fix: move 0.4.0 section above 0.3.2 to restore newest-first ordering in CHANGELOG.md

Co-authored-by: mnriem <15701806+mnriem@users.noreply.github.com>
Agent-Logs-Url: https://github.com/github/spec-kit/sessions/1c1787ad-64df-4b8c-bd32-0bc5198f5029

.github/workflows/docs.yml

@@ -64,5 +64,5 @@ jobs:
     steps:
       - name: Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@v5
+        uses: actions/deploy-pages@v4
 

.github/workflows/release-trigger.yml

@@ -100,16 +100,18 @@ jobs:
               COMMITS="- Initial release"
             fi
 
-            # Create new changelog entry — insert after the marker comment
-            NEW_ENTRY=$(printf '%s\n' \
-              "" \
-              "## [${{ steps.version.outputs.version }}] - $DATE" \
-              "" \
-              "### Changed" \
-              "" \
-              "$COMMITS")
-
-            awk -v entry="$NEW_ENTRY" '/<!-- insert new changelog below this comment -->/ { print; print entry; next } {print}' CHANGELOG.md > CHANGELOG.md.tmp
+            # Create new changelog entry
+            {
+              head -n 8 CHANGELOG.md
+              echo ""
+              echo "## [${{ steps.version.outputs.version }}] - $DATE"
+              echo ""
+              echo "### Changes"
+              echo ""
+              echo "$COMMITS"
+              echo ""
+              tail -n +9 CHANGELOG.md
+            } > CHANGELOG.md.tmp
             mv CHANGELOG.md.tmp CHANGELOG.md
 
             echo "✅ Updated CHANGELOG.md with commits since $PREVIOUS_TAG"

.github/workflows/scripts/create-release-packages.ps1

@@ -202,7 +202,8 @@ agent: $basename
 }
 
 # Create skills in <skills_dir>\<name>\SKILL.md format.
-# Skills use hyphenated names (e.g. speckit-plan).
+# Most agents use hyphenated names (e.g. speckit-plan); Kimi is the
+# current dotted-name exception (e.g. speckit.plan).
 #
 # Technical debt note:
 # Keep SKILL.md frontmatter aligned with `install_ai_skills()` and extension
@@ -462,7 +463,7 @@ function Build-Variant {
         'kimi' {
             $skillsDir = Join-Path $baseDir ".kimi/skills"
             New-Item -ItemType Directory -Force -Path $skillsDir | Out-Null
-            New-Skills -SkillsDir $skillsDir -ScriptVariant $Script -AgentName 'kimi'
+            New-Skills -SkillsDir $skillsDir -ScriptVariant $Script -AgentName 'kimi' -Separator '.'
         }
         'trae' {
             $rulesDir = Join-Path $baseDir ".trae/rules"

.github/workflows/scripts/create-release-packages.sh

@@ -140,7 +140,8 @@ EOF
 }
 
 # Create skills in <skills_dir>/<name>/SKILL.md format.
-# Skills use hyphenated names (e.g. speckit-plan).
+# Most agents use hyphenated names (e.g. speckit-plan); Kimi is the
+# current dotted-name exception (e.g. speckit.plan).
 #
 # Technical debt note:
 # Keep SKILL.md frontmatter aligned with `install_ai_skills()` and extension
@@ -320,7 +321,7 @@ build_variant() {
       generate_commands vibe md "\$ARGUMENTS" "$base_dir/.vibe/prompts" "$script" ;;
     kimi)
       mkdir -p "$base_dir/.kimi/skills"
-      create_skills "$base_dir/.kimi/skills" "$script" "kimi" ;;
+      create_skills "$base_dir/.kimi/skills" "$script" "kimi" "." ;;
     trae)
       mkdir -p "$base_dir/.trae/rules"
       generate_commands trae md "\$ARGUMENTS" "$base_dir/.trae/rules" "$script" ;;

README.md

@@ -22,10 +22,7 @@
 - [🤔 What is Spec-Driven Development?](#-what-is-spec-driven-development)
 - [⚡ Get Started](#-get-started)
 - [📽️ Video Overview](#️-video-overview)
-- [🧩 Community Extensions](#-community-extensions)
-- [🎨 Community Presets](#-community-presets)
 - [🚶 Community Walkthroughs](#-community-walkthroughs)
-- [🛠️ Community Friends](#️-community-friends)
 - [🤖 Supported AI Agents](#-supported-ai-agents)
 - [🔧 Specify CLI Reference](#-specify-cli-reference)
 - [🧩 Making Spec Kit Your Own: Extensions & Presets](#-making-spec-kit-your-own-extensions--presets)
@@ -158,56 +155,6 @@ Want to see Spec Kit in action? Watch our [video overview](https://www.youtube.c
 
 [![Spec Kit video header](/media/spec-kit-video-header.jpg)](https://www.youtube.com/watch?v=a9eR1xsfvHg&pp=0gcJCckJAYcqIYzv)
 
-## 🧩 Community Extensions
-
-The following community-contributed extensions are available in [`catalog.community.json`](extensions/catalog.community.json):
-
-**Categories:** `docs` — reads, validates, or generates spec artifacts · `code` — reviews, validates, or modifies source code · `process` — orchestrates workflow across phases · `integration` — syncs with external platforms · `visibility` — reports on project health or progress
-
-**Effect:** `Read-only` — produces reports without modifying files · `Read+Write` — modifies files, creates artifacts, or updates specs
-
-| Extension | Purpose | Category | Effect | URL |
-|-----------|---------|----------|--------|-----|
-| AI-Driven Engineering (AIDE) | A structured 7-step workflow for building new projects from scratch with AI assistants — from vision through implementation | `process` | Read+Write | [aide](https://github.com/mnriem/spec-kit-extensions/tree/main/aide) |
-| Archive Extension | Archive merged features into main project memory. | `docs` | Read+Write | [spec-kit-archive](https://github.com/stn1slv/spec-kit-archive) |
-| Azure DevOps Integration | Sync user stories and tasks to Azure DevOps work items using OAuth authentication | `integration` | Read+Write | [spec-kit-azure-devops](https://github.com/pragya247/spec-kit-azure-devops) |
-| 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) |
-| Cognitive Squad | Multi-agent cognitive system with Triadic Model: understanding, internalization, application — with quality gates, backpropagation verification, and self-healing | `docs` | Read+Write | [cognitive-squad](https://github.com/Testimonial/cognitive-squad) |
-| Conduct Extension | Orchestrates spec-kit phases via sub-agent delegation to reduce context pollution. | `process` | Read+Write | [spec-kit-conduct-ext](https://github.com/twbrandon7/spec-kit-conduct-ext) |
-| DocGuard — CDD Enforcement | Canonical-Driven Development enforcement. Validates, scores, and traces project documentation with automated checks, AI-driven workflows, and spec-kit hooks. Zero NPM runtime dependencies. | `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) |
-| Fleet Orchestrator | Orchestrate a full feature lifecycle with human-in-the-loop gates across all SpecKit phases | `process` | Read+Write | [spec-kit-fleet](https://github.com/sharathsatish/spec-kit-fleet) |
-| Iterate | Iterate on spec documents with a two-phase define-and-apply workflow — refine specs mid-implementation and go straight back to building | `docs` | Read+Write | [spec-kit-iterate](https://github.com/imviancagrace/spec-kit-iterate) |
-| Jira Integration | Create Jira Epics, Stories, and Issues from spec-kit specifications and task breakdowns with configurable hierarchy and custom field support | `integration` | Read+Write | [spec-kit-jira](https://github.com/mbachorik/spec-kit-jira) |
-| 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) |
-| Presetify | Create and validate presets and preset catalogs | `process` | Read+Write | [presetify](https://github.com/mnriem/spec-kit-extensions/tree/main/presetify) |
-| Project Health Check | Diagnose a Spec Kit project and report health issues across structure, agents, features, scripts, extensions, and git | `visibility` | Read-only | [spec-kit-doctor](https://github.com/KhawarHabibKhan/spec-kit-doctor) |
-| Project Status | Show current SDD workflow progress — active feature, artifact status, task completion, workflow phase, and extensions summary | `visibility` | Read-only | [spec-kit-status](https://github.com/KhawarHabibKhan/spec-kit-status) |
-| Ralph Loop | Autonomous implementation loop using AI agent CLI | `code` | Read+Write | [spec-kit-ralph](https://github.com/Rubiss/spec-kit-ralph) |
-| Reconcile Extension | Reconcile implementation drift by surgically updating feature artifacts. | `docs` | Read+Write | [spec-kit-reconcile](https://github.com/stn1slv/spec-kit-reconcile) |
-| 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) |
-| 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) |
-| Spec Sync | Detect and resolve drift between specs and implementation. AI-assisted resolution with human approval | `docs` | Read+Write | [spec-kit-sync](https://github.com/bgervin/spec-kit-sync) |
-| Understanding | Automated requirements quality analysis — 31 deterministic metrics against IEEE/ISO standards with experimental energy-based ambiguity detection | `docs` | Read-only | [understanding](https://github.com/Testimonial/understanding) |
-| V-Model Extension Pack | Enforces V-Model paired generation of development specs and test specs with full traceability | `docs` | Read+Write | [spec-kit-v-model](https://github.com/leocamello/spec-kit-v-model) |
-| Verify Extension | Post-implementation quality gate that validates implemented code against specification artifacts | `code` | Read-only | [spec-kit-verify](https://github.com/ismaelJimenez/spec-kit-verify) |
-| Verify Tasks Extension | Detect phantom completions: tasks marked [X] in tasks.md with no real implementation | `code` | Read-only | [spec-kit-verify-tasks](https://github.com/datastone-inc/spec-kit-verify-tasks) |
-
-To submit your own extension, see the [Extension Publishing Guide](extensions/EXTENSION-PUBLISHING-GUIDE.md).
-
-## 🎨 Community Presets
-
-The following community-contributed presets customize how Spec Kit behaves — overriding templates, commands, and terminology without changing any tooling. Presets are available in [`catalog.community.json`](presets/catalog.community.json):
-
-| Preset | Purpose | Provides | Requires | URL |
-|--------|---------|----------|----------|-----|
-| AIDE In-Place Migration | Adapts the AIDE extension workflow for in-place technology migrations (X → Y pattern) — adds migration objectives, verification gates, knowledge documents, and behavioral equivalence criteria | 2 templates, 8 commands | AIDE extension | [spec-kit-presets](https://github.com/mnriem/spec-kit-presets) |
-| Pirate Speak (Full) | Transforms all Spec Kit output into pirate speak — specs become "Voyage Manifests", plans become "Battle Plans", tasks become "Crew Assignments" | 6 templates, 9 commands | — | [spec-kit-presets](https://github.com/mnriem/spec-kit-presets) |
-
-To build and publish your own preset, see the [Presets Publishing Guide](presets/PUBLISHING.md).
-
 ## 🚶 Community Walkthroughs
 
