}{agent_config['extension']}"
            self._ensure_inside(dest_file, commands_dir)
            dest_file.parent.mkdir(parents=True, exist_ok=True)
@@ -759,7 +721,6 @@ class CommandRegistrar:
                            source_id,
                            cmd_file,
                            project_root,
-                            extension_id=extension_id,
                        )
                    elif agent_config["format"] == "markdown":
                        alias_output = self.render_markdown_command(
@@ -777,9 +738,6 @@ class CommandRegistrar:
                        raise ValueError(
                            f"Unsupported format: {agent_config['format']}"
                        )
-
-                    if agent_config["extension"] != "/SKILL.md" and _integration is not None:
-                        alias_output = _integration.post_process_command_content(alias_output)
                else:
                    # For other agents, reuse the primary output
                    alias_output = output
@@ -792,7 +750,6 @@ class CommandRegistrar:
                            source_id,
                            cmd_file,
                            project_root,
-                            extension_id=extension_id,
                        )

                alias_file = (
@@ -924,7 +881,6 @@ class CommandRegistrar:
        context_note: str = None,
        link_outputs: bool = False,
        create_missing_active_skills_dir: bool = False,
-        extension_id: Optional[str] = None,
    ) -> Dict[str, List[str]]:
        """Register commands for all detected agents in the project.

@@ -941,7 +897,6 @@ class CommandRegistrar:
                Recovery requires active skills mode (or Kimi's existing native
                skills directory) and is skipped when safe resolution or
                creation fails.
-            extension_id: Extension id when rendering extension-owned commands.

        Returns:
            Dictionary mapping agent names to list of registered commands
@@ -1044,7 +999,6 @@ class CommandRegistrar:
                        context_note=context_note,
                        _resolved_dir=agent_dir,
                        link_outputs=link_outputs,
-                        extension_id=extension_id,
                    )
                    if registered:
                        results[agent_name] = registered
@@ -1069,7 +1023,6 @@ class CommandRegistrar:
        project_root: Path,
        context_note: Optional[str] = None,
        link_outputs: bool = False,
-        extension_id: Optional[str] = None,
    ) -> Dict[str, List[str]]:
        """Register commands for all non-skill agents in the project.

@@ -1085,7 +1038,6 @@ class CommandRegistrar:
            context_note: Custom context comment for markdown output
            link_outputs: If True, create dev-mode symlinks for rendered
                command files when supported by the OS.
-            extension_id: Extension id when rendering extension-owned commands.

        Returns:
            Dictionary mapping agent names to list of registered commands
@@ -1114,7 +1066,6 @@ class CommandRegistrar:
                        context_note=context_note,
                        _resolved_dir=agent_dir,
                        link_outputs=link_outputs,
-                        extension_id=extension_id,
                    )
                    if registered:
                        results[agent_name] = registered
--- a/src/specify_cli/bundler/commands_impl/catalog_config.py
+++ b/src/specify_cli/bundler/commands_impl/catalog_config.py
@@ -95,11 +95,7 @@ def _is_local_path(url: str) -> bool:
    """True when *url* denotes a local filesystem path rather than a URL."""
    if _WINDOWS_DRIVE_RE.match(url):
        return True
-    try:
-        scheme = urlparse(url).scheme.lower()
-    except ValueError:
-        # Malformed URLs (e.g. an unclosed IPv6 bracket) are not local paths.
-        return False
+    scheme = urlparse(url).scheme.lower()
    return scheme not in _REMOTE_SCHEMES


@@ -141,10 +137,7 @@ def add_source(
    url = url.strip()
    if not url:
        raise BundlerError("A catalog url is required.")
-    try:
-        parsed = urlparse(url)
-    except ValueError as exc:
-        raise BundlerError(f"Invalid catalog url: '{url}'.") from exc
+    parsed = urlparse(url)
    if not (parsed.scheme or parsed.path):
        raise BundlerError(f"Invalid catalog url: '{url}'.")
    # Reject unsupported URL schemes (e.g. ssh://, ftp://) up front so they are
@@ -155,20 +148,6 @@ def add_source(
            f"Unsupported catalog url scheme '{parsed.scheme}://' in '{url}'. "
            "Use http(s)://, file://, builtin://, or a local path."
        )
-    if parsed.scheme.lower() in {"http", "https"}:
-        # Mirror specify_cli.catalogs._validate_catalog_url (#3209/#3210):
-        # HTTPS only (HTTP just for localhost), and check hostname, not
-        # netloc — netloc is truthy for host-less URLs like "https://:8080"
-        # or "https://user@". Validating here keeps junk out of
-        # bundle-catalogs.yml instead of failing later at fetch time.
-        is_localhost = parsed.hostname in ("localhost", "127.0.0.1", "::1")
-        if parsed.scheme.lower() != "https" and not is_localhost:
-            raise BundlerError(
-                f"Catalog url must use HTTPS (got {parsed.scheme}://). "
-                "HTTP is only allowed for localhost."
-            )
-        if not parsed.hostname:
-            raise BundlerError(f"Catalog url must be a valid URL with a host: {url}")

    url = _canonicalize_url(url)
    install_policy = InstallPolicy.parse(policy)
--- a/src/specify_cli/bundler/services/adapters.py
+++ b/src/specify_cli/bundler/services/adapters.py
@@ -75,11 +75,7 @@ def _validate_remote_url(source_id: str, url: str) -> None:
            f"Catalog '{source_id}' URL must use HTTPS (got {parsed.scheme}://). "
            "HTTP is only allowed for localhost."
        )
-    # Check hostname, not netloc: netloc is truthy for host-less URLs like
-    # "https://:8080" or "https://user@...", so requiring netloc would let
-    # those through even though they carry no host. hostname is None in those
-    # cases. Mirrors the fix in ``specify_cli.catalogs`` (#3210).
-    if not parsed.hostname:
+    if not parsed.netloc:
        raise BundlerError(
            f"Catalog '{source_id}' URL must be a valid URL with a host: {url}"
        )
--- a/src/specify_cli/bundler/services/catalog_stack.py
+++ b/src/specify_cli/bundler/services/catalog_stack.py
@@ -88,25 +88,17 @@ class CatalogStack:
        Results are sorted by bundle id for deterministic output.
        """
        needle = query.strip().lower()
-        # Resolve each id to its highest-precedence entry FIRST, then filter by
-        # the query. Claiming an id only when it matches would let a lower-
-        # precedence entry with the same id surface when the highest-precedence
-        # one doesn't match the query — but that shadowed entry is not what
-        # `resolve()`/install would use, so search would advertise a bundle
-        # (name, version, author) the user can never actually get.
-        resolved: dict[str, ResolvedBundle] = {}
+        seen: dict[str, ResolvedBundle] = {}
        for source in self._sources:
            for bundle_id, entry in self._entries_for(source).items():
-                if bundle_id in resolved:
+                if bundle_id in seen:
                    continue
-                resolved[bundle_id] = ResolvedBundle(
+                if needle and not _matches(entry, needle):
+                    continue
+                seen[bundle_id] = ResolvedBundle(
                    entry=entry.with_provenance(source), source=source
                )
-        return [
-            resolved[k]
-            for k in sorted(resolved)
-            if not needle or _matches(resolved[k].entry, needle)
-        ]
+        return [seen[k] for k in sorted(seen)]


 def _matches(entry: CatalogEntry, needle: str) -> bool:
--- a/src/specify_cli/bundler/services/installer.py
+++ b/src/specify_cli/bundler/services/installer.py
@@ -130,28 +130,6 @@ def install_bundle(
            done.append(component)
            result.installed.append(component)
            contributed.append(component)
-
-        # On update (refresh), uninstall components this bundle used to own
-        # that the new version no longer ships. Otherwise they are dropped
-        # from the record below (contributed only holds plan.components) yet
-        # left on disk — permanently orphaned, since no bundle record can
-        # ever remove them. A stale component still owned by another bundle
-        # is kept installed and simply de-attributed here (it stays in that
-        # bundle's record). Mirrors remove_bundle's refcount logic.
-        if refresh and existing is not None:
-            planned = {(c.kind, c.id) for c in plan.components}
-            still_needed = components_still_needed(
-                records, exclude_bundle_id=plan.bundle_id
-            )
-            for component in existing.contributed_components:
-                key = (component.kind, component.id)
-                if key in planned:
-                    continue
-                if key in still_needed:
-                    continue
-                if installer.is_installed(project_root, component):
-                    installer.remove(project_root, component)
-                    result.uninstalled.append(component)
    except BundlerError:
        _rollback(project_root, installer, done)
        raise
--- a/src/specify_cli/extensions/init.py
+++ b/src/specify_cli/extensions/init.py
@@ -1075,11 +1075,9 @@ class ExtensionManager:
                        pass  # best-effort cleanup
                continue
            frontmatter, body = registrar.parse_frontmatter(content)
-            frontmatter = registrar._adjust_script_paths(
-                frontmatter, extension_id=manifest.id
-            )
+            frontmatter = registrar._adjust_script_paths(frontmatter)
            body = registrar.resolve_skill_placeholders(
-                selected_ai, frontmatter, body, self.project_root, extension_id=manifest.id
+                selected_ai, frontmatter, body, self.project_root
            )

            original_desc = frontmatter.get("description", "")
@@ -1960,7 +1958,6 @@ class CommandRegistrar:
            project_root,
            context_note=context_note,
            link_outputs=link_outputs,
-            extension_id=manifest.id,
        )

    def register_commands_for_all_agents(
@@ -1981,7 +1978,6 @@ class CommandRegistrar:
            context_note=context_note,
            link_outputs=link_outputs,
            create_missing_active_skills_dir=create_missing_active_skills_dir,
-            extension_id=manifest.id,
        )

    def unregister_commands(
@@ -2692,12 +2688,7 @@ class ConfigManager:
            return {}

        try:
-            data = yaml.safe_load(file_path.read_text(encoding="utf-8"))
-            # Coerce a non-mapping root (list/scalar, or None for an empty
-            # file) to {} so callers that iterate/merge the result — e.g.
-            # _merge_configs' .items() — never crash. Mirrors the same
-            # non-dict-root guard in get_project_config().
-            return data if isinstance(data, dict) else {}
+            return yaml.safe_load(file_path.read_text(encoding="utf-8")) or {}
        except (yaml.YAMLError, OSError, UnicodeError):
            return {}

--- a/src/specify_cli/integrations/agy/init.py
+++ b/src/specify_cli/integrations/agy/init.py
@@ -89,11 +89,7 @@ class AgyIntegration(SkillsIntegration):
        output_json: bool = True,
    ) -> list[str] | None:
        # agy does not support --model or JSON output; both params are ignored
-        args = [self._resolve_executable(), "--print", prompt]
-        # Honor SPECKIT_INTEGRATION_AGY_EXTRA_ARGS (operator-supplied flags),
-        # appended after the positional prompt like the devin integration.
-        self._apply_extra_args_env_var(args)
-        return args
+        return [self._resolve_executable(), "--print", prompt]

    def setup(
        self,
--- a/src/specify_cli/integrations/base.py
+++ b/src/specify_cli/integrations/base.py
@@ -123,19 +123,6 @@ class IntegrationBase(ABC):
    integration that sets this flag.
    """

-    def post_process_command_content(self, content: str) -> str:
-        """Transform command content after format rendering.
-
-        Called by ``register_commands()`` for non-skills format types
-        (Markdown, TOML, YAML) after the command has been rendered into
-        its target format and before writing to disk.  Skills-format
-        agents use ``post_process_skill_content()`` instead.
-
-        Subclasses may override to inject agent-specific content.
-        The default implementation returns *content* unchanged.
-        """
-        return content
-
    # -- Public API -------------------------------------------------------

    @classmethod
@@ -1191,18 +1178,12 @@ class YamlIntegration(IntegrationBase):
            default_flow_style=False,
        ).strip()

-        # Indent the body for YAML block scalar. Use an explicit indentation
-        # indicator ("|2") rather than a bare "|": YAML infers a plain block
-        # scalar's indentation from its first non-empty line, so a body whose
-        # first line is itself indented (e.g. a markdown code block or a nested
-        # list item) would make the parser expect that deeper indent for the
-        # whole block and reject the later, less-indented lines. Pinning the
-        # indent to 2 keeps the recipe parseable whatever the body looks like.
+        # Indent the body for YAML block scalar
        indented = "\n".join(f"  {line}" for line in body.split("\n"))

        lines = [
            header_yaml,
-            "prompt: |2",
+            "prompt: |",
            indented,
            "",
            f"# Source: {source_id}",
--- a/src/specify_cli/integrations/hermes/init.py
+++ b/src/specify_cli/integrations/hermes/init.py
@@ -253,11 +253,6 @@ class HermesIntegration(SkillsIntegration):
        """
        args = [self._resolve_executable(), "chat", "-Q"]

-        # Operator-supplied SPECKIT_INTEGRATION_HERMES_EXTRA_ARGS go here —
-        # after the base command but before Spec Kit's canonical -m/--json/-s/-q
-        # flags — so they can't displace or clobber them (mirrors opencode).
-        self._apply_extra_args_env_var(args)
-
        if model:
            args.extend(["-m", model])
        if output_json:
--- a/src/specify_cli/workflows/_commands.py
+++ b/src/specify_cli/workflows/_commands.py
@@ -50,17 +50,7 @@ workflow_step_catalog_app = typer.Typer(
 workflow_step_app.add_typer(workflow_step_catalog_app, name="catalog")


-def _error_console(json_output: bool):
-    """Console for error text: stderr under ``--json`` so the JSON stdout
-    stream stays parseable, the normal console otherwise. Mirrors the
-    stderr-only error routing already used by ``specify bundle``.
-    """
-    return err_console if json_output else console
-
-
-def _parse_input_values(
-    input_values: list[str] | None, *, json_output: bool = False
-) -> dict[str, Any]:
+def _parse_input_values(input_values: list[str] | None) -> dict[str, Any]:
    """Parse repeated ``key=value`` CLI inputs into a dict.

    Shared by ``workflow run`` and ``workflow resume``. Exits with an error
@@ -69,9 +59,7 @@ def _parse_input_values(
    inputs: dict[str, Any] = {}
    for kv in input_values or []:
        if "=" not in kv:
-            _error_console(json_output).print(
-                f"[red]Error:[/red] Invalid input format: {kv!r} (expected key=value)"
-            )
+            console.print(f"[red]Error:[/red] Invalid input format: {kv!r} (expected key=value)")
            raise typer.Exit(1)
        key, _, value = kv.partition("=")
        inputs[key.strip()] = value.strip()
@@ -347,26 +335,25 @@ def workflow_run(
    if not json_output:
        engine.on_step_start = lambda sid, label: console.print(f"  \u25b8 [{sid}] {label} \u2026")

-    err = _error_console(json_output)
    try:
        definition = engine.load_workflow(source_path if is_file_source else source)
    except FileNotFoundError:
-        err.print(f"[red]Error:[/red] Workflow not found: {source}")
+        console.print(f"[red]Error:[/red] Workflow not found: {source}")
        raise typer.Exit(1)
    except ValueError as exc:
-        err.print(f"[red]Error:[/red] Invalid workflow: {exc}")
+        console.print(f"[red]Error:[/red] Invalid workflow: {exc}")
        raise typer.Exit(1)

    # Validate
    errors = engine.validate(definition)
    if errors:
-        err.print("[red]Workflow validation failed:[/red]")
-        for verr in errors:
-            err.print(f"  • {verr}")
+        console.print("[red]Workflow validation failed:[/red]")
+        for err in errors:
+            console.print(f"  • {err}")
        raise typer.Exit(1)

    # Parse inputs
-    inputs = _parse_input_values(input_values, json_output=json_output)
+    inputs = _parse_input_values(input_values)

    if not json_output:
        console.print(f"\n[bold cyan]Running workflow:[/bold cyan] {definition.name} ({definition.id})")
@@ -376,10 +363,10 @@ def workflow_run(
        with _stdout_to_stderr_when(json_output):
            state = engine.execute(definition, inputs)
    except ValueError as exc:
-        err.print(f"[red]Error:[/red] {exc}")
+        console.print(f"[red]Error:[/red] {exc}")
        raise typer.Exit(1)
    except Exception as exc:
-        err.print(f"[red]Workflow failed:[/red] {exc}")
+        console.print(f"[red]Workflow failed:[/red] {exc}")
        raise typer.Exit(1)

    if json_output:
@@ -424,20 +411,19 @@ def workflow_resume(
    if not json_output:
        engine.on_step_start = lambda sid, label: console.print(f"  \u25b8 [{sid}] {label} \u2026")

-    inputs = _parse_input_values(input_values, json_output=json_output)
-    err = _error_console(json_output)
+    inputs = _parse_input_values(input_values)

    try:
        with _stdout_to_stderr_when(json_output):
            state = engine.resume(run_id, inputs or None)
    except FileNotFoundError:
-        err.print(f"[red]Error:[/red] Run not found: {run_id}")
+        console.print(f"[red]Error:[/red] Run not found: {run_id}")
        raise typer.Exit(1)
    except ValueError as exc:
-        err.print(f"[red]Error:[/red] {exc}")
+        console.print(f"[red]Error:[/red] {exc}")
        raise typer.Exit(1)
    except Exception as exc:
-        err.print(f"[red]Resume failed:[/red] {exc}")
+        console.print(f"[red]Resume failed:[/red] {exc}")
        raise typer.Exit(1)

    if json_output:
--- a/src/specify_cli/workflows/expressions.py
+++ b/src/specify_cli/workflows/expressions.py
@@ -183,65 +183,6 @@ def _is_single_expression(stripped: str) -> bool:
    return True


-def _interpolate_expressions(template: str, namespace: dict[str, Any]) -> str:
-    """Substitute every top-level ``{{ ... }}`` block in *template*, quote-aware.
-
-    Walks the template and, for each block, finds the closing ``}}`` that lies
-    outside string literals -- the same quote-scanning used by
-    ``_is_single_expression``. This keeps a literal ``}}`` inside a string
-    argument (e.g. ``| default('}}')``) from prematurely closing a block.
-
-    ``_EXPR_PATTERN.sub`` cannot do this: its non-greedy body stops at the first
-    ``}}`` regardless of quoting, so in a multi-expression template any block
-    whose argument contains a literal ``}}`` is captured truncated and mis-parsed
-    (raising ``ValueError`` from the filter parser). #3208/#3228 fixed exactly
-    this for the single-expression fast path but left the interpolation path on
-    the old regex.
-    """
-    out: list[str] = []
-    i = 0
-    n = len(template)
-    while i < n:
-        start = template.find("{{", i)
-        if start == -1:
-            out.append(template[i:])
-            break
-        out.append(template[i:start])
-        # Scan for the block-closing ``}}`` that is outside any string literal.
-        j = start + 2
-        quote: str | None = None
-        close = -1
-        while j < n:
-            ch = template[j]
-            if quote is not None:
-                if ch == quote:
-                    quote = None
-            elif ch in ("'", '"'):
-                quote = ch
-            elif ch == "}" and j + 1 < n and template[j + 1] == "}":
-                close = j
-                break
-            j += 1
-        if close == -1:
-            # No quote-aware close. Two sub-cases, both kept identical to the old
-            # regex so a malformed template is never silently hidden:
-            #   * a raw ``}}`` still exists in the tail (e.g. an unbalanced quote
-            #     in a filter arg swallowed the real delimiter) -- fall back to
-            #     that first raw ``}}`` and evaluate, letting the parser surface
-            #     a ValueError just as ``_EXPR_PATTERN.sub`` would have.
-            #   * no ``}}`` at all -- a genuinely unterminated ``{{``; leave the
-            #     tail verbatim, again matching the regex (which cannot match).
-            raw_close = template.find("}}", start + 2)
-            if raw_close == -1:
-                out.append(template[start:])
-                break
-            close = raw_close
-        val = _evaluate_simple_expression(template[start + 2:close].strip(), namespace)
-        out.append(str(val) if val is not None else "")
-        i = close + 2
-    return "".join(out)
-
-
 def _split_top_level_commas(text: str) -> list[str]:
    """Split *text* on commas that are not inside quotes or nested brackets.

@@ -467,34 +408,15 @@ def _evaluate_simple_expression(expr: str, namespace: dict[str, Any]) -> Any:
    return _resolve_dot_path(namespace, expr)


-def _coerce_number(value: Any) -> Any:
-    """Return *value* as int/float if it is a numeric string, else unchanged."""
-    if isinstance(value, str):
-        try:
-            return float(value) if "." in value else int(value)
-        except ValueError:
-            return value
-    return value
-
-
 def _safe_compare(left: Any, right: Any, op: str) -> bool:
-    """Compare two values for ordering, coercing numeric strings when possible.
-
-    Numeric coercion is applied only when *both* operands look numeric, so a
-    pair like ``"10"`` and ``"9"`` compares as numbers (10 > 9). When either
-    side is a non-numeric string, both fall back to their original values and
-    are compared directly -- so ordinary strings (dates, semver-ish tags,
-    names) compare lexicographically the way Python does, instead of every
-    such comparison silently returning ``False`` after a failed int()/float()
-    coercion. A genuinely incomparable pair (e.g. number vs non-numeric string)
-    raises ``TypeError`` and yields ``False``.
-    """
-    cl, cr = _coerce_number(left), _coerce_number(right)
-    # Only use the coerced numbers when both converted; otherwise a numeric
-    # string paired with a plain string would become an int-vs-str mismatch
-    # (always False) rather than a lexicographic string comparison.
-    if isinstance(cl, (int, float)) and isinstance(cr, (int, float)):
-        left, right = cl, cr
+    """Safely compare two values, coercing types when possible."""
+    try:
+        if isinstance(left, str):
+            left = float(left) if "." in left else int(left)
+        if isinstance(right, str):
+            right = float(right) if "." in right else int(right)
+    except (ValueError, TypeError):
+        return False
    try:
        if op == ">":
            return left > right  # type: ignore[operator]
@@ -550,11 +472,12 @@ def evaluate_expression(template: str, context: Any) -> Any:
    if _is_single_expression(stripped):
        return _evaluate_simple_expression(stripped[2:-2].strip(), namespace)

-    # Multi-expression: interpolate each block inline. Uses a quote-aware scan
-    # (not ``_EXPR_PATTERN.sub``) so a literal ``}}`` inside a string argument
-    # in any block does not close that block early -- matching the handling the
-    # single-expression path above already got in #3208/#3228.
-    return _interpolate_expressions(template, namespace)
+    # Multi-expression: string interpolation
+    def _replacer(m: re.Match[str]) -> str:
+        val = _evaluate_simple_expression(m.group(1).strip(), namespace)
+        return str(val) if val is not None else ""
+
+    return _EXPR_PATTERN.sub(_replacer, template)


 def evaluate_condition(condition: str, context: Any) -> bool:
--- a/src/specify_cli/workflows/steps/fan_in/init.py
+++ b/src/specify_cli/workflows/steps/fan_in/init.py
@@ -58,13 +58,4 @@ class FanInStep(StepBase):
                f"Fan-in step {config.get('id', '?')!r}: "
                f"'wait_for' must be a non-empty list of step IDs."
            )
-        output = config.get("output")
-        if output is not None and not isinstance(output, dict):
-            # execute() silently coerces a non-mapping output to {}, so the
-            # author's declared aggregation keys would vanish with no error.
-            # Reject at validation, mirroring the command-step (#3262) fix.
-            errors.append(
-                f"Fan-in step {config.get('id', '?')!r}: 'output' must be a "
-                f"mapping of key -> expression, got {type(output).__name__}."
-            )
        return errors
--- a/src/specify_cli/workflows/steps/gate/init.py
+++ b/src/specify_cli/workflows/steps/gate/init.py
@@ -73,14 +73,7 @@ class GateStep(StepBase):
        choice = self._prompt(self._compose_prompt(message, show_file), options)
        output["choice"] = choice

-        # Match rejection case-insensitively. ``_prompt`` echoes the option's
-        # original casing, and ``validate`` accepts a reject option
-        # case-insensitively (``o.lower() in {"reject", "abort"}``), so a gate
-        # authored as ``options: [Approve, Reject]`` passes validation. Comparing
-        # ``choice`` case-sensitively here would then treat a ``Reject`` pick as
-        # approval and silently skip the abort — the reject path must agree with
-        # the check that let the option through.
-        if choice.lower() in ("reject", "abort"):
+        if choice in ("reject", "abort"):
            if on_reject == "abort":
                output["aborted"] = True
                return StepResult(
--- a/src/specify_cli/workflows/steps/shell/init.py
+++ b/src/specify_cli/workflows/steps/shell/init.py
@@ -90,16 +90,6 @@ class ShellStep(StepBase):
            errors.append(
                f"Shell step {config.get('id', '?')!r} is missing 'run' field."
            )
-        elif not isinstance(config["run"], str):
-            # execute() str()-coerces run and invokes it under shell=True, so a
-            # null or list 'run' would run the Python repr ('None', "['echo']")
-            # as a command. Reject non-strings at validation, mirroring the
-            # command-step input/options and gate options type checks. An
-            # expression like "{{ ... }}" is still a str, so it stays valid.
-            errors.append(
-                f"Shell step {config.get('id', '?')!r}: 'run' must be a string, "
-                f"got {type(config['run']).__name__}."
-            )
        output_format = config.get("output_format")
        if output_format is not None and output_format != "json":
            errors.append(
--- a/tests/extensions/git/test_git_extension.py
+++ b/tests/extensions/git/test_git_extension.py
@@ -122,10 +122,10 @@ def _run_bash(script_name: str, cwd: Path, *args: str, env_extra: dict | None =
    )


-def _run_pwsh(script_name: str, cwd: Path, *args: str, env_extra: dict | None = None) -> subprocess.CompletedProcess:
+def _run_pwsh(script_name: str, cwd: Path, *args: str) -> subprocess.CompletedProcess:
    """Run an extension PowerShell script."""
    script = cwd / ".specify" / "extensions" / "git" / "scripts" / "powershell" / script_name
-    env = {**os.environ, **_GIT_ENV, **(env_extra or {})}
+    env = {**os.environ, **_GIT_ENV}
    return subprocess.run(
        ["pwsh", "-NoProfile", "-File", str(script), *args],
        cwd=cwd,
@@ -320,15 +320,6 @@ class TestCreateFeatureBash:
        assert rt.returncode == 0, rt.stderr
        assert "HAS_GIT" not in rt.stdout

-    def test_help_documents_branch_prefix(self, tmp_path: Path):
-        """--help documents both template config knobs."""
-        project = _setup_project(tmp_path)
-        result = _run_bash("create-new-feature-branch.sh", project, "--help")
-
-        assert result.returncode == 0
-        assert "branch_template" in result.stdout
-        assert "branch_prefix" in result.stdout
-
    def test_branch_name_short_word_case_sensitivity(self, tmp_path: Path):
        """A short word is dropped from the derived branch name unless it appears
        as an acronym in UPPERCASE in the description (case-sensitive, must match the
@@ -372,183 +363,6 @@ class TestCreateFeatureBash:
        data = json.loads(result.stdout)
        assert data["FEATURE_NUM"] == "003"