 See Spec-Driven Development in action across different scenarios with these community-contributed walkthroughs:
@@ -224,16 +171,6 @@ See Spec-Driven Development in action across different scenarios with these comm
 
 - **[Greenfield Spring Boot MVC with a custom preset](https://github.com/mnriem/spec-kit-pirate-speak-preset-demo)** — Builds a Spring Boot MVC application from scratch using a custom pirate-speak preset, demonstrating how presets can reshape the entire spec-kit experience: specifications become "Voyage Manifests," plans become "Battle Plans," and tasks become "Crew Assignments" — all generated in full pirate vernacular without changing any tooling.
 
-- **[Greenfield Spring Boot + React with a custom extension](https://github.com/mnriem/spec-kit-aide-extension-demo)** — Walks through the **AIDE extension**, a community extension that adds an alternative spec-driven workflow to spec-kit with high-level specs (vision) and low-level specs (work items) organized in a 7-step iterative lifecycle: vision → roadmap → progress tracking → work queue → work items → execution → feedback loops. Uses a family trading platform (Spring Boot 4, React 19, PostgreSQL, Docker Compose) as the scenario to illustrate how the extension mechanism lets you plug in a different style of spec-driven development without changing any core tooling — truly utilizing the "Kit" in Spec Kit.
-
-## 🛠️ Community Friends
-
-Community projects that extend, visualize, or build on Spec Kit:
-
-- **[cc-sdd](https://github.com/rhuss/cc-sdd)** - A Claude Code plugin that adds composable traits on top of Spec Kit with [Superpowers](https://github.com/obra/superpowers)-based quality gates, spec/code review, git worktree isolation, and parallel implementation via agent teams.
-
-- **[Spec Kit Assistant](https://marketplace.visualstudio.com/items?itemName=rfsales.speckit-assistant)** — A VS Code extension that provides a visual orchestrator for the full SDD workflow (constitution → specification → planning → tasks → implementation) with phase status visualization, an interactive task checklist, DAG visualization, and support for Claude, Gemini, GitHub Copilot, and OpenAI backends. Requires the `specify` CLI in your PATH.
-
 ## 🤖 Supported AI Agents
 
 | Agent                                                                                | Support | Notes                                                                                                                                     |
@@ -292,7 +229,7 @@ The `specify` command supports the following options:
 | `--skip-tls`           | Flag     | Skip SSL/TLS verification (not recommended)                                                                                                                                                                                                                                                                                                                                               |
 | `--debug`              | Flag     | Enable detailed debug output for troubleshooting                                                                                                                                                                                                                                                                                                                                          |
 | `--github-token`       | Option   | GitHub token for API requests (or set GH_TOKEN/GITHUB_TOKEN env variable)                                                                                                                                                                                                                                                                                                                 |
-| `--ai-skills`          | Flag     | Install Prompt.MD templates as agent skills in agent-specific `skills/` directory (requires `--ai`). Extension commands are also auto-registered as skills when extensions are added later.                                                                                                                                                                                               |
+| `--ai-skills`          | Flag     | Install Prompt.MD templates as agent skills in agent-specific `skills/` directory (requires `--ai`)                                                                                                                                                                                                                                                                                       |
 | `--branch-numbering`   | Option   | Branch numbering strategy: `sequential` (default — `001`, `002`, `003`) or `timestamp` (`YYYYMMDD-HHMMSS`). Timestamp mode is useful for distributed teams to avoid numbering conflicts                                                                                                                                                                                                  |
 
 ### Examples
@@ -443,7 +380,7 @@ specify extension add <extension-name>
 
 For example, extensions could add Jira integration, post-implementation code review, V-Model test traceability, or project health diagnostics.
 
-See the [Extensions README](./extensions/README.md) for the full guide and how to build and publish your own. Browse the [community extensions](#-community-extensions) above for what's available.
+See the [Extensions README](./extensions/README.md) for the full guide, the complete community catalog, and how to build and publish your own.
 
 ### Presets — Customize Existing Workflows
 

TESTING.md

@@ -1,79 +0,0 @@
-# Manual Testing Guide
-
-Any change that affects a slash command's behavior requires manually testing that command through an AI agent and submitting results with the PR.
-
-## Process
-
-1. **Identify affected commands** — use the [prompt below](#determining-which-tests-to-run) to have your agent analyze your changed files and determine which commands need testing.
-2. **Set up a test project** — scaffold from your local branch (see [Setup](#setup)).
-3. **Run each affected command** — invoke it in your agent, verify it completes successfully, and confirm it produces the expected output (files created, scripts executed, artifacts populated).
-4. **Run prerequisites first** — commands that depend on earlier commands (e.g., `/speckit.tasks` requires `/speckit.plan` which requires `/speckit.specify`) must be run in order.
-5. **Report results** — paste the [reporting template](#reporting-results) into your PR with pass/fail for each command tested.
-
-## Setup
-
-```bash
-# Install the CLI from your local branch
-cd <spec-kit-repo>
-uv venv .venv
-source .venv/bin/activate  # On Windows: .venv\Scripts\activate
-uv pip install -e .
-
-# Initialize a test project using your local changes
-specify init /tmp/speckit-test --ai <agent> --offline
-cd /tmp/speckit-test
-
-# Open in your agent
-```
-
-## Reporting results
-
-Paste this into your PR:
-
-~~~markdown
-## Manual test results
-
-**Agent**: [e.g., GitHub Copilot in VS Code]  |  **OS/Shell**: [e.g., macOS/zsh]
-
-| Command tested | Notes |
-|----------------|-------|
-| `/speckit.command` | |
-~~~
-
-## Determining which tests to run
-
-Copy this prompt into your agent. Include the agent's response (selected tests plus a brief explanation of the mapping) in your PR.
-
-~~~text
-Read TESTING.md, then run `git diff --name-only main` to get my changed files.
-For each changed file, determine which slash commands it affects by reading
-the command templates in templates/commands/ to understand what each command
-invokes. Use these mapping rules:
-
-- templates/commands/X.md → the command it defines
-- scripts/bash/Y.sh or scripts/powershell/Y.ps1 → every command that invokes that script (grep templates/commands/ for the script name). Also check transitive dependencies: if the changed script is sourced by other scripts (e.g., common.sh is sourced by create-new-feature.sh, check-prerequisites.sh, setup-plan.sh, update-agent-context.sh), then every command invoking those downstream scripts is also affected
-- templates/Z-template.md → every command that consumes that template during execution
-- src/specify_cli/*.py → CLI commands (`specify init`, `specify check`, `specify extension *`, `specify preset *`); test the affected CLI command and, for init/scaffolding changes, at minimum test /speckit.specify
-- extensions/X/commands/* → the extension command it defines
-- extensions/X/scripts/* → every extension command that invokes that script
-- extensions/X/extension.yml or config-template.yml → every command in that extension. Also check if the manifest defines hooks (look for `hooks:` entries like `before_specify`, `after_implement`, etc.) — if so, the core commands those hooks attach to are also affected
-- presets/*/* → test preset scaffolding via `specify init` with the preset
-- pyproject.toml → packaging/bundling; test `specify init` and verify bundled assets
-
-Include prerequisite tests (e.g., T5 requires T3 requires T1).
-
-Output in this format:
-
-### Test selection reasoning
-
-| Changed file | Affects | Test | Why |
-|---|---|---|---|
-| (path) | (command) | T# | (reason) |
-
-### Required tests
-
-Number each test sequentially (T1, T2, ...). List prerequisite tests first.
-
-- T1: /speckit.command — (reason)
-- T2: /speckit.command — (reason)
-~~~

extensions/EXTENSION-DEVELOPMENT-GUIDE.md

@@ -523,7 +523,7 @@ Submit to the community catalog for public discovery:
 