-    def test_branch_template_adds_author_and_app_namespace(self, tmp_path: Path):
-        """branch_template namespaces generated branch names for monorepos."""
-        project = _setup_project(tmp_path / "app-a")
-        subprocess.run(["git", "config", "user.name", "jdoe"], cwd=project, check=True)
-        _write_config(project, 'branch_template: "{author}/{app}/{number}-{slug}"\n')
-
-        result = _run_bash(
-            "create-new-feature-branch.sh", project,
-            "--json", "--short-name", "guided-tour", "Add guided tour",
-        )
-
-        assert result.returncode == 0, result.stderr
-        data = json.loads(result.stdout)
-        assert data["BRANCH_NAME"] == "jdoe/app-a/001-guided-tour"
-        assert data["FEATURE_NUM"] == "001"
-
-    def test_branch_prefix_shorthand_adds_namespace(self, tmp_path: Path):
-        """branch_prefix expands to a namespace before the default branch shape."""
-        project = _setup_project(tmp_path / "app-a")
-        _write_config(project, 'branch_prefix: "features/{app}"\n')
-
-        result = _run_bash(
-            "create-new-feature-branch.sh", project,
-            "--json", "--short-name", "guided-tour", "Add guided tour",
-        )
-
-        assert result.returncode == 0, result.stderr
-        data = json.loads(result.stdout)
-        assert data["BRANCH_NAME"] == "features/app-a/001-guided-tour"
-        assert data["FEATURE_NUM"] == "001"
-
-    def test_branch_template_scopes_number_after_numeric_app_namespace(self, tmp_path: Path):
-        """Numeric-looking namespace segments must not be parsed as feature numbers."""
-        project = _setup_project(tmp_path / "2026-app")
-        subprocess.run(["git", "config", "user.name", "jdoe"], cwd=project, check=True)
-        _write_config(project, 'branch_template: "{author}/{app}/{number}-{slug}"\n')
-        subprocess.run(["git", "branch", "jdoe/2026-app/007-existing"], cwd=project, check=True)
-
-        result = _run_bash(
-            "create-new-feature-branch.sh", project,
-            "--json", "--dry-run", "--short-name", "next", "Next feature",
-        )
-
-        assert result.returncode == 0, result.stderr
-        data = json.loads(result.stdout)
-        assert data["BRANCH_NAME"] == "jdoe/2026-app/008-next"
-        assert data["FEATURE_NUM"] == "008"
-
-    def test_branch_template_ignores_malformed_timestamp_branches_when_numbering(self, tmp_path: Path):
-        """Malformed timestamp-looking branches must not inflate sequential numbering."""
-        project = _setup_project(tmp_path / "app-a")
-        subprocess.run(["git", "config", "user.name", "jdoe"], cwd=project, check=True)
-        _write_config(project, 'branch_template: "{author}/{app}/{number}-{slug}"\n')
-        subprocess.run(["git", "branch", "jdoe/app-a/007-existing"], cwd=project, check=True)
-        subprocess.run(["git", "branch", "jdoe/app-a/2026031-143022-invalid"], cwd=project, check=True)
-        subprocess.run(["git", "branch", "jdoe/app-a/20260319-143022"], cwd=project, check=True)
-
-        result = _run_bash(
-            "create-new-feature-branch.sh", project,
-            "--json", "--dry-run", "--short-name", "next", "Next feature",
-        )
-
-        assert result.returncode == 0, result.stderr
-        data = json.loads(result.stdout)
-        assert data["BRANCH_NAME"] == "jdoe/app-a/008-next"
-        assert data["FEATURE_NUM"] == "008"
-
-    def test_branch_template_scopes_existing_branch_numbers(self, tmp_path: Path):
-        """Templated branch numbering ignores branches outside the current namespace."""
-        project = _setup_project(tmp_path / "app-a")
-        subprocess.run(["git", "config", "user.name", "jdoe"], cwd=project, check=True)
-        _write_config(project, 'branch_template: "{author}/{app}/{number}-{slug}"\n')
-        subprocess.run(["git", "branch", "jdoe/app-a/007-existing"], cwd=project, check=True)
-        subprocess.run(["git", "branch", "jdoe/app-b/010-other-app"], cwd=project, check=True)
-
-        result = _run_bash(
-            "create-new-feature-branch.sh", project,
-            "--json", "--dry-run", "--short-name", "next", "Next feature",
-        )
-
-        assert result.returncode == 0, result.stderr
-        data = json.loads(result.stdout)
-        assert data["BRANCH_NAME"] == "jdoe/app-a/008-next"
-        assert data["FEATURE_NUM"] == "008"
-
-    def test_branch_template_requires_number_token(self, tmp_path: Path):
-        """Configured templates must include {number} so generated branches validate."""
-        project = _setup_project(tmp_path / "app-a")
-        _write_config(project, 'branch_template: "{author}/{app}/{slug}"\n')
-
-        result = _run_bash(
-            "create-new-feature-branch.sh", project,
-            "--json", "--dry-run", "--short-name", "guided-tour", "Add guided tour",
-        )
-
-        assert result.returncode != 0
-        assert "branch_template" in result.stderr
-        assert "{number}" in result.stderr
-
-    def test_branch_template_requires_feature_segment_to_start_with_number(self, tmp_path: Path):
-        """Templates must render a final path segment that validation accepts."""
-        project = _setup_project(tmp_path / "app-a")
-        _write_config(project, 'branch_template: "{author}/{app}/feature-{number}"\n')
-
-        result = _run_bash(
-            "create-new-feature-branch.sh", project,
-            "--json", "--dry-run", "--short-name", "guided-tour", "Add guided tour",
-        )
-
-        assert result.returncode != 0
-        assert "branch_template" in result.stderr
-        assert "{number}-" in result.stderr
-
-    def test_branch_template_rejects_slug_before_number(self, tmp_path: Path):
-        """{slug} before {number} would make branch-number scanning slug-specific."""
-        project = _setup_project(tmp_path / "app-a")
-        _write_config(project, 'branch_template: "{author}/{slug}/{number}-{slug}"\n')
-
-        result = _run_bash(
-            "create-new-feature-branch.sh", project,
-            "--json", "--dry-run", "--short-name", "guided-tour", "Add guided tour",
-        )
-
-        assert result.returncode != 0
-        assert "branch_template" in result.stderr
-        assert "{slug}" in result.stderr
-        assert "{number}" in result.stderr
-
-    def test_git_branch_name_override_extracts_number_after_namespace(self, tmp_path: Path):
-        """GIT_BRANCH_NAME extracts FEATURE_NUM from a namespaced branch."""
-        project = _setup_project(tmp_path / "app-a")
-        result = _run_bash(
-            "create-new-feature-branch.sh", project,
-            "--json", "Ignored description",
-            env_extra={"GIT_BRANCH_NAME": "jdoe/app-a/042-custom-branch"},
-        )
-
-        assert result.returncode == 0, result.stderr
-        data = json.loads(result.stdout)
-        assert data["BRANCH_NAME"] == "jdoe/app-a/042-custom-branch"
-        assert data["FEATURE_NUM"] == "042"
-
-    def test_git_branch_name_override_ignores_numeric_namespace_segments(self, tmp_path: Path):
-        """GIT_BRANCH_NAME uses the feature segment, not numeric namespace segments."""
-        project = _setup_project(tmp_path / "2026-app")
-        result = _run_bash(
-            "create-new-feature-branch.sh", project,
-            "--json", "Ignored description",
-            env_extra={"GIT_BRANCH_NAME": "jdoe/2026-app/042-custom-branch"},
-        )
-
-        assert result.returncode == 0, result.stderr
-        data = json.loads(result.stdout)
-        assert data["BRANCH_NAME"] == "jdoe/2026-app/042-custom-branch"
-        assert data["FEATURE_NUM"] == "042"
-
-    def test_git_branch_name_override_without_feature_marker_preserves_full_name(self, tmp_path: Path):
-        """GIT_BRANCH_NAME without a feature marker keeps the historical FEATURE_NUM."""
-        project = _setup_project(tmp_path / "app-a")
-        result = _run_bash(
-            "create-new-feature-branch.sh", project,
-            "--json", "Ignored description",
-            env_extra={"GIT_BRANCH_NAME": "jdoe/app-a/custom-branch"},
-        )
-
-        assert result.returncode == 0, result.stderr
-        data = json.loads(result.stdout)
-        assert data["BRANCH_NAME"] == "jdoe/app-a/custom-branch"
-        assert data["FEATURE_NUM"] == "jdoe/app-a/custom-branch"
-
-    def test_truncation_warning_reports_utf8_bytes(self):
-        """Bash truncation warnings should use the same byte counter as enforcement."""
-        source = (EXT_BASH / "create-new-feature-branch.sh").read_text(encoding="utf-8")
-
-        assert '_byte_length "$ORIGINAL_BRANCH_NAME"' in source
-        assert '_byte_length "$BRANCH_NAME"' in source
-
    def test_dry_run_counts_branches_checked_out_in_worktrees(self, tmp_path: Path):
        """Branches checked out in sibling worktrees still reserve their prefix."""
        project = _setup_project(tmp_path / "project")
@@ -670,15 +484,6 @@ class TestCreateFeaturePowerShell:
        assert rt.returncode == 0, rt.stderr
        assert "HAS_GIT" not in rt.stdout

-    def test_help_documents_branch_prefix(self, tmp_path: Path):
-        """-Help documents both template config knobs."""
-        project = _setup_project(tmp_path)
-        result = _run_pwsh("create-new-feature-branch.ps1", project, "-Help")
-
-        assert result.returncode == 0
-        assert "branch_template" in result.stdout
-        assert "branch_prefix" in result.stdout
-
    def test_branch_name_short_word_case_sensitivity(self, tmp_path: Path):
        """PowerShell must match the bash twin: a short word is dropped unless it
        appears as an acronym in UPPERCASE (case-sensitive -cmatch, not -match)."""
@@ -720,176 +525,6 @@ class TestCreateFeaturePowerShell:
        data = json.loads(result.stdout)
        assert re.match(r"^\d{8}-\d{6}-feat$", data["BRANCH_NAME"])

-    def test_branch_template_adds_author_and_app_namespace(self, tmp_path: Path):
-        """PowerShell supports branch_template namespaces."""
-        project = _setup_project(tmp_path / "app-a")
-        subprocess.run(["git", "config", "user.name", "jdoe"], cwd=project, check=True)
-        _write_config(project, 'branch_template: "{author}/{app}/{number}-{slug}"\n')
-
-        result = _run_pwsh(
-            "create-new-feature-branch.ps1", project,
-            "-Json", "-ShortName", "guided-tour", "Add guided tour",
-        )
-
-        assert result.returncode == 0, result.stderr
-        data = json.loads(result.stdout)
-        assert data["BRANCH_NAME"] == "jdoe/app-a/001-guided-tour"
-        assert data["FEATURE_NUM"] == "001"
-
-    def test_branch_prefix_shorthand_adds_namespace(self, tmp_path: Path):
-        """PowerShell supports branch_prefix shorthand namespaces."""
-        project = _setup_project(tmp_path / "app-a")
-        _write_config(project, 'branch_prefix: "features/{app}"\n')
-
-        result = _run_pwsh(
-            "create-new-feature-branch.ps1", project,
-            "-Json", "-ShortName", "guided-tour", "Add guided tour",
-        )
-
-        assert result.returncode == 0, result.stderr
-        data = json.loads(result.stdout)
-        assert data["BRANCH_NAME"] == "features/app-a/001-guided-tour"
-        assert data["FEATURE_NUM"] == "001"
-
-    def test_branch_template_scopes_number_after_numeric_app_namespace(self, tmp_path: Path):
-        """PowerShell ignores numeric-looking namespace segments when numbering."""
-        project = _setup_project(tmp_path / "2026-app")
-        subprocess.run(["git", "config", "user.name", "jdoe"], cwd=project, check=True)
-        _write_config(project, 'branch_template: "{author}/{app}/{number}-{slug}"\n')
-        subprocess.run(["git", "branch", "jdoe/2026-app/007-existing"], cwd=project, check=True)
-
-        result = _run_pwsh(
-            "create-new-feature-branch.ps1", project,
-            "-Json", "-DryRun", "-ShortName", "next", "Next feature",
-        )
-
-        assert result.returncode == 0, result.stderr
-        data = json.loads(result.stdout)
-        assert data["BRANCH_NAME"] == "jdoe/2026-app/008-next"
-        assert data["FEATURE_NUM"] == "008"
-
-    def test_branch_template_ignores_malformed_timestamp_branches_when_numbering(self, tmp_path: Path):
-        """PowerShell skips malformed timestamp-looking refs during sequential numbering."""
-        project = _setup_project(tmp_path / "app-a")
-        subprocess.run(["git", "config", "user.name", "jdoe"], cwd=project, check=True)
-        _write_config(project, 'branch_template: "{author}/{app}/{number}-{slug}"\n')
-        subprocess.run(["git", "branch", "jdoe/app-a/007-existing"], cwd=project, check=True)
-        subprocess.run(["git", "branch", "jdoe/app-a/2026031-143022-invalid"], cwd=project, check=True)
-        subprocess.run(["git", "branch", "jdoe/app-a/20260319-143022"], cwd=project, check=True)
-
-        result = _run_pwsh(
-            "create-new-feature-branch.ps1", project,
-            "-Json", "-DryRun", "-ShortName", "next", "Next feature",
-        )
-
-        assert result.returncode == 0, result.stderr
-        data = json.loads(result.stdout)
-        assert data["BRANCH_NAME"] == "jdoe/app-a/008-next"
-        assert data["FEATURE_NUM"] == "008"
-
-    def test_branch_template_scopes_existing_branch_numbers(self, tmp_path: Path):
-        """PowerShell templated numbering ignores branches outside the namespace."""
-        project = _setup_project(tmp_path / "app-a")
-        subprocess.run(["git", "config", "user.name", "jdoe"], cwd=project, check=True)
-        _write_config(project, 'branch_template: "{author}/{app}/{number}-{slug}"\n')
-        subprocess.run(["git", "branch", "jdoe/app-a/007-existing"], cwd=project, check=True)
-        subprocess.run(["git", "branch", "jdoe/app-b/010-other-app"], cwd=project, check=True)
-
-        result = _run_pwsh(
-            "create-new-feature-branch.ps1", project,
-            "-Json", "-DryRun", "-ShortName", "next", "Next feature",
-        )
-
-        assert result.returncode == 0, result.stderr
-        data = json.loads(result.stdout)
-        assert data["BRANCH_NAME"] == "jdoe/app-a/008-next"
-        assert data["FEATURE_NUM"] == "008"
-
-    def test_branch_template_requires_number_token(self, tmp_path: Path):
-        """PowerShell rejects templates without {number}."""
-        project = _setup_project(tmp_path / "app-a")
-        _write_config(project, 'branch_template: "{author}/{app}/{slug}"\n')
-
-        result = _run_pwsh(
-            "create-new-feature-branch.ps1", project,
-            "-Json", "-DryRun", "-ShortName", "guided-tour", "Add guided tour",
-        )
-
-        assert result.returncode != 0
-        assert "branch_template" in result.stderr
-        assert "{number}" in result.stderr
-
-    def test_branch_template_requires_feature_segment_to_start_with_number(self, tmp_path: Path):
-        """PowerShell rejects templates whose final segment cannot validate."""
-        project = _setup_project(tmp_path / "app-a")
-        _write_config(project, 'branch_template: "{author}/{app}/feature-{number}"\n')
-
-        result = _run_pwsh(
-            "create-new-feature-branch.ps1", project,
-            "-Json", "-DryRun", "-ShortName", "guided-tour", "Add guided tour",
-        )
-
-        assert result.returncode != 0
-        assert "branch_template" in result.stderr
-        assert "{number}-" in result.stderr
-
-    def test_branch_template_rejects_slug_before_number(self, tmp_path: Path):
-        """PowerShell rejects templates where {slug} scopes number scanning."""
-        project = _setup_project(tmp_path / "app-a")
-        _write_config(project, 'branch_template: "{author}/{slug}/{number}-{slug}"\n')
-
-        result = _run_pwsh(
-            "create-new-feature-branch.ps1", project,
-            "-Json", "-DryRun", "-ShortName", "guided-tour", "Add guided tour",
-        )
-
-        assert result.returncode != 0
-        assert "branch_template" in result.stderr
-        assert "{slug}" in result.stderr
-        assert "{number}" in result.stderr
-
-    def test_git_branch_name_override_extracts_number_after_namespace(self, tmp_path: Path):
-        """PowerShell GIT_BRANCH_NAME extracts FEATURE_NUM from a namespaced branch."""
-        project = _setup_project(tmp_path / "app-a")
-        result = _run_pwsh(
-            "create-new-feature-branch.ps1", project,
-            "-Json", "Ignored description",
-            env_extra={"GIT_BRANCH_NAME": "jdoe/app-a/042-custom-branch"},
-        )
-
-        assert result.returncode == 0, result.stderr
-        data = json.loads(result.stdout)
-        assert data["BRANCH_NAME"] == "jdoe/app-a/042-custom-branch"
-        assert data["FEATURE_NUM"] == "042"
-
-    def test_git_branch_name_override_ignores_numeric_namespace_segments(self, tmp_path: Path):
-        """PowerShell GIT_BRANCH_NAME ignores numeric namespace segments."""
-        project = _setup_project(tmp_path / "2026-app")
-        result = _run_pwsh(
-            "create-new-feature-branch.ps1", project,
-            "-Json", "Ignored description",
-            env_extra={"GIT_BRANCH_NAME": "jdoe/2026-app/042-custom-branch"},
-        )
-
-        assert result.returncode == 0, result.stderr
-        data = json.loads(result.stdout)
-        assert data["BRANCH_NAME"] == "jdoe/2026-app/042-custom-branch"
-        assert data["FEATURE_NUM"] == "042"
-
-    def test_git_branch_name_override_without_feature_marker_preserves_full_name(self, tmp_path: Path):
-        """PowerShell keeps the full override name when no feature marker exists."""
-        project = _setup_project(tmp_path / "app-a")
-        result = _run_pwsh(
-            "create-new-feature-branch.ps1", project,
-            "-Json", "Ignored description",
-            env_extra={"GIT_BRANCH_NAME": "jdoe/app-a/custom-branch"},
-        )
-
-        assert result.returncode == 0, result.stderr
-        data = json.loads(result.stdout)
-        assert data["BRANCH_NAME"] == "jdoe/app-a/custom-branch"
-        assert data["FEATURE_NUM"] == "jdoe/app-a/custom-branch"
-
    def test_no_git_graceful_degradation(self, tmp_path: Path):
        """create-new-feature-branch.ps1 works without git."""
        project = _setup_project(tmp_path, git=False)
@@ -1376,31 +1011,13 @@ class TestGitCommonBash:
        )
        assert result.returncode == 0

-    def test_check_feature_branch_accepts_nested_prefix(self, tmp_path: Path):
+    def test_check_feature_branch_rejects_nested_prefix(self, tmp_path: Path):
        project = _setup_project(tmp_path)
        script = project / ".specify" / "extensions" / "git" / "scripts" / "bash" / "git-common.sh"
        result = subprocess.run(
            ["bash", "-c", f'source "{script}" && check_feature_branch "feat/fix/001-x" "true"'],
            capture_output=True, text=True,
        )
-        assert result.returncode == 0
-
-    def test_check_feature_branch_rejects_nested_prefix_without_number(self, tmp_path: Path):
-        project = _setup_project(tmp_path)
-        script = project / ".specify" / "extensions" / "git" / "scripts" / "bash" / "git-common.sh"
-        result = subprocess.run(
-            ["bash", "-c", f'source "{script}" && check_feature_branch "feat/fix/no-number" "true"'],
-            capture_output=True, text=True,
-        )
-        assert result.returncode != 0
-
-    def test_check_feature_branch_rejects_numeric_namespace_without_feature_number(self, tmp_path: Path):
-        project = _setup_project(tmp_path)
-        script = project / ".specify" / "extensions" / "git" / "scripts" / "bash" / "git-common.sh"
-        result = subprocess.run(
-            ["bash", "-c", f'source "{script}" && check_feature_branch "jdoe/2026-app/no-number" "true"'],
-            capture_output=True, text=True,
-        )
        assert result.returncode != 0


@@ -1420,33 +1037,3 @@ class TestGitCommonPowerShell:
            text=True,
        )
        assert result.returncode == 0
-
-    def test_test_feature_branch_accepts_nested_prefix(self, tmp_path: Path):
-        project = _setup_project(tmp_path)
-        script = project / ".specify" / "extensions" / "git" / "scripts" / "powershell" / "git-common.ps1"
-        result = subprocess.run(
-            [
-                "pwsh",
-                "-NoProfile",
-                "-Command",
-                f'. "{script}"; if (Test-FeatureBranch -Branch "jdoe/app-a/001-x" -HasGit $true) {{ exit 0 }} else {{ exit 1 }}',
-            ],
-            capture_output=True,
-            text=True,
-        )
-        assert result.returncode == 0
-
-    def test_test_feature_branch_rejects_numeric_namespace_without_feature_number(self, tmp_path: Path):
-        project = _setup_project(tmp_path)
-        script = project / ".specify" / "extensions" / "git" / "scripts" / "powershell" / "git-common.ps1"
-        result = subprocess.run(
-            [
-                "pwsh",
-                "-NoProfile",
-                "-Command",
-                f'. "{script}"; if (Test-FeatureBranch -Branch "jdoe/2026-app/no-number" -HasGit $true) {{ exit 0 }} else {{ exit 1 }}',
-            ],
-            capture_output=True,
-            text=True,
-        )
-        assert result.returncode != 0
--- a/tests/integration/test_bundler_catalog_stack.py
+++ b/tests/integration/test_bundler_catalog_stack.py
@@ -71,47 +71,6 @@ def test_search_dedupes_by_precedence_and_filters():
    assert [r.entry.id for r in qa_only] == ["beta"]


-def test_search_does_not_surface_a_shadowed_lower_precedence_entry():
-    """Search must resolve each id at its highest-precedence source, then
-    filter — never fall through to a shadowed lower-precedence entry the query
-    happens to match.
-
-    If the query matched only the lower-precedence copy of an id, search used
-    to return that copy, even though `resolve()`/install always use the
-    higher-precedence one. That advertised a bundle (name/version/source) the
-    user could never actually get.
-    """
-    sources = [_source("high", 1, "install-allowed"), _source("low", 2, "install-allowed")]
-    payloads = {
-        # Highest-precedence entry for 'shared' does NOT match "widget".
-        "high": catalog_payload({
-            "shared": catalog_entry_dict(
-                "shared", name="Alpha Tool", role="developer",
-                description="nothing relevant", version="2.0.0",
-            ),
-        }),
-        # Lower-precedence entry for the same id DOES match "widget".
-        "low": catalog_payload({
-            "shared": catalog_entry_dict(
-                "shared", name="Searchable Widget", version="1.0.0",
-            ),
-        }),
-    }
-    stack = _stack(sources, payloads)
-
-    # resolve() uses the high-precedence entry.
-    assert stack.resolve("shared").source.id == "high"
-
-    # A query that only the shadowed low-precedence entry matches returns
-    # nothing — search agrees with resolve().
-    assert stack.search("widget") == []
-
-    # And a query the high-precedence entry matches returns it (from 'high').
-    alpha = stack.search("alpha tool")
-    assert [r.entry.id for r in alpha] == ["shared"]
-    assert alpha[0].source.id == "high"
-
-
 def test_unreachable_source_raises_named_error():
    def fetcher(src):
        raise RuntimeError("boom")
--- a/tests/integration/test_bundler_install_flow.py
+++ b/tests/integration/test_bundler_install_flow.py
@@ -220,68 +220,3 @@ def test_pre_existing_component_is_not_attributed_or_removed(tmp_path: Path):

    remove_bundle(tmp_path, "demo-bundle", installer)
    assert ("extensions", "ext-a") in installer.installed
-
-
-def _bundle(manifest_id, ext_ids, *, version="1.0.0"):
-    data = valid_manifest_dict()
-    data["bundle"]["id"] = manifest_id
-    data["bundle"]["version"] = version
-    data["provides"] = {
-        "extensions": [{"id": e, "version": version} for e in ext_ids]
-    }
-    return BundleManifest.from_dict(data)
-
-
-def test_update_uninstalls_components_dropped_by_new_version(tmp_path: Path):
-    """`bundle update` must uninstall components the new version no longer
-    ships, instead of orphaning them (installed on disk, tracked by nothing)."""
-    make_project(tmp_path)
-    installer = FakeInstaller()
-
-    man_v1 = _bundle("demo", ["ext-a", "ext-b"])
-    install_bundle(tmp_path, _plan(man_v1), installer, manifest=man_v1)
-    assert ("extensions", "ext-b") in installer.installed
-
-    man_v2 = _bundle("demo", ["ext-a"], version="2.0.0")
-    result = install_bundle(
-        tmp_path, _plan(man_v2), installer, manifest=man_v2, refresh=True
-    )
-
-    # ext-b was dropped by v2 -> uninstalled and reported.
-    assert ("extensions", "ext-b") in installer.remove_calls
-    assert ("extensions", "ext-b") in {(c.kind, c.id) for c in result.uninstalled}
-    assert ("extensions", "ext-b") not in installer.installed
-    assert ("extensions", "ext-a") in installer.installed
-
-    # The saved record lists only ext-a.
-    rec = next(r for r in load_records(tmp_path) if r.bundle_id == "demo")
-    keys = {(c.kind, c.id) for c in rec.contributed_components}
-    assert ("extensions", "ext-a") in keys
-    assert ("extensions", "ext-b") not in keys
-
-
-def test_update_keeps_component_still_needed_by_sibling_bundle(tmp_path: Path):
-    """A dropped component still owned by another bundle stays installed."""
-    make_project(tmp_path)
-    installer = FakeInstaller()
-
-    man_sib = _bundle("sibling", ["ext-b"])
-    install_bundle(tmp_path, _plan(man_sib), installer, manifest=man_sib)
-
-    man_v1 = _bundle("demo", ["ext-a", "ext-b"])
-    install_bundle(tmp_path, _plan(man_v1), installer, manifest=man_v1)
-
-    man_v2 = _bundle("demo", ["ext-a"], version="2.0.0")
-    install_bundle(
-        tmp_path, _plan(man_v2), installer, manifest=man_v2, refresh=True
-    )
-
-    # ext-b is still needed by 'sibling' -> not removed, stays installed.
-    assert ("extensions", "ext-b") not in installer.remove_calls
-    assert ("extensions", "ext-b") in installer.installed
-
-    # But demo's record no longer attributes it.
-    rec = next(r for r in load_records(tmp_path) if r.bundle_id == "demo")
-    assert ("extensions", "ext-b") not in {
-        (c.kind, c.id) for c in rec.contributed_components
-    }
--- a/tests/integrations/conftest.py
+++ b/tests/integrations/conftest.py
@@ -1,24 +1,8 @@
 """Shared test helpers for integration tests."""

-import pytest
-
 from specify_cli.integrations.base import MarkdownIntegration


-@pytest.fixture(autouse=True)
-def _isolate_integration_home(monkeypatch: pytest.MonkeyPatch, tmp_path):
-    """Keep integration tests from reading or writing the real user home."""
-    home = tmp_path / "home"
-    for path in (home, home / ".cache", home / ".config", home / ".local" / "share"):
-        path.mkdir(parents=True, exist_ok=True)
-
-    monkeypatch.setenv("HOME", str(home))
-    monkeypatch.setenv("USERPROFILE", str(home))
-    monkeypatch.setenv("XDG_CACHE_HOME", str(home / ".cache"))
-    monkeypatch.setenv("XDG_CONFIG_HOME", str(home / ".config"))
-    monkeypatch.setenv("XDG_DATA_HOME", str(home / ".local" / "share"))
-
-
 class StubIntegration(MarkdownIntegration):
    """Minimal concrete integration for testing."""

--- a/tests/integrations/test_home_isolation.py
+++ b/tests/integrations/test_home_isolation.py
@@ -1,21 +0,0 @@
-"""Regression tests for integration-test environment isolation."""
-
-from __future__ import annotations
-
-import os
-from pathlib import Path
-
-
-def test_integration_tests_use_tmp_home(tmp_path: Path) -> None:
-    home = tmp_path / "home"
-
-    assert Path(os.environ["HOME"]) == home
-    assert Path(os.environ["USERPROFILE"]) == home
-    assert Path(os.environ["XDG_CACHE_HOME"]) == home / ".cache"
-    assert Path(os.environ["XDG_CONFIG_HOME"]) == home / ".config"
-    assert Path(os.environ["XDG_DATA_HOME"]) == home / ".local" / "share"
-
-    assert home.is_dir()
-    assert (home / ".cache").is_dir()
-    assert (home / ".config").is_dir()
-    assert (home / ".local" / "share").is_dir()
--- a/tests/integrations/test_integration_agy.py
+++ b/tests/integrations/test_integration_agy.py
@@ -81,26 +81,6 @@ class TestAgyBuildExecArgs:
        result = i.build_exec_args("my prompt", output_json=False)
        assert result == ["agy", "--print", "my prompt"]

-    def test_build_exec_args_honors_extra_args(self, monkeypatch):
-        """SPECKIT_INTEGRATION_AGY_EXTRA_ARGS must be appended after the prompt.
-
-        agy previously skipped _apply_extra_args_env_var entirely, so the
-        documented per-integration extra-args hook was silently ignored
-        (same class as the merged cursor-agent fix #3265).
-        """
-        from specify_cli.integrations import get_integration
-        monkeypatch.setenv("SPECKIT_INTEGRATION_AGY_EXTRA_ARGS", "--verbose")
-        i = get_integration("agy")
-        assert i.build_exec_args("my prompt") == [
-            "agy", "--print", "my prompt", "--verbose",
-        ]
-
-    def test_build_exec_args_honors_executable_override(self, monkeypatch):
-        from specify_cli.integrations import get_integration
-        monkeypatch.setenv("SPECKIT_INTEGRATION_AGY_EXECUTABLE", "/custom/agy")
-        i = get_integration("agy")
-        assert i.build_exec_args("my prompt")[0] == "/custom/agy"
-

 class TestAgyHookCommandNote:
    """Verify dot-to-hyphen normalization note is injected into hook sections."""
--- a/tests/integrations/test_integration_base_yaml.py
+++ b/tests/integrations/test_integration_base_yaml.py
@@ -184,23 +184,6 @@ class YamlIntegrationTests:
        assert "scripts:" not in parsed["prompt"]
        assert "---" not in parsed["prompt"]

-    def test_yaml_prompt_with_indented_first_line_stays_valid(self):
-        """A body whose first line is indented must still parse.
-
-        A bare ``|`` block scalar infers its indentation from the first
-        non-empty line, so a body starting with an indented line (e.g. a
-        markdown code block or nested list item) made the parser expect that
-        deeper indent for the whole block and reject the later, shallower
-        lines. The explicit ``|2`` indicator pins the indent so it parses."""
-        body = "    indented first line\nback to normal\n    indented again"
-        rendered = YamlIntegration._render_yaml("Title", "Desc", body, "src")
-
-        yaml_lines = [
-            ln for ln in rendered.split("\n") if not ln.startswith("# Source:")
-        ]
-        parsed = yaml.safe_load("\n".join(yaml_lines))
-        assert parsed["prompt"].rstrip("\n") == body
-
    def test_plan_command_has_no_context_placeholder(self, tmp_path):
        """The generated plan command must not carry a context-file placeholder.