 1. **Fork** spec-kit repository
 2. **Add entry** to `extensions/catalog.community.json`
-3. **Update** the Community Extensions table in `README.md` with your extension
+3. **Update** `extensions/README.md` with your extension
 4. **Create PR** following the [Extension Publishing Guide](EXTENSION-PUBLISHING-GUIDE.md)
 5. **After merge**, your extension becomes available:
    - Users can browse `catalog.community.json` to discover your extension

extensions/EXTENSION-PUBLISHING-GUIDE.md

@@ -204,9 +204,9 @@ Edit `extensions/catalog.community.json` and add your extension:
 - Use current timestamp for `created_at` and `updated_at`
 - Update the top-level `updated_at` to current time
 
-### 3. Update Community Extensions Table
+### 3. Update Extensions README
 
-Add your extension to the Community Extensions table in the project root `README.md`:
+Add your extension to the Available Extensions table in `extensions/README.md`:
 
 ```markdown
 | Your Extension Name | Brief description of what it does | `<category>` | <effect> | [repo-name](https://github.com/your-org/spec-kit-your-extension) |
@@ -234,7 +234,7 @@ Insert your extension in alphabetical order in the table.
 git checkout -b add-your-extension
 
 # Commit your changes
-git add extensions/catalog.community.json README.md
+git add extensions/catalog.community.json extensions/README.md
 git commit -m "Add your-extension to community catalog
 
 - Extension ID: your-extension
@@ -273,7 +273,7 @@ Brief description of what your extension does.
 - [x] All commands working
 - [x] No security vulnerabilities
 - [x] Added to extensions/catalog.community.json
-- [x] Added to Community Extensions table in README.md
+- [x] Added to extensions/README.md Available Extensions table
 
 ### Testing
 Tested on:

extensions/EXTENSION-USER-GUIDE.md

@@ -187,21 +187,6 @@ Provided commands:
    Check: .specify/extensions/jira/
 ```
 
-### Automatic Agent Skill Registration
-
-If your project was initialized with `--ai-skills`, extension commands are **automatically registered as agent skills** during installation. This ensures that extensions are discoverable by agents that use the [agentskills.io](https://agentskills.io) skill specification.
-
-```text
-✓ Extension installed successfully!
-
-Jira Integration (v1.0.0)
-  ...
-
-✓ 3 agent skill(s) auto-registered
-```
-
-When an extension is removed, its corresponding skills are also cleaned up automatically. Pre-existing skills that were manually customized are never overwritten.
-
 ---
 
 ## Using Extensions

extensions/README.md

@@ -68,9 +68,36 @@ specify extension add --from https://github.com/org/spec-kit-ext/archive/refs/ta
 
 ## Available Community Extensions
 
-See the [Community Extensions](../README.md#-community-extensions) section in the main README for the full list of available community-contributed extensions.
+The following community-contributed extensions are available in [`catalog.community.json`](catalog.community.json):
 
-For the raw catalog data, see [`catalog.community.json`](catalog.community.json).
+**Categories:** `docs` — reads, validates, or generates spec artifacts · `code` — reviews, validates, or modifies source code · `process` — orchestrates workflow across phases · `integration` — syncs with external platforms · `visibility` — reports on project health or progress
+
+**Effect:** `Read-only` — produces reports without modifying files · `Read+Write` — modifies files, creates artifacts, or updates specs
+
+| Extension | Purpose | Category | Effect | URL |
+|-----------|---------|----------|--------|-----|
+| Archive Extension | Archive merged features into main project memory. | `docs` | Read+Write | [spec-kit-archive](https://github.com/stn1slv/spec-kit-archive) |
+| Azure DevOps Integration | Sync user stories and tasks to Azure DevOps work items using OAuth authentication | `integration` | Read+Write | [spec-kit-azure-devops](https://github.com/pragya247/spec-kit-azure-devops) |
+| 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) |
+| Cognitive Squad | Multi-agent cognitive system with Triadic Model: understanding, internalization, application — with quality gates, backpropagation verification, and self-healing | `docs` | Read+Write | [cognitive-squad](https://github.com/Testimonial/cognitive-squad) |
+| Conduct Extension | Orchestrates spec-kit phases via sub-agent delegation to reduce context pollution. | `process` | Read+Write | [spec-kit-conduct-ext](https://github.com/twbrandon7/spec-kit-conduct-ext) |
+| DocGuard — CDD Enforcement | Canonical-Driven Development enforcement. Validates, scores, and traces project documentation with automated checks, AI-driven workflows, and spec-kit hooks. Zero NPM runtime dependencies. | `docs` | Read+Write | [spec-kit-docguard](https://github.com/raccioly/docguard) |
+| Fleet Orchestrator | Orchestrate a full feature lifecycle with human-in-the-loop gates across all SpecKit phases | `process` | Read+Write | [spec-kit-fleet](https://github.com/sharathsatish/spec-kit-fleet) |
+| Iterate | Iterate on spec documents with a two-phase define-and-apply workflow — refine specs mid-implementation and go straight back to building | `docs` | Read+Write | [spec-kit-iterate](https://github.com/imviancagrace/spec-kit-iterate) |
+| Jira Integration | Create Jira Epics, Stories, and Issues from spec-kit specifications and task breakdowns with configurable hierarchy and custom field support | `integration` | Read+Write | [spec-kit-jira](https://github.com/mbachorik/spec-kit-jira) |
+| 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) |
+| Project Health Check | Diagnose a Spec Kit project and report health issues across structure, agents, features, scripts, extensions, and git | `visibility` | Read-only | [spec-kit-doctor](https://github.com/KhawarHabibKhan/spec-kit-doctor) |
+| Project Status | Show current SDD workflow progress — active feature, artifact status, task completion, workflow phase, and extensions summary | `visibility` | Read-only | [spec-kit-status](https://github.com/KhawarHabibKhan/spec-kit-status) |
+| Ralph Loop | Autonomous implementation loop using AI agent CLI | `code` | Read+Write | [spec-kit-ralph](https://github.com/Rubiss/spec-kit-ralph) |
+| Reconcile Extension | Reconcile implementation drift by surgically updating feature artifacts. | `docs` | Read+Write | [spec-kit-reconcile](https://github.com/stn1slv/spec-kit-reconcile) |
+| 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) |
+| 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) |
+| Spec Sync | Detect and resolve drift between specs and implementation. AI-assisted resolution with human approval | `docs` | Read+Write | [spec-kit-sync](https://github.com/bgervin/spec-kit-sync) |
+| Understanding | Automated requirements quality analysis — 31 deterministic metrics against IEEE/ISO standards with experimental energy-based ambiguity detection | `docs` | Read-only | [understanding](https://github.com/Testimonial/understanding) |
+| V-Model Extension Pack | Enforces V-Model paired generation of development specs and test specs with full traceability | `docs` | Read+Write | [spec-kit-v-model](https://github.com/leocamello/spec-kit-v-model) |
+| Verify Extension | Post-implementation quality gate that validates implemented code against specification artifacts | `code` | Read-only | [spec-kit-verify](https://github.com/ismaelJimenez/spec-kit-verify) |
+| Verify Tasks Extension | Detect phantom completions: tasks marked [X] in tasks.md with no real implementation | `code` | Read-only | [spec-kit-verify-tasks](https://github.com/datastone-inc/spec-kit-verify-tasks) |
 