--- a/tests/integrations/test_integration_hermes.py
+++ b/tests/integrations/test_integration_hermes.py
@@ -353,38 +353,3 @@ class TestHermesInitFlow:
            if "agent-context" not in d.name
        ]
        assert local_skills == [], f"Local skills dir should be empty, got: {local_skills}"
-
-
-class TestHermesBuildExecArgs:
-    """CLI dispatch argv, including the operator extra-args env hook."""
-
-    def test_build_exec_args_default_shape(self):
-        i = get_integration("hermes")
-        assert i.build_exec_args("/speckit-plan hi", output_json=True) == [
-            "hermes", "chat", "-Q", "--json", "-s", "speckit-plan", "-q", "hi",
-        ]
-
-    def test_build_exec_args_honors_extra_args(self, monkeypatch):
-        """SPECKIT_INTEGRATION_HERMES_EXTRA_ARGS is injected before the
-        canonical -m/--json/-s/-q flags (same env hook as codex/opencode/
-        devin; hermes previously skipped _apply_extra_args_env_var entirely).
-        """
-        monkeypatch.setenv(
-            "SPECKIT_INTEGRATION_HERMES_EXTRA_ARGS", "--temperature 0.2"
-        )
-        i = get_integration("hermes")
-        args = i.build_exec_args("/speckit-plan hi", output_json=True)
-        assert args == [
-            "hermes", "chat", "-Q", "--temperature", "0.2",
-            "--json", "-s", "speckit-plan", "-q", "hi",
-        ]
-        # Injected before the canonical flags so it can't displace them.
-        assert args.index("--temperature") < args.index("--json")
-        assert args.index("--temperature") < args.index("-s")
-
-    def test_build_exec_args_honors_executable_override(self, monkeypatch):
-        monkeypatch.setenv(
-            "SPECKIT_INTEGRATION_HERMES_EXECUTABLE", "/custom/hermes"
-        )
-        i = get_integration("hermes")
-        assert i.build_exec_args("/speckit-plan hi")[0] == "/custom/hermes"
--- a/tests/integrations/test_registry.py
+++ b/tests/integrations/test_registry.py
@@ -48,19 +48,6 @@ def _multi_install_safe_pairs() -> list[tuple[str, str]]:
    ]


-def _multi_install_safe_orders() -> list[list[str]]:
-    safe_keys = _multi_install_safe_keys()
-    if len(safe_keys) < 2:
-        return [safe_keys]
-    return [safe_keys[index:] + safe_keys[:index] for index in range(len(safe_keys))]
-
-
-def _multi_install_safe_order_id(ordered_keys: list[str]) -> str:
-    if not ordered_keys:
-        return "no-safe-integrations"
-    return f"init-{ordered_keys[0]}"
-
-
 def _posix_path(value: str | None) -> str | None:
    if not value:
        return None
@@ -100,6 +87,16 @@ def _paths_overlap(first: str | None, second: str | None) -> bool:
        return False


+def _path_is_inside(path: str | None, directory: str | None) -> bool:
+    if not path or not directory:
+        return False
+    try:
+        PurePosixPath(path).relative_to(PurePosixPath(directory))
+        return True
+    except ValueError:
+        return False
+
+
 class TestRegistry:
    def test_registry_is_dict(self):
        assert isinstance(INTEGRATION_REGISTRY, dict)
@@ -165,15 +162,6 @@ class TestRegistrarKeyAlignment:
 class TestMultiInstallSafeContracts:
    """Declared safe integrations must stay isolated from each other."""

-    def test_safe_install_orders_rotate_each_integration_through_init(self):
-        safe_keys = _multi_install_safe_keys()
-        orders = _multi_install_safe_orders()
-
-        assert len(safe_keys) >= 2
-        assert [order[0] for order in orders] == safe_keys
-        assert len({tuple(order) for order in orders}) == len(safe_keys)
-        assert all(sorted(order) == safe_keys for order in orders)
-
    @pytest.mark.parametrize("key", _multi_install_safe_keys())
    def test_safe_integrations_have_static_isolated_paths(self, key):
        assert _integration_root_dir(key), (
@@ -199,77 +187,62 @@ class TestMultiInstallSafeContracts:
            f"{_integration_commands_dir(second)!r}"
        )

-    @pytest.mark.parametrize(
-        "ordered_keys",
-        _multi_install_safe_orders(),
-        ids=_multi_install_safe_order_id,
-    )
+    @pytest.mark.parametrize(("first", "second"), _multi_install_safe_pairs())
    def test_safe_integrations_have_disjoint_manifests(
        self,
        tmp_path,
-        ordered_keys,
+        first,
+        second,
    ):
-        # The pairwise disjointness contract is only meaningful with at least
-        # two safe integrations. Guard so a shrunken registry fails loudly here
-        # rather than passing vacuously (or tripping over ordered_keys[0] below).
-        assert len(ordered_keys) >= 2, (
-            f"expected at least two multi-install-safe integrations, got {ordered_keys}"
-        )
+        for initial, additional in ((first, second), (second, first)):
+            project_root = tmp_path / f"project-{initial}-{additional}"
+            project_root.mkdir()
+            runner = CliRunner()

-        project_root = tmp_path / "project"
-        project_root.mkdir()
-        runner = CliRunner()
+            original_cwd = os.getcwd()
+            try:
+                os.chdir(project_root)
+                init_result = runner.invoke(
+                    app,
+                    [
+                        "init",
+                        "--here",
+                        "--integration",
+                        initial,
+                        "--script",
+                        "sh",
+                        "--ignore-agent-tools",
+                    ],
+                    catch_exceptions=False,
+                )
+                assert init_result.exit_code == 0, init_result.output

-        # Install every safe integration once into a single project, then assert
-        # pairwise manifest isolation. Each safe integration writes only to its
-        # own (disjoint) directories and always records what it writes, so a
-        # manifest's contents are independent of install order and of which other
-        # integrations are co-installed. The parametrized rotations keep the
-        # aggregate setup while placing each safe integration first once, so each
-        # one still exercises the `specify init --integration ...` path.
-        original_cwd = os.getcwd()
-        try:
-            os.chdir(project_root)
-            init_result = runner.invoke(
-                app,
-                [
-                    "init",
-                    "--here",
-                    "--integration",
-                    ordered_keys[0],
-                    "--script",
-                    "sh",
-                    "--ignore-agent-tools",
-                ],
-                catch_exceptions=False,
-            )
-            assert init_result.exit_code == 0, init_result.output
-
-            for key in ordered_keys[1:]:
                install_result = runner.invoke(
                    app,
-                    ["integration", "install", key, "--script", "sh"],
+                    ["integration", "install", additional, "--script", "sh"],
                    catch_exceptions=False,
                )
                assert install_result.exit_code == 0, install_result.output
-        finally:
-            os.chdir(original_cwd)
+            finally:
+                os.chdir(original_cwd)

-        integrations_dir = project_root / ".specify" / "integrations"
-        manifests = {}
-        for key in ordered_keys:
-            manifest = json.loads(
-                (integrations_dir / f"{key}.manifest.json").read_text(encoding="utf-8")
+            initial_manifest = json.loads(
+                (
+                    project_root / ".specify" / "integrations" / f"{initial}.manifest.json"
+                ).read_text(encoding="utf-8")
+            )
+            additional_manifest = json.loads(
+                (
+                    project_root / ".specify" / "integrations" / f"{additional}.manifest.json"
+                ).read_text(encoding="utf-8")
            )
-            files = manifest.get("files", {})
-            assert isinstance(files, dict), f"{key} manifest files must be an object"
-            manifests[key] = set(files.keys())

-        for first, second in _multi_install_safe_pairs():
-            overlap = manifests[first] & manifests[second]
-            assert not overlap, (
-                f"{first} and {second} are declared multi-install safe but both manage "
-                f"these files: {sorted(overlap)}"
+            initial_files = set(initial_manifest.get("files", {}))
+            additional_files = set(additional_manifest.get("files", {}))
+
+            assert initial_files.isdisjoint(additional_files), (
+                f"{initial} and {additional} are declared multi-install safe but both manage "
+                f"these files: {sorted(initial_files & additional_files)}"
            )