 
 ## Adding Your Extension

extensions/catalog.community.json

@@ -3,39 +3,6 @@
   "updated_at": "2026-03-19T12:08:20Z",
   "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/extensions/catalog.community.json",
   "extensions": {
-    "aide": {
-      "name": "AI-Driven Engineering (AIDE)",
-      "id": "aide",
-      "description": "A structured 7-step workflow for building new projects from scratch with AI assistants — from vision through implementation.",
-      "author": "mnriem",
-      "version": "1.0.0",
-      "download_url": "https://github.com/mnriem/spec-kit-extensions/releases/download/aide-v1.0.0/aide.zip",
-      "repository": "https://github.com/mnriem/spec-kit-extensions",
-      "homepage": "https://github.com/mnriem/spec-kit-extensions",
-      "documentation": "https://github.com/mnriem/spec-kit-extensions/blob/main/aide/README.md",
-      "changelog": "https://github.com/mnriem/spec-kit-extensions/blob/main/aide/CHANGELOG.md",
-      "license": "MIT",
-      "requires": {
-        "speckit_version": ">=0.2.0"
-      },
-      "provides": {
-        "commands": 7,
-        "hooks": 0
-      },
-      "tags": [
-        "workflow",
-        "project-management",
-        "ai-driven",
-        "new-project",
-        "planning",
-        "experimental"
-      ],
-      "verified": false,
-      "downloads": 0,
-      "stars": 0,
-      "created_at": "2026-03-18T00:00:00Z",
-      "updated_at": "2026-03-18T00:00:00Z"
-    },
     "archive": {
       "name": "Archive Extension",
       "id": "archive",
@@ -106,35 +73,6 @@
       "created_at": "2026-03-03T00:00:00Z",
       "updated_at": "2026-03-03T00:00:00Z"
     },
-    "checkpoint": {
-      "name": "Checkpoint Extension",
-      "id": "checkpoint",
-      "description": "An extension to 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.",
-      "author": "aaronrsun",
-      "version": "1.0.0",
-      "download_url": "https://github.com/aaronrsun/spec-kit-checkpoint/archive/refs/tags/v1.0.0.zip",
-      "repository": "https://github.com/aaronrsun/spec-kit-checkpoint",
-      "homepage": "https://github.com/aaronrsun/spec-kit-checkpoint",
-      "documentation": "https://github.com/aaronrsun/spec-kit-checkpoint/blob/main/README.md",
-      "changelog": "https://github.com/aaronrsun/spec-kit-checkpoint/blob/main/CHANGELOG.md",
-      "license": "MIT",
-      "requires": {
-        "speckit_version": ">=0.1.0"
-      },
-      "provides": {
-        "commands": 1,
-        "hooks": 0
-      },
-      "tags": [
-        "checkpoint",
-        "commit"
-      ],
-      "verified": false,
-      "downloads": 0,
-      "stars": 0,
-      "created_at": "2026-03-22T00:00:00Z",
-      "updated_at": "2026-03-22T00:00:00Z"
-    },
     "cleanup": {
       "name": "Cleanup Extension",
       "id": "cleanup",
@@ -314,37 +252,6 @@
       "created_at": "2026-03-13T00:00:00Z",
       "updated_at": "2026-03-13T00:00:00Z"
     },
-    "extensify": {
-      "name": "Extensify",
-      "id": "extensify",
-      "description": "Create and validate extensions and extension catalogs.",
-      "author": "mnriem",
-      "version": "1.0.0",
-      "download_url": "https://github.com/mnriem/spec-kit-extensions/releases/download/extensify-v1.0.0/extensify.zip",
-      "repository": "https://github.com/mnriem/spec-kit-extensions",
-      "homepage": "https://github.com/mnriem/spec-kit-extensions",
-      "documentation": "https://github.com/mnriem/spec-kit-extensions/blob/main/extensify/README.md",
-      "changelog": "https://github.com/mnriem/spec-kit-extensions/blob/main/extensify/CHANGELOG.md",
-      "license": "MIT",
-      "requires": {
-        "speckit_version": ">=0.2.0"
-      },
-      "provides": {
-        "commands": 4,
-        "hooks": 0
-      },
-      "tags": [
-        "extensions",
-        "workflow",
-        "validation",
-        "experimental"
-      ],
-      "verified": false,
-      "downloads": 0,
-      "stars": 0,
-      "created_at": "2026-03-18T00:00:00Z",
-      "updated_at": "2026-03-18T00:00:00Z"
-    },
     "fleet": {
       "name": "Fleet Orchestrator",
       "id": "fleet",
@@ -437,37 +344,6 @@
       "created_at": "2026-03-05T00:00:00Z",
       "updated_at": "2026-03-05T00:00:00Z"
     },
-    "presetify": {
-      "name": "Presetify",
-      "id": "presetify",
-      "description": "Create and validate presets and preset catalogs.",
-      "author": "mnriem",
-      "version": "1.0.0",
-      "download_url": "https://github.com/mnriem/spec-kit-extensions/releases/download/presetify-v1.0.0/presetify.zip",
-      "repository": "https://github.com/mnriem/spec-kit-extensions",
-      "homepage": "https://github.com/mnriem/spec-kit-extensions",
-      "documentation": "https://github.com/mnriem/spec-kit-extensions/blob/main/presetify/README.md",
-      "changelog": "https://github.com/mnriem/spec-kit-extensions/blob/main/presetify/CHANGELOG.md",
-      "license": "MIT",
-      "requires": {
-        "speckit_version": ">=0.2.0"
-      },
-      "provides": {
-        "commands": 4,
-        "hooks": 0
-      },
-      "tags": [
-        "presets",
-        "workflow",
-        "templates",
-        "experimental"
-      ],
-      "verified": false,
-      "downloads": 0,
-      "stars": 0,
-      "created_at": "2026-03-18T00:00:00Z",
-      "updated_at": "2026-03-18T00:00:00Z"
-    },
     "ralph": {
       "name": "Ralph Loop",
       "id": "ralph",

presets/catalog.community.json

@@ -1,58 +1,6 @@
 {
   "schema_version": "1.0",
-  "updated_at": "2026-03-24T00:00:00Z",
+  "updated_at": "2026-03-09T00:00:00Z",
   "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/presets/catalog.community.json",
-  "presets": {
-    "aide-in-place": {
-      "name": "AIDE In-Place Migration",
-      "id": "aide-in-place",
-      "version": "1.0.0",
-      "description": "Adapts the AIDE workflow for in-place technology migrations (X → Y pattern). Overrides vision, roadmap, progress, and work item commands with migration-specific guidance.",
-      "author": "mnriem",
-      "repository": "https://github.com/mnriem/spec-kit-presets",
-      "download_url": "https://github.com/mnriem/spec-kit-presets/releases/download/aide-in-place-v1.0.0/aide-in-place.zip",
-      "homepage": "https://github.com/mnriem/spec-kit-presets",
-      "documentation": "https://github.com/mnriem/spec-kit-presets/blob/main/aide-in-place/README.md",
-      "license": "MIT",
-      "requires": {
-        "speckit_version": ">=0.2.0",
-        "extensions": ["aide"]
-      },
-      "provides": {
-        "templates": 2,
-        "commands": 8
-      },
-      "tags": [
-        "migration",
-        "in-place",
-        "brownfield",
-        "aide"
-      ]
-    },
-    "pirate": {
-      "name": "Pirate Speak (Full)",
-      "id": "pirate",
-      "version": "1.0.0",
-      "description": "Arrr! Transforms all Spec Kit output into pirate speak. Specs, plans, and tasks be written fer scallywags.",
-      "author": "mnriem",
-      "repository": "https://github.com/mnriem/spec-kit-presets",
-      "download_url": "https://github.com/mnriem/spec-kit-presets/releases/download/pirate-v1.0.0/pirate.zip",
-      "homepage": "https://github.com/mnriem/spec-kit-presets",
-      "documentation": "https://github.com/mnriem/spec-kit-presets/blob/main/pirate/README.md",
-      "license": "MIT",
-      "requires": {
-        "speckit_version": ">=0.1.0"
-      },
-      "provides": {
-        "templates": 6,
-        "commands": 9
-      },
-      "tags": [
-        "pirate",
-        "theme",
-        "fun",
-        "experimental"
-      ]
-    }
-  }
+  "presets": {}
 }

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "specify-cli"
-version = "0.4.3"
+version = "0.4.0"
 description = "Specify CLI, part of GitHub Spec Kit. A tool to bootstrap your projects for Spec-Driven Development (SDD)."
 requires-python = ">=3.11"
 dependencies = [

scripts/bash/common.sh

@@ -1,48 +1,15 @@
 #!/usr/bin/env bash
 # Common functions and variables for all scripts
 
-# Find repository root by searching upward for .specify directory
-# This is the primary marker for spec-kit projects
-find_specify_root() {
-    local dir="${1:-$(pwd)}"
-    # Normalize to absolute path to prevent infinite loop with relative paths
-    # Use -- to handle paths starting with - (e.g., -P, -L)
-    dir="$(cd -- "$dir" 2>/dev/null && pwd)" || return 1
-    local prev_dir=""
-    while true; do
-        if [ -d "$dir/.specify" ]; then
-            echo "$dir"
-            return 0
-        fi
-        # Stop if we've reached filesystem root or dirname stops changing
-        if [ "$dir" = "/" ] || [ "$dir" = "$prev_dir" ]; then
-            break
-        fi
-        prev_dir="$dir"
-        dir="$(dirname "$dir")"
-    done
-    return 1
-}
-
-# Get repository root, prioritizing .specify directory over git
-# This prevents using a parent git repo when spec-kit is initialized in a subdirectory
+# Get repository root, with fallback for non-git repositories
 get_repo_root() {
-    # First, look for .specify directory (spec-kit's own marker)
-    local specify_root
-    if specify_root=$(find_specify_root); then
-        echo "$specify_root"
-        return
-    fi
-
-    # Fallback to git if no .specify found
     if git rev-parse --show-toplevel >/dev/null 2>&1; then
         git rev-parse --show-toplevel
-        return
+    else
+        # Fall back to script location for non-git repos
+        local script_dir="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+        (cd "$script_dir/../../.." && pwd)
     fi
-
-    # Final fallback to script location for non-git repos
-    local script_dir="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
-    (cd "$script_dir/../../.." && pwd)
 }
 
 # Get current branch, with fallback for non-git repositories
@@ -53,14 +20,14 @@ get_current_branch() {
         return
     fi
 
-    # Then check git if available at the spec-kit root (not parent)
-    local repo_root=$(get_repo_root)
-    if has_git; then
-        git -C "$repo_root" rev-parse --abbrev-ref HEAD
+    # Then check git if available
+    if git rev-parse --abbrev-ref HEAD >/dev/null 2>&1; then
+        git rev-parse --abbrev-ref HEAD
         return
     fi
 
     # For non-git repos, try to find the latest feature directory
+    local repo_root=$(get_repo_root)
     local specs_dir="$repo_root/specs"
 
     if [[ -d "$specs_dir" ]]; then
@@ -101,17 +68,9 @@ get_current_branch() {
     echo "main"  # Final fallback
 }
 
-# Check if we have git available at the spec-kit root level
-# Returns true only if git is installed and the repo root is inside a git work tree
-# Handles both regular repos (.git directory) and worktrees/submodules (.git file)
+# Check if we have git available
 has_git() {
-    # First check if git command is available (before calling get_repo_root which may use git)
-    command -v git >/dev/null 2>&1 || return 1
-    local repo_root=$(get_repo_root)
-    # Check if .git exists (directory or file for worktrees/submodules)
-    [ -e "$repo_root/.git" ] || return 1
-    # Verify it's actually a valid git work tree
-    git -C "$repo_root" rev-parse --is-inside-work-tree >/dev/null 2>&1
+    git rev-parse --show-toplevel >/dev/null 2>&1
 }
 
 check_feature_branch() {

scripts/bash/create-new-feature.sh

@@ -80,6 +80,19 @@ if [ -z "$FEATURE_DESCRIPTION" ]; then
     exit 1
 fi
 
+# Function to find the repository root by searching for existing project markers
+find_repo_root() {
+    local dir="$1"
+    while [ "$dir" != "/" ]; do
+        if [ -d "$dir/.git" ] || [ -d "$dir/.specify" ]; then
+            echo "$dir"
+            return 0
+        fi
+        dir="$(dirname "$dir")"
+    done
+    return 1
+}
+
 # Function to get highest number from specs directory
 get_highest_from_specs() {
     local specs_dir="$1"
@@ -89,9 +102,9 @@ get_highest_from_specs() {
         for dir in "$specs_dir"/*; do
             [ -d "$dir" ] || continue
             dirname=$(basename "$dir")
-            # Match sequential prefixes (>=3 digits), but skip timestamp dirs.
-            if echo "$dirname" | grep -Eq '^[0-9]{3,}-' && ! echo "$dirname" | grep -Eq '^[0-9]{8}-[0-9]{6}-'; then
-                number=$(echo "$dirname" | grep -Eo '^[0-9]+')
+            # Only match sequential prefixes (###-*), skip timestamp dirs
+            if echo "$dirname" | grep -q '^[0-9]\{3\}-'; then
+                number=$(echo "$dirname" | grep -o '^[0-9]\{3\}')
                 number=$((10#$number))
                 if [ "$number" -gt "$highest" ]; then
                     highest=$number
@@ -115,9 +128,9 @@ get_highest_from_branches() {
             # Clean branch name: remove leading markers and remote prefixes
             clean_branch=$(echo "$branch" | sed 's/^[* ]*//; s|^remotes/[^/]*/||')
             
-            # Extract sequential feature number (>=3 digits), skip timestamp branches.
-            if echo "$clean_branch" | grep -Eq '^[0-9]{3,}-' && ! echo "$clean_branch" | grep -Eq '^[0-9]{8}-[0-9]{6}-'; then
-                number=$(echo "$clean_branch" | grep -Eo '^[0-9]+' || echo "0")
+            # Extract feature number if branch matches pattern ###-*
+            if echo "$clean_branch" | grep -q '^[0-9]\{3\}-'; then
+                number=$(echo "$clean_branch" | grep -o '^[0-9]\{3\}' || echo "0")
                 number=$((10#$number))
                 if [ "$number" -gt "$highest" ]; then
                     highest=$number
@@ -158,16 +171,21 @@ clean_branch_name() {
     echo "$name" | tr '[:upper:]' '[:lower:]' | sed 's/[^a-z0-9]/-/g' | sed 's/-\+/-/g' | sed 's/^-//' | sed 's/-$//'
 }
 
-# Resolve repository root using common.sh functions which prioritize .specify over git
+# Resolve repository root. Prefer git information when available, but fall back
+# to searching for repository markers so the workflow still functions in repositories that
+# were initialised with --no-git.
 SCRIPT_DIR="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 source "$SCRIPT_DIR/common.sh"
 
-REPO_ROOT=$(get_repo_root)
-
-# Check if git is available at this repo root (not a parent)
-if has_git; then
+if git rev-parse --show-toplevel >/dev/null 2>&1; then
+    REPO_ROOT=$(git rev-parse --show-toplevel)
     HAS_GIT=true
 else
+    REPO_ROOT="$(find_repo_root "$SCRIPT_DIR")"
+    if [ -z "$REPO_ROOT" ]; then
+        echo "Error: Could not determine repository root. Please run this script from within the repository." >&2
+        exit 1
+    fi
     HAS_GIT=false
 fi
 

scripts/powershell/common.ps1

@@ -1,39 +1,7 @@
 #!/usr/bin/env pwsh
 # Common PowerShell functions analogous to common.sh
 
-# Find repository root by searching upward for .specify directory
-# This is the primary marker for spec-kit projects
-function Find-SpecifyRoot {
-    param([string]$StartDir = (Get-Location).Path)
-
-    # Normalize to absolute path to prevent issues with relative paths
-    # Use -LiteralPath to handle paths with wildcard characters ([, ], *, ?)
-    $resolved = Resolve-Path -LiteralPath $StartDir -ErrorAction SilentlyContinue
-    $current = if ($resolved) { $resolved.Path } else { $null }
-    if (-not $current) { return $null }
-
-    while ($true) {
-        if (Test-Path -LiteralPath (Join-Path $current ".specify") -PathType Container) {
-            return $current
-        }
-        $parent = Split-Path $current -Parent
-        if ([string]::IsNullOrEmpty($parent) -or $parent -eq $current) {
-            return $null
-        }
-        $current = $parent
-    }
-}
-
-# Get repository root, prioritizing .specify directory over git
-# This prevents using a parent git repo when spec-kit is initialized in a subdirectory
 function Get-RepoRoot {
-    # First, look for .specify directory (spec-kit's own marker)
-    $specifyRoot = Find-SpecifyRoot
-    if ($specifyRoot) {
-        return $specifyRoot
-    }
-
-    # Fallback to git if no .specify found
     try {
         $result = git rev-parse --show-toplevel 2>$null
         if ($LASTEXITCODE -eq 0) {
@@ -42,10 +10,9 @@ function Get-RepoRoot {
     } catch {
         # Git command failed
     }
-
-    # Final fallback to script location for non-git repos
-    # Use -LiteralPath to handle paths with wildcard characters
-    return (Resolve-Path -LiteralPath (Join-Path $PSScriptRoot "../../..")).Path
+    
+    # Fall back to script location for non-git repos
+    return (Resolve-Path (Join-Path $PSScriptRoot "../../..")).Path
 }
 
 function Get-CurrentBranch {
@@ -53,21 +20,19 @@ function Get-CurrentBranch {
     if ($env:SPECIFY_FEATURE) {
         return $env:SPECIFY_FEATURE
     }
-
-    # Then check git if available at the spec-kit root (not parent)
-    $repoRoot = Get-RepoRoot
-    if (Test-HasGit) {
-        try {
-            $result = git -C $repoRoot rev-parse --abbrev-ref HEAD 2>$null
-            if ($LASTEXITCODE -eq 0) {
-                return $result
-            }
-        } catch {
-            # Git command failed
+    
+    # Then check git if available
+    try {
+        $result = git rev-parse --abbrev-ref HEAD 2>$null
+        if ($LASTEXITCODE -eq 0) {
+            return $result
         }
+    } catch {
+        # Git command failed
     }
-
+    
     # For non-git repos, try to find the latest feature directory
+    $repoRoot = Get-RepoRoot
     $specsDir = Join-Path $repoRoot "specs"
     
     if (Test-Path $specsDir) {
@@ -104,23 +69,9 @@ function Get-CurrentBranch {
     return "main"
 }
 