--- a/tests/test_check_prerequisites_python_parity.py
+++ b/tests/test_check_prerequisites_python_parity.py
@@ -1,339 +0,0 @@
-"""Parity tests for the Python check-prerequisites PoC."""
-
-from __future__ import annotations
-
-import json
-import os
-import shutil
-import subprocess
-import sys
-from pathlib import Path
-
-import pytest
-
-from tests.conftest import requires_bash
-
-PROJECT_ROOT = Path(__file__).resolve().parent.parent
-COMMON_SH = PROJECT_ROOT / "scripts" / "bash" / "common.sh"
-CHECK_PREREQS_SH = PROJECT_ROOT / "scripts" / "bash" / "check-prerequisites.sh"
-COMMON_PS = PROJECT_ROOT / "scripts" / "powershell" / "common.ps1"
-CHECK_PREREQS_PS = PROJECT_ROOT / "scripts" / "powershell" / "check-prerequisites.ps1"
-COMMON_PY = PROJECT_ROOT / "scripts" / "python" / "common.py"
-CHECK_PREREQS_PY = PROJECT_ROOT / "scripts" / "python" / "check_prerequisites.py"
-
-HAS_PWSH = shutil.which("pwsh") is not None
-_WINDOWS_POWERSHELL = (
-    shutil.which("powershell.exe") or shutil.which("powershell")
-) if os.name == "nt" else None
-
-
-def _install_scripts(repo: Path) -> None:
-    bash_dir = repo / ".specify" / "scripts" / "bash"
-    bash_dir.mkdir(parents=True, exist_ok=True)
-    shutil.copy(COMMON_SH, bash_dir / "common.sh")
-    shutil.copy(CHECK_PREREQS_SH, bash_dir / "check-prerequisites.sh")
-
-    ps_dir = repo / ".specify" / "scripts" / "powershell"
-    ps_dir.mkdir(parents=True, exist_ok=True)
-    shutil.copy(COMMON_PS, ps_dir / "common.ps1")
-    shutil.copy(CHECK_PREREQS_PS, ps_dir / "check-prerequisites.ps1")
-
-    py_dir = repo / ".specify" / "scripts" / "python"
-    py_dir.mkdir(parents=True, exist_ok=True)
-    shutil.copy(COMMON_PY, py_dir / "common.py")
-    shutil.copy(CHECK_PREREQS_PY, py_dir / "check_prerequisites.py")
-
-
-def _write_feature_json(
-    repo: Path, feature_directory: str = "specs/001-my-feature"
-) -> None:
-    (repo / ".specify" / "feature.json").write_text(
-        json.dumps({"feature_directory": feature_directory}, separators=(",", ":"))
-        + "\n",
-        encoding="utf-8",
-    )
-
-
-def _clean_env() -> dict[str, str]:
-    env = os.environ.copy()
-    for key in list(env):
-        if key.startswith("SPECIFY_"):
-            env.pop(key)
-    return env
-
-
-def _git_init(repo: Path) -> None:
-    subprocess.run(["git", "init", "-q"], cwd=repo, check=True)
-    subprocess.run(
-        ["git", "config", "user.email", "test@example.com"], cwd=repo, check=True
-    )
-    subprocess.run(["git", "config", "user.name", "Test User"], cwd=repo, check=True)
-    subprocess.run(
-        ["git", "commit", "--allow-empty", "-m", "init", "-q"], cwd=repo, check=True
-    )
-
-
-@pytest.fixture
-def prereq_repo(tmp_path: Path) -> Path:
-    repo = tmp_path / "proj"
-    repo.mkdir()
-    _git_init(repo)
-    (repo / ".specify").mkdir()
-    _install_scripts(repo)
-    return repo
-
-
-def _py_cmd(repo: Path, *args: str) -> list[str]:
-    script = repo / ".specify" / "scripts" / "python" / "check_prerequisites.py"
-    return [sys.executable, str(script), *args]
-
-
-def _repo_copy_py_cmd(repo: Path, *args: str) -> list[str]:
-    script = repo / "scripts" / "python" / "check_prerequisites.py"
-    return [sys.executable, str(script), *args]
-
-
-def _bash_cmd(repo: Path, *args: str) -> list[str]:
-    script = repo / ".specify" / "scripts" / "bash" / "check-prerequisites.sh"
-    return ["bash", str(script), *args]
-
-
-def _ps_cmd(repo: Path, *args: str) -> list[str]:
-    script = repo / ".specify" / "scripts" / "powershell" / "check-prerequisites.ps1"
-    exe = "pwsh" if HAS_PWSH else _WINDOWS_POWERSHELL
-    return [exe, "-NoProfile", "-File", str(script), *args]
-
-
-def _run(
-    cmd: list[str], repo: Path, env: dict[str, str] | None = None
-) -> subprocess.CompletedProcess[str]:
-    return subprocess.run(
-        cmd,
-        cwd=repo,
-        capture_output=True,
-        text=True,
-        check=False,
-        env=env or _clean_env(),
-    )
-
-
-def _json_stdout(result: subprocess.CompletedProcess[str]) -> object:
-    return json.loads(result.stdout)
-
-
-def _normalize_status_text(text: str) -> str:
-    return (
-        text.replace("  ✓ ", "  [OK] ")
-        .replace("  ✗ ", "  [FAIL] ")
-        .replace("\r\n", "\n")
-    )
-
-
-def _normalize_help_text(text: str) -> str:
-    normalized = text.replace("\r\n", "\n").replace(
-        "check-prerequisites.sh", "check_prerequisites.py"
-    )
-    return "\n".join("" if not line.strip() else line for line in normalized.split("\n"))
-
-
-@requires_bash
-@pytest.mark.parametrize(
-    "args",
-    [
-        ("--json",),
-        ("--json", "--include-tasks"),
-        ("--json", "--require-tasks", "--include-tasks"),
-        ("--json", "--paths-only"),
-    ],
-)
-def test_python_json_output_matches_bash(prereq_repo: Path, args: tuple[str, ...]) -> None:
-    feat = prereq_repo / "specs" / "001-my-feature"
-    feat.mkdir(parents=True)
-    (feat / "plan.md").write_text("# plan\n", encoding="utf-8")
-    (feat / "tasks.md").write_text("# tasks\n", encoding="utf-8")
-    (feat / "research.md").write_text("# research\n", encoding="utf-8")
-    (feat / "data-model.md").write_text("# model\n", encoding="utf-8")
-    (feat / "quickstart.md").write_text("# quickstart\n", encoding="utf-8")
-    (feat / "contracts" / "v1").mkdir(parents=True)
-    _write_feature_json(prereq_repo)
-
-    bash = _run(_bash_cmd(prereq_repo, *args), prereq_repo)
-    py = _run(_py_cmd(prereq_repo, *args), prereq_repo)
-
-    assert py.returncode == bash.returncode == 0
-    assert py.stderr == bash.stderr == ""
-    assert _json_stdout(py) == _json_stdout(bash)
-
-
-@requires_bash
-def test_python_text_output_matches_bash(prereq_repo: Path) -> None:
-    feat = prereq_repo / "specs" / "001-my-feature"
-    feat.mkdir(parents=True)
-    (feat / "plan.md").write_text("# plan\n", encoding="utf-8")
-    (feat / "contracts").mkdir()
-    _write_feature_json(prereq_repo)
-
-    bash = _run(_bash_cmd(prereq_repo, "--include-tasks"), prereq_repo)
-    py = _run(_py_cmd(prereq_repo, "--include-tasks"), prereq_repo)
-
-    assert py.returncode == bash.returncode == 0
-    assert py.stderr == bash.stderr == ""
-    assert _normalize_status_text(py.stdout) == _normalize_status_text(bash.stdout)
-
-
-@requires_bash
-def test_python_help_output_matches_bash(prereq_repo: Path) -> None:
-    bash = _run(_bash_cmd(prereq_repo, "--help"), prereq_repo)
-    py = _run(_py_cmd(prereq_repo, "--help"), prereq_repo)
-
-    assert py.returncode == bash.returncode == 0
-    assert py.stderr == bash.stderr == ""
-    assert _normalize_help_text(py.stdout) == _normalize_help_text(bash.stdout)
-
-
-@requires_bash
-def test_python_unknown_option_matches_bash_error_shape(prereq_repo: Path) -> None:
-    bash = _run(_bash_cmd(prereq_repo, "--bogus"), prereq_repo)
-    py = _run(_py_cmd(prereq_repo, "--bogus"), prereq_repo)
-
-    assert py.returncode == bash.returncode == 1
-    assert py.stdout == bash.stdout == ""
-    assert py.stderr == bash.stderr
-
-
-@pytest.mark.skipif(not (HAS_PWSH or _WINDOWS_POWERSHELL), reason="no PowerShell available")
-@pytest.mark.parametrize(
-    ("py_args", "ps_args"),
-    [
-        (("--json",), ("-Json",)),
-        (("--json", "--include-tasks"), ("-Json", "-IncludeTasks")),
-        (
-            ("--json", "--require-tasks", "--include-tasks"),
-            ("-Json", "-RequireTasks", "-IncludeTasks"),
-        ),
-        (("--json", "--paths-only"), ("-Json", "-PathsOnly")),
-    ],
-    ids=[
-        "json",
-        "json_include_tasks",
-        "json_require_tasks_include_tasks",
-        "json_paths_only",
-    ],
-)
-def test_python_json_output_matches_powershell(
-    prereq_repo: Path, py_args: tuple[str, ...], ps_args: tuple[str, ...]
-) -> None:
-    feat = prereq_repo / "specs" / "001-my-feature"
-    feat.mkdir(parents=True)
-    (feat / "plan.md").write_text("# plan\n", encoding="utf-8")
-    (feat / "tasks.md").write_text("# tasks\n", encoding="utf-8")
-    (feat / "research.md").write_text("# research\n", encoding="utf-8")
-    (feat / "data-model.md").write_text("# model\n", encoding="utf-8")
-    (feat / "quickstart.md").write_text("# quickstart\n", encoding="utf-8")
-    (feat / "contracts" / "v1").mkdir(parents=True)
-    _write_feature_json(prereq_repo)
-
-    ps = _run(_ps_cmd(prereq_repo, *ps_args), prereq_repo)
-    py = _run(_py_cmd(prereq_repo, *py_args), prereq_repo)
-
-    assert py.returncode == ps.returncode == 0
-    assert py.stderr == ps.stderr == ""
-    assert _json_stdout(py) == _json_stdout(ps)
-
-
-def test_python_repo_copy_script_file_fallback_finds_repo_root(tmp_path: Path) -> None:
-    repo = tmp_path / "proj"
-    outside = tmp_path / "outside"
-    repo.mkdir()
-    outside.mkdir()
-    _git_init(repo)
-    (repo / ".specify").mkdir()
-    _write_feature_json(repo)
-    (repo / "specs" / "001-my-feature").mkdir(parents=True)
-
-    py_dir = repo / "scripts" / "python"
-    py_dir.mkdir(parents=True)
-    shutil.copy(COMMON_PY, py_dir / "common.py")
-    shutil.copy(CHECK_PREREQS_PY, py_dir / "check_prerequisites.py")
-
-    py = _run(_repo_copy_py_cmd(repo, "--json", "--paths-only"), outside)
-
-    assert py.returncode == 0, py.stderr
-    assert Path(_json_stdout(py)["REPO_ROOT"]) == repo
-
-
-def test_python_paths_only_does_not_persist_feature_json(prereq_repo: Path) -> None:
-    (prereq_repo / "specs" / "001-my-feature").mkdir(parents=True)
-    (prereq_repo / "specs" / "002-other").mkdir(parents=True)
-    _write_feature_json(prereq_repo, "specs/001-my-feature")
-    feature_json = prereq_repo / ".specify" / "feature.json"
-    before = feature_json.read_text(encoding="utf-8")
-    env = _clean_env()
-    env["SPECIFY_FEATURE_DIRECTORY"] = "specs/002-other"
-
-    py = _run(_py_cmd(prereq_repo, "--json", "--paths-only"), prereq_repo, env=env)
-
-    assert py.returncode == 0, py.stderr
-    assert "002-other" in _json_stdout(py)["FEATURE_DIR"]
-    assert feature_json.read_text(encoding="utf-8") == before
-
-
-def test_python_normal_mode_persists_feature_json(prereq_repo: Path) -> None:
-    (prereq_repo / "specs" / "001-my-feature").mkdir(parents=True)
-    feat = prereq_repo / "specs" / "002-other"
-    feat.mkdir(parents=True)
-    (feat / "plan.md").write_text("# plan\n", encoding="utf-8")
-    _write_feature_json(prereq_repo, "specs/001-my-feature")
-    env = _clean_env()
-    env["SPECIFY_FEATURE_DIRECTORY"] = "specs/002-other"
-
-    py = _run(_py_cmd(prereq_repo, "--json"), prereq_repo, env=env)
-
-    assert py.returncode == 0, py.stderr
-    data = json.loads(
-        (prereq_repo / ".specify" / "feature.json").read_text(encoding="utf-8")
-    )
-    assert data["feature_directory"] == "specs/002-other"
-
-
-@pytest.mark.parametrize(
-    ("args", "expected"),
-    [
-        (("--json",), "Feature directory not found"),
-        (("--json",), "plan.md not found"),
-        (("--json", "--require-tasks"), "tasks.md not found"),
-    ],
-    ids=["missing_feature_context", "missing_plan", "missing_tasks"],
-)
-def test_python_negative_errors_are_stderr_only(
-    tmp_path: Path, args: tuple[str, ...], expected: str
-) -> None:
-    repo = tmp_path / "proj"
-    repo.mkdir()
-    _git_init(repo)
-    (repo / ".specify").mkdir()
-    _install_scripts(repo)
-
-    if expected in {"plan.md not found", "tasks.md not found"}:
-        feat = repo / "specs" / "001-my-feature"
-        feat.mkdir(parents=True)
-        _write_feature_json(repo)
-        if expected == "tasks.md not found":
-            (feat / "plan.md").write_text("# plan\n", encoding="utf-8")
-
-    py = _run(_py_cmd(repo, *args), repo)
-
-    assert py.returncode != 0
-    assert expected in py.stderr
-    assert expected not in py.stdout
-    assert py.stdout.strip() == ""
-
-
-def test_python_branch_falls_back_to_feature_dir_basename(prereq_repo: Path) -> None:
-    (prereq_repo / "specs" / "001-my-feature").mkdir(parents=True)
-    _write_feature_json(prereq_repo)
-
-    py = _run(_py_cmd(prereq_repo, "--json", "--paths-only"), prereq_repo)
-
-    assert py.returncode == 0, py.stderr
-    assert _json_stdout(py)["BRANCH"] == "001-my-feature"
--- a/tests/test_extension_skills.py
+++ b/tests/test_extension_skills.py
@@ -850,67 +850,6 @@ class TestExtensionSkillRegistration:
        assert ".specify/templates/checklist.md" in content
        assert ".specify/memory/constitution.md" in content

-    def test_skill_registration_uses_extension_local_script_paths(self, project_dir, temp_dir):
-        """Auto-registered skills should not rewrite extension scripts into core scripts."""
-        _create_init_options(project_dir, ai="claude", ai_skills=True)
-        skills_dir = _create_skills_dir(project_dir, ai="claude")
-
-        ext_dir = temp_dir / "scripted-ext"
-        ext_dir.mkdir()
-        manifest_data = {
-            "schema_version": "1.0",
-            "extension": {
-                "id": "scripted-ext",
-                "name": "Scripted Extension",
-                "version": "1.0.0",
-                "description": "Test",
-            },
-            "requires": {"speckit_version": ">=0.1.0"},
-            "provides": {
-                "commands": [
-                    {
-                        "name": "speckit.scripted-ext.check",
-                        "file": "commands/check.md",
-                        "description": "Scripted check command",
-                    }
-                ]
-            },
-        }
-        with open(ext_dir / "extension.yml", "w") as f:
-            yaml.safe_dump(manifest_data, f)
-
-        (ext_dir / "commands").mkdir()
-        (ext_dir / "scripts" / "bash").mkdir(parents=True)
-        (ext_dir / "scripts" / "bash" / "resolve-skill.sh").write_text(
-            "#!/usr/bin/env bash\n"
-        )
-        (ext_dir / "scripts" / "bash" / "ensure-skills.sh").write_text(
-            "#!/usr/bin/env bash\n"
-        )
-        (ext_dir / "commands" / "check.md").write_text(
-            "---\n"
-            "description: Scripted check command\n"
-            "scripts:\n"
-            '  sh: scripts/bash/resolve-skill.sh "{ARGS}"\n'
-            "---\n\n"
-            "Run {SCRIPT}\n"
-            "Then run scripts/bash/ensure-skills.sh.\n"
-        )
-
-        manager = ExtensionManager(project_dir)
-        manager.install_from_directory(ext_dir, "0.1.0", register_commands=False)
-
-        content = (skills_dir / "speckit-scripted-ext-check" / "SKILL.md").read_text()
-        assert "{SCRIPT}" not in content
-        assert "{ARGS}" not in content
-        assert (
-            '.specify/extensions/scripted-ext/scripts/bash/resolve-skill.sh "$ARGUMENTS"'
-            in content
-        )
-        assert ".specify/extensions/scripted-ext/scripts/bash/ensure-skills.sh" in content
-        assert ".specify/scripts/bash/resolve-skill.sh" not in content
-        assert ".specify/scripts/bash/ensure-skills.sh" not in content
-
    def test_missing_command_file_skipped(self, skills_project, temp_dir):
        """Commands with missing source files should be skipped gracefully."""
        project_dir, skills_dir = skills_project
--- a/tests/test_extensions.py
+++ b/tests/test_extensions.py
@@ -31,7 +31,6 @@ from specify_cli.extensions import (
    ExtensionRegistry,
    ExtensionManager,
    CommandRegistrar,
-    ConfigManager,
    HookExecutor,
    ExtensionCatalog,
    ExtensionError,
@@ -1147,12 +1146,10 @@ class TestExtensionManager:
            context_note=None,
            link_outputs=False,
            create_missing_active_skills_dir=False,
-            extension_id=None,
        ):
            captured["create_missing_active_skills_dir"] = (
                create_missing_active_skills_dir
            )
-            captured["extension_id"] = extension_id
            return {}

        monkeypatch.setattr(
@@ -1166,7 +1163,6 @@ class TestExtensionManager:
        registrar.register_commands_for_all_agents(manifest, extension_dir, project_dir)

        assert captured["create_missing_active_skills_dir"] is False
-        assert captured["extension_id"] == manifest.id

    def test_install_duplicate(self, extension_dir, project_dir):
        """Test installing already installed extension."""
@@ -1698,29 +1694,6 @@ $ARGUMENTS
        assert adjusted["scripts"]["sh"] == ".specify/extensions/test-ext/scripts/setup.sh {ARGS}"
        assert adjusted["scripts"]["ps"] == ".specify/scripts/powershell/setup-plan.ps1 {ARGS}"

-    def test_adjust_script_paths_rewrites_extension_top_level_scripts(self):
-        """Extension command-local scripts should resolve under the installed extension."""
-        from specify_cli.agents import CommandRegistrar as AgentCommandRegistrar
-
-        registrar = AgentCommandRegistrar()
-        original = {
-            "scripts": {
-                "sh": "scripts/bash/resolve-skill.sh {ARGS}",
-                "ps": "../../scripts/powershell/setup-plan.ps1 -Json",
-            }
-        }
-
-        adjusted = registrar._adjust_script_paths(original, extension_id="test-ext")
-
-        assert (
-            adjusted["scripts"]["sh"]
-            == ".specify/extensions/test-ext/scripts/bash/resolve-skill.sh {ARGS}"
-        )
-        assert (
-            adjusted["scripts"]["ps"]
-            == ".specify/scripts/powershell/setup-plan.ps1 -Json"
-        )
-
    def test_rewrite_project_relative_paths_preserves_extension_local_body_paths(self):
        """Body rewrites should preserve extension-local assets while fixing top-level refs."""
        from specify_cli.agents import CommandRegistrar as AgentCommandRegistrar
@@ -1735,24 +1708,6 @@ $ARGUMENTS
        assert ".specify/extensions/test-ext/templates/spec.md" in rewritten
        assert ".specify/scripts/bash/setup-plan.sh" in rewritten

-    def test_rewrite_project_relative_paths_uses_extension_context_for_scripts(self):
-        """Extension source bodies treat top-level scripts/ as extension-local."""
-        from specify_cli.agents import CommandRegistrar as AgentCommandRegistrar
-
-        body = (
-            "Run scripts/bash/ensure-skills.sh\n"
-            "Fallback ../../scripts/bash/setup-plan.sh\n"
-            "Read templates/checklist.md\n"
-        )
-
-        rewritten = AgentCommandRegistrar.rewrite_project_relative_paths(
-            body, extension_id="test-ext"
-        )
-
-        assert ".specify/extensions/test-ext/scripts/bash/ensure-skills.sh" in rewritten
-        assert ".specify/scripts/bash/setup-plan.sh" in rewritten
-        assert ".specify/templates/checklist.md" in rewritten
-
    def test_render_toml_command_handles_embedded_triple_double_quotes(self):
        """TOML renderer should stay valid when body includes triple double-quotes."""
        from specify_cli.agents import CommandRegistrar as AgentCommandRegistrar
@@ -7537,52 +7492,3 @@ def test_extension_wrapper_resolves_ghes_asset_when_host_configured(tmp_path, mo
    )
    assert resolved == "https://ghes.example/api/v3/repos/o/r/releases/assets/7"
    assert captured == ["https://ghes.example/api/v3/repos/o/r/releases/tags/v1"]
-
-
-class TestConfigManagerNonMappingYaml:
-    """A non-mapping YAML config root must not crash config/hook resolution."""
-
-    def _make(self, tmp_path, body: str):
-        ext_dir = tmp_path / ".specify" / "extensions" / "jira"
-        ext_dir.mkdir(parents=True)
-        (ext_dir / "jira-config.yml").write_text(body, encoding="utf-8")
-        return ConfigManager(tmp_path, "jira")
-
-    def test_get_config_coerces_list_root(self, tmp_path):
-        """A YAML list root previously raised AttributeError in _merge_configs."""
-        cm = self._make(tmp_path, "- foo\n- bar\n")
-        assert cm.get_config() == {}
-
-    def test_get_config_coerces_scalar_root(self, tmp_path):
-        cm = self._make(tmp_path, "just a string\n")
-        assert cm.get_config() == {}
-
-    def test_has_value_and_get_value_do_not_raise(self, tmp_path):
-        cm = self._make(tmp_path, "- foo\n")
-        assert cm.has_value("anything") is False
-        assert cm.get_value("anything") is None
-
-    def test_valid_local_config_layers_over_list_root_project_config(self, tmp_path):
-        """A malformed project config must not block a valid local config."""
-        ext_dir = tmp_path / ".specify" / "extensions" / "jira"
-        ext_dir.mkdir(parents=True)
-        (ext_dir / "jira-config.yml").write_text("- foo\n- bar\n", encoding="utf-8")
-        (ext_dir / "local-config.yml").write_text(
-            "notifications:\n  enabled: true\n", encoding="utf-8"
-        )
-        cm = ConfigManager(tmp_path, "jira")
-        assert cm.get_value("notifications.enabled") is True
-
-    def test_hook_condition_returns_false_without_raising(self, tmp_path):
-        """`config.x is set` on a scalar-root config must evaluate cleanly.
-
-        Before the fix, _merge_configs raised AttributeError and the
-        exception was swallowed by should_execute_hook, silently disabling
-        every config-based hook for the extension. Assert on
-        _evaluate_condition directly so the crash isn't masked.
-        """
-        ext_dir = tmp_path / ".specify" / "extensions" / "jira"
-        ext_dir.mkdir(parents=True)
-        (ext_dir / "jira-config.yml").write_text("just a string\n", encoding="utf-8")
-        executor = HookExecutor(tmp_path)
-        assert executor._evaluate_condition("config.x is set", "jira") is False
--- a/tests/test_post_process.py
+++ b/tests/test_post_process.py
@@ -1,245 +0,0 @@
-"""Tests for post_process_command_content() hook on IntegrationBase.
-
-Verifies that the generalized post-processing hook:
- Runs for non-skills format types (Markdown, TOML, YAML)
- Does NOT run for skills-format agents
- Default no-op returns content unchanged
- Exceptions propagate to caller
-"""
-
-from __future__ import annotations
-
-from unittest.mock import patch
-
-import pytest
-
-from specify_cli.agents import CommandRegistrar
-from specify_cli.integrations.base import IntegrationBase
-
-
-@pytest.fixture
-def registrar():
-    return CommandRegistrar()
-
-
-@pytest.fixture
-def ext_dir(tmp_path):
-    """Create a mock extension with a simple command template."""
-    ext = tmp_path / "extension"
-    ext.mkdir()
-    cmd_dir = ext / "commands"
-    cmd_dir.mkdir()
-    return ext, cmd_dir
-
-
-def _write_cmd(cmd_dir, name="review.md", body="Review the code.\n"):
-    cmd_file = cmd_dir / name
-    cmd_file.write_text(
-        f"---\ndescription: Test command\n---\n\n{body}",
-        encoding="utf-8",
-    )
-    return cmd_file
-
-
-class TestDefaultNoOp:
-    def test_returns_content_unchanged(self):
-        base = IntegrationBase()
-        content = "Some command content\nwith multiple lines."
-        assert base.post_process_command_content(content) == content
-
-    def test_empty_string(self):
-        base = IntegrationBase()
-        assert base.post_process_command_content("") == ""
-
-
-class TestMarkdownAgentPostProcess:
-    def test_opencode_post_process_applied(
-        self, tmp_path, registrar, ext_dir, monkeypatch
-    ):
-        ext, cmd_dir = ext_dir
-        _write_cmd(cmd_dir)
-
-        from specify_cli.integrations import get_integration
-
-        opencode = get_integration("opencode")
-        marker = "<!-- POST_PROCESSED -->"
-
-        def _inject_marker(self, content):
-            return content + marker
-
-        monkeypatch.setattr(
-            opencode.__class__, "post_process_command_content", _inject_marker
-        )
-
-        commands = [{"name": "speckit.test.review", "file": "commands/review.md"}]
-        registrar.register_commands(
-            "opencode", commands, "test-ext", ext, tmp_path
-        )
-
-        cmd_output = tmp_path / ".opencode" / "commands" / "speckit.test.review.md"
-        assert cmd_output.exists()
-        content = cmd_output.read_text(encoding="utf-8")
-        assert marker in content
-
-
-class TestTomlAgentPostProcess:
-    def test_gemini_post_process_applied(
-        self, tmp_path, registrar, ext_dir, monkeypatch
-    ):
-        ext, cmd_dir = ext_dir
-        _write_cmd(cmd_dir)
-
-        from specify_cli.integrations import get_integration
-
-        gemini = get_integration("gemini")
-        marker = "# POST_PROCESSED"
-
-        def _inject_marker(self, content):
-            return content + f"\n{marker}\n"
-
-        monkeypatch.setattr(
-            gemini.__class__, "post_process_command_content", _inject_marker
-        )
-
-        commands = [{"name": "speckit.test.review", "file": "commands/review.md"}]
-        registrar.register_commands(
-            "gemini", commands, "test-ext", ext, tmp_path
-        )
-
-        cmd_output = tmp_path / ".gemini" / "commands" / "speckit.test.review.toml"
-        assert cmd_output.exists()
-        content = cmd_output.read_text(encoding="utf-8")
-        assert marker in content
-
-
-class TestYamlAgentPostProcess:
-    def test_goose_post_process_applied(
-        self, tmp_path, registrar, ext_dir, monkeypatch
-    ):
-        ext, cmd_dir = ext_dir
-        _write_cmd(cmd_dir)
-
-        from specify_cli.integrations import get_integration
-
-        goose = get_integration("goose")
-        marker = "# POST_PROCESSED"
-
-        def _inject_marker(self, content):
-            return content + f"\n{marker}\n"
-
-        monkeypatch.setattr(
-            goose.__class__, "post_process_command_content", _inject_marker
-        )
-
-        commands = [{"name": "speckit.test.review", "file": "commands/review.md"}]
-        registrar.register_commands(
-            "goose", commands, "test-ext", ext, tmp_path
-        )
-
-        cmd_output = tmp_path / ".goose" / "recipes" / "speckit.test.review.yaml"
-        assert cmd_output.exists()
-        content = cmd_output.read_text(encoding="utf-8")
-        assert marker in content
-
-
-class TestSkillsAgentExcluded:
-    def test_claude_post_process_not_called(
-        self, tmp_path, registrar, ext_dir, monkeypatch
-    ):
-        ext, cmd_dir = ext_dir
-        _write_cmd(cmd_dir)
-
-        from specify_cli.integrations import get_integration
-
-        claude = get_integration("claude")
-        marker = "<!-- SHOULD_NOT_APPEAR -->"
-
-        def _inject_marker(self, content):
-            return content + marker
-
-        monkeypatch.setattr(
-            claude.__class__, "post_process_command_content", _inject_marker
-        )
-
-        commands = [{"name": "speckit.test.review", "file": "commands/review.md"}]
-        registrar.register_commands(
-            "claude", commands, "test-ext", ext, tmp_path
-        )
-
-        skill_file = (
-            tmp_path / ".claude" / "skills" / "speckit-test-review" / "SKILL.md"
-        )
-        assert skill_file.exists()
-        content = skill_file.read_text(encoding="utf-8")
-        assert marker not in content
-
-    def test_skills_agent_method_never_called(
-        self, tmp_path, registrar, ext_dir
-    ):
-        ext, cmd_dir = ext_dir
-        _write_cmd(cmd_dir)
-
-        from specify_cli.integrations import get_integration
-
-        claude = get_integration("claude")
-        commands = [{"name": "speckit.test.review", "file": "commands/review.md"}]
-
-        with patch.object(
-            claude.__class__, "post_process_command_content", wraps=claude.post_process_command_content
-        ) as mock_method:
-            registrar.register_commands(
-                "claude", commands, "test-ext", ext, tmp_path
-            )
-            mock_method.assert_not_called()
-
-
-class TestExceptionPropagation:
-    def test_hook_exception_propagates(
-        self, tmp_path, registrar, ext_dir, monkeypatch
-    ):
-        ext, cmd_dir = ext_dir
-        _write_cmd(cmd_dir)
-
-        from specify_cli.integrations import get_integration
-
-        opencode = get_integration("opencode")
-
-        def _raise(self, content):
-            raise RuntimeError("Hook failed")
-
-        monkeypatch.setattr(
-            opencode.__class__, "post_process_command_content", _raise
-        )
-
-        commands = [{"name": "speckit.test.review", "file": "commands/review.md"}]
-        with pytest.raises(RuntimeError, match="Hook failed"):
-            registrar.register_commands(
-                "opencode", commands, "test-ext", ext, tmp_path
-            )
-
-
-class TestRegressionPlainTemplate:
-    @pytest.mark.parametrize(
-        "agent,path_pattern",
-        [
-            ("claude", ".claude/skills/speckit-test-plain/SKILL.md"),
-            ("opencode", ".opencode/commands/speckit.test.plain.md"),
-        ],
-        ids=["skills", "markdown"],
-    )
-    def test_plain_template_unchanged(
-        self, tmp_path, registrar, ext_dir, agent, path_pattern
-    ):
-        ext, cmd_dir = ext_dir
-        body_text = "This is a plain command with no special content.\n"
-        _write_cmd(cmd_dir, name="plain.md", body=body_text)
-
-        commands = [{"name": "speckit.test.plain", "file": "commands/plain.md"}]
-        registrar.register_commands(
-            agent, commands, "test-ext", ext, tmp_path
-        )
-
-        output_file = tmp_path / path_pattern
-        assert output_file.exists(), f"Output file missing for {agent}"
-        content = output_file.read_text(encoding="utf-8")
-        assert body_text.strip() in content, f"Body text missing in {agent} output"
--- a/tests/test_workflow_run_without_project.py
+++ b/tests/test_workflow_run_without_project.py
@@ -322,87 +322,3 @@ class TestWorkflowRunWithoutProject:

        assert result.exit_code != 0
        assert ".specify path exists but is not a directory" in result.output
-
-
-class TestWorkflowRunJsonErrorStream:
-    """Under --json, error text must go to stderr so stdout stays parseable."""
-
-    def _bad_workflow(self, tmp_path):
-        wf = tmp_path / "bad.yml"
-        wf.write_text(
-            yaml.dump(
-                {
-                    "schema_version": "1.0",
-                    "workflow": {
-                        "id": "bad-wf",
-                        "name": "Bad",
-                        "version": "1.0.0",
-                        "description": "fails validation",
-                    },
-                    # shell step missing required 'run' -> validation error
-                    "steps": [{"id": "s", "type": "shell"}],
-                }
-            ),
-            encoding="utf-8",
-        )
-        return wf
-
-    def test_run_json_validation_error_not_on_stdout(self, tmp_path):
-        from typer.testing import CliRunner
-        from specify_cli import app
-
-        wf = self._bad_workflow(tmp_path)
-        runner = CliRunner()
-        old = os.getcwd()
-        try:
-            os.chdir(tmp_path)
-            result = runner.invoke(
-                app, ["workflow", "run", str(wf), "--json"], catch_exceptions=False
-            )
-        finally:
-            os.chdir(old)
-
-        assert result.exit_code == 1
-        # stdout must carry only JSON (here: nothing) — never human error text.
-        assert "validation failed" not in result.stdout
-        assert "Error" not in result.stdout
-        # The message is routed to stderr instead.
-        assert "validation failed" in result.stderr
-
-    def test_run_json_invalid_input_not_on_stdout(self, tmp_path):
-        from typer.testing import CliRunner
-        from specify_cli import app
-
-        # A valid single-shell workflow so we get past load/validate to
-        # _parse_input_values, which rejects the malformed --input.
-        wf = tmp_path / "ok.yml"
-        wf.write_text(
-            yaml.dump(
-                {
-                    "schema_version": "1.0",
-                    "workflow": {
-                        "id": "ok-wf",
-                        "name": "OK",
-                        "version": "1.0.0",
-                        "description": "x",
-                    },
-                    "steps": [{"id": "s", "type": "shell", "run": "echo hi"}],
-                }
-            ),
-            encoding="utf-8",
-        )
-        runner = CliRunner()
-        old = os.getcwd()
-        try:
-            os.chdir(tmp_path)
-            result = runner.invoke(
-                app,
-                ["workflow", "run", str(wf), "--json", "--input", "no-equals"],
-                catch_exceptions=False,
-            )
-        finally:
-            os.chdir(old)
-
-        assert result.exit_code == 1
-        assert "Invalid input format" not in result.stdout
-        assert "Invalid input format" in result.stderr
--- a/tests/test_workflows.py
+++ b/tests/test_workflows.py
@@ -260,60 +260,6 @@ class TestExpressions:
        ctx = StepContext(inputs={"text": "uses }} syntax"})
        assert evaluate_expression("{{ inputs.text | contains('}}') }}", ctx) is True