-# Check if we have git available at the spec-kit root level
-# Returns true only if git is installed and the repo root is inside a git work tree
-# Handles both regular repos (.git directory) and worktrees/submodules (.git file)
 function Test-HasGit {
-    # First check if git command is available (before calling Get-RepoRoot which may use git)
-    if (-not (Get-Command git -ErrorAction SilentlyContinue)) {
-        return $false
-    }
-    $repoRoot = Get-RepoRoot
-    # Check if .git exists (directory or file for worktrees/submodules)
-    # Use -LiteralPath to handle paths with wildcard characters
-    if (-not (Test-Path -LiteralPath (Join-Path $repoRoot ".git"))) {
-        return $false
-    }
-    # Verify it's actually a valid git work tree
     try {
-        $null = git -C $repoRoot rev-parse --is-inside-work-tree 2>$null
+        git rev-parse --show-toplevel 2>$null | Out-Null
         return ($LASTEXITCODE -eq 0)
     } catch {
         return $false

scripts/powershell/create-new-feature.ps1

@@ -5,7 +5,7 @@ param(
     [switch]$Json,
     [string]$ShortName,
     [Parameter()]
-    [long]$Number = 0,
+    [int]$Number = 0,
     [switch]$Timestamp,
     [switch]$Help,
     [Parameter(Position = 0, ValueFromRemainingArguments = $true)]
@@ -45,18 +45,39 @@ if ([string]::IsNullOrWhiteSpace($featureDesc)) {
     exit 1
 }
 
+# Resolve repository root. Prefer git information when available, but fall back
+# to searching for repository markers so the workflow still functions in repositories that
+# were initialized with --no-git.
+function Find-RepositoryRoot {
+    param(
+        [string]$StartDir,
+        [string[]]$Markers = @('.git', '.specify')
+    )
+    $current = Resolve-Path $StartDir
+    while ($true) {
+        foreach ($marker in $Markers) {
+            if (Test-Path (Join-Path $current $marker)) {
+                return $current
+            }
+        }
+        $parent = Split-Path $current -Parent
+        if ($parent -eq $current) {
+            # Reached filesystem root without finding markers
+            return $null
+        }
+        $current = $parent
+    }
+}
+
 function Get-HighestNumberFromSpecs {
     param([string]$SpecsDir)
     
-    [long]$highest = 0
+    $highest = 0
     if (Test-Path $SpecsDir) {
         Get-ChildItem -Path $SpecsDir -Directory | ForEach-Object {
-            # Match sequential prefixes (>=3 digits), but skip timestamp dirs.
-            if ($_.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 = $num
-                }
+            if ($_.Name -match '^(\d{3})-') {
+                $num = [int]$matches[1]
+                if ($num -gt $highest) { $highest = $num }
             }
         }
     }
@@ -66,7 +87,7 @@ function Get-HighestNumberFromSpecs {
 function Get-HighestNumberFromBranches {
     param()
     
-    [long]$highest = 0
+    $highest = 0
     try {
         $branches = git branch -a 2>$null
         if ($LASTEXITCODE -eq 0) {
@@ -74,12 +95,10 @@ function Get-HighestNumberFromBranches {
                 # Clean branch name: remove leading markers and remote prefixes
                 $cleanBranch = $branch.Trim() -replace '^\*?\s+', '' -replace '^remotes/[^/]+/', ''
                 
-                # Extract sequential feature number (>=3 digits), skip timestamp branches.
-                if ($cleanBranch -match '^(\d{3,})-' -and $cleanBranch -notmatch '^\d{8}-\d{6}-') {
-                    [long]$num = 0
-                    if ([long]::TryParse($matches[1], [ref]$num) -and $num -gt $highest) {
-                        $highest = $num
-                    }
+                # Extract feature number if branch matches pattern ###-*
+                if ($cleanBranch -match '^(\d{3})-') {
+                    $num = [int]$matches[1]
+                    if ($num -gt $highest) { $highest = $num }
                 }
             }
         }
@@ -120,14 +139,26 @@ function ConvertTo-CleanBranchName {
     
     return $Name.ToLower() -replace '[^a-z0-9]', '-' -replace '-{2,}', '-' -replace '^-', '' -replace '-$', ''
 }
-# Load common functions (includes Get-RepoRoot, Test-HasGit, Resolve-Template)
+$fallbackRoot = (Find-RepositoryRoot -StartDir $PSScriptRoot)
+if (-not $fallbackRoot) {
+    Write-Error "Error: Could not determine repository root. Please run this script from within the repository."
+    exit 1
+}
+
+# Load common functions (includes Resolve-Template)
 . "$PSScriptRoot/common.ps1"
 
-# Use common.ps1 functions which prioritize .specify over git
-$repoRoot = Get-RepoRoot
-
-# Check if git is available at this repo root (not a parent)
-$hasGit = Test-HasGit
+try {
+    $repoRoot = git rev-parse --show-toplevel 2>$null
+    if ($LASTEXITCODE -eq 0) {
+        $hasGit = $true
+    } else {
+        throw "Git not available"
+    }
+} catch {
+    $repoRoot = $fallbackRoot
+    $hasGit = $false
+}
 
 Set-Location $repoRoot
 
@@ -295,3 +326,4 @@ if ($Json) {
     Write-Output "HAS_GIT: $hasGit"
     Write-Output "SPECIFY_FEATURE environment variable set to: $branchName"
 }
+

src/specify_cli/__init__.py

@@ -1490,6 +1490,12 @@ def load_init_options(project_path: Path) -> dict[str, Any]:
         return {}
 
 
+# Agent-specific skill directory overrides for agents whose skills directory
+# doesn't follow the standard <agent_folder>/skills/ pattern
+AGENT_SKILLS_DIR_OVERRIDES = {
+    "codex": ".agents/skills",  # Codex agent layout override
+}
+
 # Default skills directory for agents not in AGENT_CONFIG
 DEFAULT_SKILLS_DIR = ".agents/skills"
 
@@ -1522,9 +1528,13 @@ SKILL_DESCRIPTIONS = {
 def _get_skills_dir(project_path: Path, selected_ai: str) -> Path:
     """Resolve the agent-specific skills directory for the given AI assistant.
 
-    Uses ``AGENT_CONFIG[agent]["folder"] + "skills"`` and falls back to
-    ``DEFAULT_SKILLS_DIR`` for unknown agents.
+    Uses ``AGENT_SKILLS_DIR_OVERRIDES`` first, then falls back to
+    ``AGENT_CONFIG[agent]["folder"] + "skills"``, and finally to
+    ``DEFAULT_SKILLS_DIR``.
     """
+    if selected_ai in AGENT_SKILLS_DIR_OVERRIDES:
+        return project_path / AGENT_SKILLS_DIR_OVERRIDES[selected_ai]
+
     agent_config = AGENT_CONFIG.get(selected_ai, {})
     agent_folder = agent_config.get("folder", "")
     if agent_folder:
@@ -1638,7 +1648,10 @@ def install_ai_skills(
                 command_name = command_name[len("speckit."):]
             if command_name.endswith(".agent"):
                 command_name = command_name[:-len(".agent")]
-            skill_name = f"speckit-{command_name.replace('.', '-')}"
+            if selected_ai == "kimi":
+                skill_name = f"speckit.{command_name}"
+            else:
+                skill_name = f"speckit-{command_name}"
 
             # Create skill directory (additive — never removes existing content)
             skill_dir = skills_dir / skill_name
@@ -1717,64 +1730,8 @@ def _has_bundled_skills(project_path: Path, selected_ai: str) -> bool:
     if not skills_dir.is_dir():
         return False
 
-    return any(skills_dir.glob("speckit-*/SKILL.md"))
-
-
-def _migrate_legacy_kimi_dotted_skills(skills_dir: Path) -> tuple[int, int]:
-    """Migrate legacy Kimi dotted skill dirs (speckit.xxx) to hyphenated format.
-
-    Temporary migration helper:
-    - Intended removal window: after 2026-06-25.
-    - Purpose: one-time cleanup for projects initialized before Kimi moved to
-      hyphenated skills (speckit-xxx).
-
-    Returns:
-        Tuple[migrated_count, removed_count]
-        - migrated_count: old dotted dir renamed to hyphenated dir
-        - removed_count: old dotted dir deleted when equivalent hyphenated dir existed
-    """
-    if not skills_dir.is_dir():
-        return (0, 0)
-
-    migrated_count = 0
-    removed_count = 0
-
-    for legacy_dir in sorted(skills_dir.glob("speckit.*")):
-        if not legacy_dir.is_dir():
-            continue
-        if not (legacy_dir / "SKILL.md").exists():
-            continue
-
-        suffix = legacy_dir.name[len("speckit."):]
-        if not suffix:
-            continue
-
-        target_dir = skills_dir / f"speckit-{suffix.replace('.', '-')}"
-
-        if not target_dir.exists():
-            shutil.move(str(legacy_dir), str(target_dir))
-            migrated_count += 1
-            continue
-
-        # If the new target already exists, avoid destructive cleanup unless
-        # both SKILL.md files are byte-identical.
-        target_skill = target_dir / "SKILL.md"
-        legacy_skill = legacy_dir / "SKILL.md"
-        if target_skill.is_file():
-            try:
-                if target_skill.read_bytes() == legacy_skill.read_bytes():
-                    # Preserve legacy directory when it contains extra user files.
-                    has_extra_entries = any(
-                        child.name != "SKILL.md" for child in legacy_dir.iterdir()
-                    )
-                    if not has_extra_entries:
-                        shutil.rmtree(legacy_dir)
-                        removed_count += 1
-            except OSError:
-                # Best-effort migration: preserve legacy dir on read failures.
-                pass
-
-    return (migrated_count, removed_count)
+    pattern = "speckit.*/SKILL.md" if selected_ai == "kimi" else "speckit-*/SKILL.md"
+    return any(skills_dir.glob(pattern))
 
 
 AGENT_SKILLS_MIGRATIONS = {
@@ -2137,33 +2094,16 @@ def init(
 
             ensure_constitution_from_template(project_path, tracker=tracker)
 
-            # Determine skills directory and migrate any legacy Kimi dotted skills.
-            migrated_legacy_kimi_skills = 0
-            removed_legacy_kimi_skills = 0
-            skills_dir: Optional[Path] = None
-            if selected_ai in NATIVE_SKILLS_AGENTS:
-                skills_dir = _get_skills_dir(project_path, selected_ai)
-                if selected_ai == "kimi" and skills_dir.is_dir():
-                    (
-                        migrated_legacy_kimi_skills,
-                        removed_legacy_kimi_skills,
-                    ) = _migrate_legacy_kimi_dotted_skills(skills_dir)
-
             if ai_skills:
                 if selected_ai in NATIVE_SKILLS_AGENTS:
+                    skills_dir = _get_skills_dir(project_path, selected_ai)
                     bundled_found = _has_bundled_skills(project_path, selected_ai)
                     if bundled_found:
-                        detail = f"bundled skills → {skills_dir.relative_to(project_path)}"
-                        if migrated_legacy_kimi_skills or removed_legacy_kimi_skills:
-                            detail += (
-                                f" (migrated {migrated_legacy_kimi_skills}, "
-                                f"removed {removed_legacy_kimi_skills} legacy Kimi dotted skills)"
-                            )
                         if tracker:
                             tracker.start("ai-skills")
-                            tracker.complete("ai-skills", detail)
+                            tracker.complete("ai-skills", f"bundled skills → {skills_dir.relative_to(project_path)}")
                         else:
-                            console.print(f"[green]✓[/green] Using {detail}")
+                            console.print(f"[green]✓[/green] Using bundled agent skills in {skills_dir.relative_to(project_path)}/")
                     else:
                         # Compatibility fallback: convert command templates to skills
                         # when an older template archive does not include native skills.
@@ -2348,7 +2288,7 @@ def init(
         if codex_skill_mode:
             return f"$speckit-{name}"
         if kimi_skill_mode:
-            return f"/skill:speckit-{name}"
+            return f"/skill:speckit.{name}"
         return f"/speckit.{name}"
 
     steps_lines.append(f"{step_num}. Start using {usage_label} with your AI agent:")
@@ -3654,15 +3594,6 @@ def extension_add(
         for cmd in manifest.commands:
             console.print(f"  • {cmd['name']} - {cmd.get('description', '')}")
 
-        # Report agent skills registration
-        reg_meta = manager.registry.get(manifest.id)
-        reg_skills = reg_meta.get("registered_skills", []) if reg_meta else []
-        # Normalize to guard against corrupted registry entries
-        if not isinstance(reg_skills, list):
-            reg_skills = []
-        if reg_skills:
-            console.print(f"\n[green]✓[/green] {len(reg_skills)} agent skill(s) auto-registered")
-
         console.print("\n[yellow]⚠[/yellow]  Configuration may be required")
         console.print(f"   Check: .specify/extensions/{manifest.id}/")
 
@@ -3701,19 +3632,14 @@ def extension_remove(
     installed = manager.list_installed()
     extension_id, display_name = _resolve_installed_extension(extension, installed, "remove")
 
-    # Get extension info for command and skill counts
+    # Get extension info for command count
     ext_manifest = manager.get_extension(extension_id)
     cmd_count = len(ext_manifest.commands) if ext_manifest else 0
-    reg_meta = manager.registry.get(extension_id)
-    raw_skills = reg_meta.get("registered_skills") if reg_meta else None
-    skill_count = len(raw_skills) if isinstance(raw_skills, list) else 0
 
     # Confirm removal
     if not force:
         console.print("\n[yellow]⚠  This will remove:[/yellow]")
         console.print(f"   • {cmd_count} commands from AI agent")
-        if skill_count:
-            console.print(f"   • {skill_count} agent skill(s)")
         console.print(f"   • Extension directory: .specify/extensions/{extension_id}/")
         if not keep_config:
             console.print("   • Config files (will be backed up)")

src/specify_cli/agents.py

@@ -10,8 +10,6 @@ from pathlib import Path
 from typing import Dict, List, Any
 
 import platform
-import re
-from copy import deepcopy
 import yaml
 
 
@@ -213,52 +211,24 @@ class CommandRegistrar:
         return f"---\n{yaml_str}---\n"
 
     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
-        `scripts` and `agent_scripts` keys (for example `../../scripts/`,
-        `../../templates/`, `../../memory/`, `scripts/`, `templates/`, and
-        `memory/`) to the `.specify/...` paths used in generated projects.
+        """Adjust script paths from extension-relative to repo-relative.
 
         Args:
             frontmatter: Frontmatter dictionary
 
         Returns:
-            Modified frontmatter with normalized project paths
+            Modified frontmatter with adjusted paths
         """
-        frontmatter = deepcopy(frontmatter)
-
         for script_key in ("scripts", "agent_scripts"):
             scripts = frontmatter.get(script_key)
             if not isinstance(scripts, dict):
                 continue
 
             for key, script_path in scripts.items():
-                if isinstance(script_path, str):
-                    scripts[key] = self._rewrite_project_relative_paths(script_path)
+                if isinstance(script_path, str) and script_path.startswith("../../scripts/"):
+                    scripts[key] = f".specify/scripts/{script_path[14:]}"
         return frontmatter
 
-    @staticmethod
-    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
-
-        for old, new in (
-            ("../../memory/", ".specify/memory/"),
-            ("../../scripts/", ".specify/scripts/"),
-            ("../../templates/", ".specify/templates/"),
-        ):
-            text = text.replace(old, new)
-
-        # 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/', r"\1.specify/scripts/", text)
-        text = re.sub(r'(^|[\s`"\'(])(?:\.?/)?templates/', r"\1.specify/templates/", text)
-
-        return text.replace(".specify/.specify/", ".specify/").replace(".specify.specify/", ".specify/")
-
     def render_markdown_command(
         self,
         frontmatter: dict,
@@ -307,25 +277,9 @@ class CommandRegistrar:
         toml_lines.append(f"# Source: {source_id}")
         toml_lines.append("")
 
-        # Keep TOML output valid even when body contains triple-quote delimiters.
-        # Prefer multiline forms, then fall back to escaped basic string.
-        if '"""' not in body:
-            toml_lines.append('prompt = """')
-            toml_lines.append(body)
-            toml_lines.append('"""')
-        elif "'''" not in body:
-            toml_lines.append("prompt = '''")
-            toml_lines.append(body)
-            toml_lines.append("'''")
-        else:
-            escaped_body = (
-                body.replace("\\", "\\\\")
-                .replace('"', '\\"')
-                .replace("\n", "\\n")
-                .replace("\r", "\\r")
-                .replace("\t", "\\t")
-            )
-            toml_lines.append(f'prompt = "{escaped_body}"')
+        toml_lines.append('prompt = """')
+        toml_lines.append(body)
+        toml_lines.append('"""')
 
         return "\n".join(toml_lines)
 
@@ -354,8 +308,8 @@ class CommandRegistrar:
         if not isinstance(frontmatter, dict):
             frontmatter = {}
 
-        if agent_name in {"codex", "kimi"}:
-            body = self.resolve_skill_placeholders(agent_name, frontmatter, body, project_root)
+        if agent_name == "codex":
+            body = self._resolve_codex_skill_placeholders(frontmatter, body, project_root)
 
         description = frontmatter.get("description", f"Spec-kit workflow command: {skill_name}")
         skill_frontmatter = {
@@ -370,8 +324,13 @@ class CommandRegistrar:
         return self.render_frontmatter(skill_frontmatter) + "\n" + body
 
     @staticmethod
-    def resolve_skill_placeholders(agent_name: str, frontmatter: dict, body: str, project_root: Path) -> str:
-        """Resolve script placeholders for skills-backed agents."""
+    def _resolve_codex_skill_placeholders(frontmatter: dict, body: str, project_root: Path) -> str:
+        """Resolve script placeholders for Codex skill overrides.
+
+        This intentionally scopes the fix to Codex, which is the newly
+        migrated runtime path in this PR. Existing Kimi behavior is left
+        unchanged for now.
+        """
         try:
             from . import load_init_options
         except ImportError:
@@ -387,11 +346,7 @@ class CommandRegistrar:
         if not isinstance(agent_scripts, dict):
             agent_scripts = {}
 