-    def test_multi_expression_with_literal_close_brace_in_argument(self):
-        """A multi-expression template with a literal ``}}`` inside a string
-        argument must interpolate, not raise. #3208/#3228 hardened the single-
-        expression fast path for literal braces but left the interpolation path
-        on ``_EXPR_PATTERN``, whose non-greedy body stops at the first ``}}`` --
-        so the block was captured truncated and the filter parser raised
-        ValueError."""
-        from specify_cli.workflows.expressions import evaluate_expression
-        from specify_cli.workflows.base import StepContext
-
-        ctx = StepContext(inputs={"name": "Bob", "missing": None})
-        # ``}}`` in the default fallback of the second block.
-        result = evaluate_expression(
-            "{{ inputs.name }}: {{ inputs.missing | default('}}') }}", ctx
-        )
-        assert result == "Bob: }}"
-        # ``}}`` in the first block, expression following it.
-        result = evaluate_expression(
-            "{{ inputs.missing | default('}}') }} / {{ inputs.name }}", ctx
-        )
-        assert result == "}} / Bob"
-
-    def test_multi_expression_with_literal_open_brace_in_argument(self):
-        """A literal ``{{`` inside a string argument in a multi-expression
-        template must not confuse block detection either."""
-        from specify_cli.workflows.expressions import evaluate_expression
-        from specify_cli.workflows.base import StepContext
-
-        ctx = StepContext(inputs={"name": "Bob", "missing": None})
-        result = evaluate_expression(
-            "{{ inputs.name }} {{ inputs.missing | default('{{') }}", ctx
-        )
-        assert result == "Bob {{"
-
-    def test_multi_expression_unbalanced_quote_still_raises(self):
-        """A malformed block (an unbalanced quote in a filter arg) must still
-        surface a ValueError, not be silently emitted verbatim.
-
-        The quote-aware scan never finds a block-closing ``}}`` when a quote is
-        left open, but a raw ``}}`` is still present in the tail. It must fall
-        back to that raw delimiter and evaluate — same as the old regex path —
-        so a typo fails loudly instead of being hidden (Copilot review on
-        #3307)."""
-        import pytest
-
-        from specify_cli.workflows.expressions import evaluate_expression
-        from specify_cli.workflows.base import StepContext
-
-        ctx = StepContext(inputs={"name": "Bob", "missing": None})
-        with pytest.raises(ValueError):
-            evaluate_expression(
-                "{{ inputs.name }} {{ inputs.missing | default('oops }}", ctx
-            )
-
    def test_comparison_equals(self):
        from specify_cli.workflows.expressions import evaluate_expression
        from specify_cli.workflows.base import StepContext
@@ -342,35 +288,6 @@ class TestExpressions:
        assert evaluate_expression("{{ steps.plan.output.task_count > 5 }}", ctx) is True
        assert evaluate_expression("{{ steps.plan.output.task_count < 5 }}", ctx) is False

-    def test_ordering_comparison_of_non_numeric_strings(self):
-        """`<`/`>`/`<=`/`>=` between non-numeric strings must compare
-        lexicographically, not silently return False.
-
-        `_safe_compare` used to coerce both operands to int/float unconditionally;
-        a non-numeric string (date, version tag, name) failed that coercion and
-        the whole comparison returned False. Ordinary strings should order the
-        way Python does; numeric strings must still compare as numbers."""
-        from specify_cli.workflows.expressions import evaluate_expression
-        from specify_cli.workflows.base import StepContext
-
-        # ISO dates compare lexicographically (correct chronological order).
-        ctx = StepContext(inputs={"d": "2026-01-01"})
-        assert evaluate_expression("{{ inputs.d < '2026-02-01' }}", ctx) is True
-        assert evaluate_expression("{{ inputs.d > '2026-02-01' }}", ctx) is False
-
-        # Plain string ordering.
-        ctx = StepContext(inputs={"name": "beta"})
-        assert evaluate_expression("{{ inputs.name > 'alpha' }}", ctx) is True
-
-        # Two numeric strings still compare numerically, not lexically
-        # ("10" > "9" is True as numbers; as strings it would be False).
-        ctx = StepContext(inputs={"v": "10"})
-        assert evaluate_expression("{{ inputs.v > '9' }}", ctx) is True
-
-        # A number vs a non-numeric string is genuinely incomparable -> False.
-        ctx = StepContext(inputs={"n": 5})
-        assert evaluate_expression("{{ inputs.n > 'abc' }}", ctx) is False
-
    def test_boolean_and(self):
        from specify_cli.workflows.expressions import evaluate_expression
        from specify_cli.workflows.base import StepContext
@@ -1266,26 +1183,6 @@ class TestShellStep:
        errors = step.validate({"id": "test"})
        assert any("missing 'run'" in e for e in errors)

-    @pytest.mark.parametrize("bad_run", [None, ["echo", "hi"], 42])
-    def test_validate_rejects_non_string_run(self, bad_run):
-        """A non-string 'run' must be rejected at validation.
-
-        execute() str()-coerces run and invokes it under shell=True, so a
-        null or list run would otherwise run the Python repr as a command.
-        """
-        from specify_cli.workflows.steps.shell import ShellStep
-
-        step = ShellStep()
-        errors = step.validate({"id": "s", "run": bad_run})
-        assert any("'run' must be a string" in e for e in errors)
-
-    def test_validate_accepts_string_and_expression_run(self):
-        from specify_cli.workflows.steps.shell import ShellStep
-
-        step = ShellStep()
-        assert step.validate({"id": "s", "run": "echo hi"}) == []
-        assert step.validate({"id": "s", "run": "{{ steps.x.output }}"}) == []
-

    def test_output_format_json_exposes_data(self, tmp_path):
        from specify_cli.workflows.steps.shell import ShellStep
@@ -2202,27 +2099,6 @@ class TestFanInStep:
        errors = step.validate({"id": "test", "wait_for": "not-a-list"})
        assert any("non-empty list" in e for e in errors)

-    @pytest.mark.parametrize("bad_output", [["{{ fan_in.results }}"], "{{ x }}", 42])
-    def test_validate_rejects_non_mapping_output(self, bad_output):
-        """A non-mapping 'output' must be rejected: execute() would otherwise
-        silently coerce it to {} and drop the declared aggregation keys."""
-        from specify_cli.workflows.steps.fan_in import FanInStep
-
-        step = FanInStep()
-        errors = step.validate(
-            {"id": "j", "wait_for": ["a"], "output": bad_output}
-        )
-        assert any("'output' must be a mapping" in e for e in errors)
-
-    def test_validate_accepts_mapping_or_absent_output(self):
-        from specify_cli.workflows.steps.fan_in import FanInStep
-
-        step = FanInStep()
-        assert step.validate(
-            {"id": "j", "wait_for": ["a"], "output": {"joined": "{{ x }}"}}
-        ) == []
-        assert step.validate({"id": "j", "wait_for": ["a"]}) == []
-

 class TestFanOutConcurrency:
    """Fan-out honors max_concurrency (WorkflowEngine._run_fan_out)."""
@@ -4101,48 +3977,6 @@ steps:
        assert state.status == RunStatus.ABORTED
        assert "should-not-run" not in state.step_results

-    def test_gate_reject_matches_case_insensitively(
-        self, project_dir, monkeypatch
-    ):
-        """A capitalised reject option (`options: [Approve, Reject]`) still
-        aborts the run. `validate` accepts a reject choice case-insensitively,
-        so the runtime reject check must agree — a case-sensitive comparison
-        would treat the echoed `Reject` as approval and silently run
-        downstream steps.
-        """
-        from specify_cli.workflows.engine import WorkflowDefinition, WorkflowEngine
-        from specify_cli.workflows.base import RunStatus
-        from specify_cli.workflows.steps.gate import GateStep
-
-        # `_prompt` echoes the option's original casing, so the operator
-        # picking "Reject" hands `execute` the capitalised string.
-        _force_gate_stdin(monkeypatch, tty=True)
-        monkeypatch.setattr(
-            GateStep, "_prompt", staticmethod(lambda _msg, _opts: "Reject")
-        )
-
-        definition = WorkflowDefinition.from_string("""
-schema_version: "1.0"
-workflow:
-  id: "gate-reject-case"
-  name: "Gate Reject Case"
-  version: "1.0.0"
-steps:
-  - id: gate-step
-    type: gate
-    message: "Approve?"
-    options: [Approve, Reject]
-    on_reject: abort
-  - id: should-not-run
-    type: shell
-    run: "echo nope"
-""")
-        engine = WorkflowEngine(project_dir)
-        state = engine.execute(definition)
-
-        assert state.status == RunStatus.ABORTED
-        assert "should-not-run" not in state.step_results
-
    def test_validation_rejects_non_bool_continue_on_error(self):
        """`continue_on_error` must be a literal boolean; coerced
        strings like `"true"` are rejected at validation time so
--- a/tests/unit/test_bundler_adapters.py
+++ b/tests/unit/test_bundler_adapters.py
@@ -69,30 +69,3 @@ def test_http_fetch_rejects_non_https_final_url(monkeypatch):
    fetcher = adapters.make_catalog_fetcher(allow_network=True)
    with pytest.raises(BundlerError, match="must use HTTPS"):
        fetcher(_source("https://example.com/c.json"))
-
-
-@pytest.mark.parametrize(
-    "url",
-    [
-        "https://:8080",          # port only, no host
-        "https://:0",
-        "https://user@",          # userinfo only, no host
-        "https://user:pw@",
-        "https://:8080/catalog.json",
-    ],
-)
-def test_validate_remote_url_rejects_host_less_urls(url):
-    """A URL with a truthy netloc but no host (``https://:8080``,
-    ``https://user@``) must be rejected.
-
-    ``urlparse`` gives these a non-empty ``netloc`` but ``hostname is None``,
-    so a ``netloc`` check would wrongly accept them. This mirrors the fix in
-    ``specify_cli.catalogs`` (#3210), which the docstring says this validator
-    mirrors."""
-    with pytest.raises(BundlerError, match="valid URL with a host"):
-        adapters._validate_remote_url("team", url)
-
-
-def test_validate_remote_url_accepts_normal_https_url():
-    # Sanity: a real host with a port still passes.
-    adapters._validate_remote_url("team", "https://example.com:8080/c.json")
--- a/tests/unit/test_bundler_catalog_config.py
+++ b/tests/unit/test_bundler_catalog_config.py
@@ -222,39 +222,3 @@ def test_add_source_allows_local_path_with_colon(tmp_path: Path, monkeypatch):
    # A relative path containing ':' but no '://' is still a local path.
    source = cc.add_source(project, "weird:name.json", policy="install-allowed", priority=50)
    assert source.url.endswith("weird:name.json") or "weird" in source.url
-
-
-def test_add_source_rejects_plain_http_for_non_localhost(tmp_path: Path):
-    project = tmp_path / "proj"
-    (project / ".specify").mkdir(parents=True)
-    with pytest.raises(BundlerError, match="HTTPS"):
-        cc.add_source(project, "http://example.com/catalog.json", policy="install-allowed", priority=50)
-
-
-def test_add_source_allows_http_for_localhost(tmp_path: Path):
-    project = tmp_path / "proj"
-    (project / ".specify").mkdir(parents=True)
-    source = cc.add_source(project, "http://localhost:8080/c.json", policy="install-allowed", priority=50)
-    assert source.url == "http://localhost:8080/c.json"
-
-
-def test_add_source_rejects_host_less_remote_urls(tmp_path: Path):
-    project = tmp_path / "proj"
-    (project / ".specify").mkdir(parents=True)
-    for url in ("https://:8080", "https://user@"):
-        with pytest.raises(BundlerError, match="host"):
-            cc.add_source(project, url, policy="install-allowed", priority=50)
-
-
-def test_add_source_wraps_invalid_ipv6_as_bundler_error(tmp_path: Path):
-    project = tmp_path / "proj"
-    (project / ".specify").mkdir(parents=True)
-    with pytest.raises(BundlerError, match="Invalid catalog url"):
-        cc.add_source(project, "https://[::1/c.json", policy="install-allowed", priority=50)
-
-
-def test_remove_source_does_not_crash_on_invalid_ipv6(tmp_path: Path):
-    project = tmp_path / "proj"
-    (project / ".specify").mkdir(parents=True)
-    with pytest.raises(BundlerError, match="No project-scoped catalog source"):
-        cc.remove_source(project, "https://[::1/c.json")