-        init_opts = load_init_options(project_root)
-        if not isinstance(init_opts, dict):
-            init_opts = {}
-
-        script_variant = init_opts.get("script")
+        script_variant = load_init_options(project_root).get("script")
         if script_variant not in {"sh", "ps"}:
             fallback_order = []
             default_variant = "ps" if platform.system().lower().startswith("win") else "sh"
@@ -421,8 +376,7 @@ class CommandRegistrar:
             agent_script_command = agent_script_command.replace("{ARGS}", "$ARGUMENTS")
             body = body.replace("{AGENT_SCRIPT}", agent_script_command)
 
-        body = body.replace("{ARGS}", "$ARGUMENTS").replace("__AGENT__", agent_name)
-        return CommandRegistrar._rewrite_project_relative_paths(body)
+        return body.replace("{ARGS}", "$ARGUMENTS").replace("__AGENT__", "codex")
 
     def _convert_argument_placeholder(self, content: str, from_placeholder: str, to_placeholder: str) -> str:
         """Convert argument placeholder format.
@@ -446,9 +400,8 @@ class CommandRegistrar:
         short_name = cmd_name
         if short_name.startswith("speckit."):
             short_name = short_name[len("speckit."):]
-        short_name = short_name.replace(".", "-")
 
-        return f"speckit-{short_name}"
+        return f"speckit.{short_name}" if agent_name == "kimi" else f"speckit-{short_name}"
 
     def register_commands(
         self,

src/specify_cli/extensions.py

@@ -510,283 +510,6 @@ class ExtensionManager:
 
         return _ignore
 
-    def _get_skills_dir(self) -> Optional[Path]:
-        """Return the active skills directory for extension skill registration.
-
-        Reads ``.specify/init-options.json`` to determine whether skills
-        are enabled and which agent was selected, then delegates to
-        the module-level ``_get_skills_dir()`` helper for the concrete path.
-
-        Kimi is treated as a native-skills agent: if ``ai == "kimi"`` and
-        ``.kimi/skills`` exists, extension installs should still propagate
-        command skills even when ``ai_skills`` is false.
-
-        Returns:
-            The skills directory ``Path``, or ``None`` if skills were not
-            enabled and no native-skills fallback applies.
-        """
-        from . import load_init_options, _get_skills_dir as resolve_skills_dir
-
-        opts = load_init_options(self.project_root)
-        if not isinstance(opts, dict):
-            opts = {}
-
-        agent = opts.get("ai")
-        if not isinstance(agent, str) or not agent:
-            return None
-
-        ai_skills_enabled = bool(opts.get("ai_skills"))
-        if not ai_skills_enabled and agent != "kimi":
-            return None
-
-        skills_dir = resolve_skills_dir(self.project_root, agent)
-        if not skills_dir.is_dir():
-            return None
-
-        return skills_dir
-
-    def _register_extension_skills(
-        self,
-        manifest: ExtensionManifest,
-        extension_dir: Path,
-    ) -> List[str]:
-        """Generate SKILL.md files for extension commands as agent skills.
-
-        For every command in the extension manifest, creates a SKILL.md
-        file in the agent's skills directory following the agentskills.io
-        specification.  This is only done when ``--ai-skills`` was used
-        during project initialisation.
-
-        Args:
-            manifest: Extension manifest.
-            extension_dir: Installed extension directory.
-
-        Returns:
-            List of skill names that were created (for registry storage).
-        """
-        skills_dir = self._get_skills_dir()
-        if not skills_dir:
-            return []
-
-        from . import load_init_options
-        from .agents import CommandRegistrar
-        import yaml
-
-        written: List[str] = []
-        opts = load_init_options(self.project_root)
-        if not isinstance(opts, dict):
-            opts = {}
-        selected_ai = opts.get("ai")
-        if not isinstance(selected_ai, str) or not selected_ai:
-            return []
-        registrar = CommandRegistrar()
-
-        for cmd_info in manifest.commands:
-            cmd_name = cmd_info["name"]
-            cmd_file_rel = cmd_info["file"]
-
-            # Guard against path traversal: reject absolute paths and ensure
-            # the resolved file stays within the extension directory.
-            cmd_path = Path(cmd_file_rel)
-            if cmd_path.is_absolute():
-                continue
-            try:
-                ext_root = extension_dir.resolve()
-                source_file = (ext_root / cmd_path).resolve()
-                source_file.relative_to(ext_root)  # raises ValueError if outside
-            except (OSError, ValueError):
-                continue
-
-            if not source_file.is_file():
-                continue
-
-            # Derive skill name from command name using the same hyphenated
-            # convention as hook rendering and preset skill registration.
-            short_name_raw = cmd_name
-            if short_name_raw.startswith("speckit."):
-                short_name_raw = short_name_raw[len("speckit."):]
-            skill_name = f"speckit-{short_name_raw.replace('.', '-')}"
-
-            # Check if skill already exists before creating the directory
-            skill_subdir = skills_dir / skill_name
-            skill_file = skill_subdir / "SKILL.md"
-            if skill_file.exists():
-                # Do not overwrite user-customized skills
-                continue
-
-            # Create skill directory; track whether we created it so we can clean
-            # up safely if reading the source file subsequently fails.
-            created_now = not skill_subdir.exists()
-            skill_subdir.mkdir(parents=True, exist_ok=True)
-
-            # Parse the command file — guard against IsADirectoryError / decode errors
-            try:
-                content = source_file.read_text(encoding="utf-8")
-            except (OSError, UnicodeDecodeError):
-                if created_now:
-                    try:
-                        skill_subdir.rmdir()  # undo the mkdir; dir is empty at this point
-                    except OSError:
-                        pass  # best-effort cleanup
-                continue
-            frontmatter, body = registrar.parse_frontmatter(content)
-            frontmatter = registrar._adjust_script_paths(frontmatter)
-            body = registrar.resolve_skill_placeholders(
-                selected_ai, frontmatter, body, self.project_root
-            )
-
-            original_desc = frontmatter.get("description", "")
-            description = original_desc or f"Extension command: {cmd_name}"
-
-            frontmatter_data = {
-                "name": skill_name,
-                "description": description,
-                "compatibility": "Requires spec-kit project structure with .specify/ directory",
-                "metadata": {
-                    "author": "github-spec-kit",
-                    "source": f"extension:{manifest.id}",
-                },
-            }
-            frontmatter_text = yaml.safe_dump(frontmatter_data, sort_keys=False).strip()
-
-            # Derive a human-friendly title from the command name
-            short_name = cmd_name
-            if short_name.startswith("speckit."):
-                short_name = short_name[len("speckit."):]
-            title_name = short_name.replace(".", " ").replace("-", " ").title()
-
-            skill_content = (
-                f"---\n"
-                f"{frontmatter_text}\n"
-                f"---\n\n"
-                f"# {title_name} Skill\n\n"
-                f"{body}\n"
-            )
-
-            skill_file.write_text(skill_content, encoding="utf-8")
-            written.append(skill_name)
-
-        return written
-
-    def _unregister_extension_skills(self, skill_names: List[str], extension_id: str) -> None:
-        """Remove SKILL.md directories for extension skills.
-
-        Called during extension removal to clean up skill files that
-        were created by ``_register_extension_skills()``.
-
-        If ``_get_skills_dir()`` returns ``None`` (e.g. the user removed
-        init-options.json or toggled ai_skills after installation), we
-        fall back to scanning all known agent skills directories so that
-        orphaned skill directories are still cleaned up.  In that case
-        each candidate directory is verified against the SKILL.md
-        ``metadata.source`` field before removal to avoid accidentally
-        deleting user-created skills with the same name.
-
-        Args:
-            skill_names: List of skill names to remove.
-            extension_id: Extension ID used to verify ownership during
-                fallback candidate scanning.
-        """
-        if not skill_names:
-            return
-
-        skills_dir = self._get_skills_dir()
-
-        if skills_dir:
-            # Fast path: we know the exact skills directory
-            for skill_name in skill_names:
-                # Guard against path traversal from a corrupted registry entry:
-                # reject names that are absolute, contain path separators, or
-                # resolve to a path outside the skills directory.
-                sn_path = Path(skill_name)
-                if sn_path.is_absolute() or len(sn_path.parts) != 1:
-                    continue
-                try:
-                    skill_subdir = (skills_dir / skill_name).resolve()
-                    skill_subdir.relative_to(skills_dir.resolve())  # raises if outside
-                except (OSError, ValueError):
-                    continue
-                if not skill_subdir.is_dir():
-                    continue
-                # Safety check: only delete if SKILL.md exists and its
-                # metadata.source matches exactly this extension — mirroring
-                # the fallback branch — so a corrupted registry entry cannot
-                # delete an unrelated user skill.
-                skill_md = skill_subdir / "SKILL.md"
-                if not skill_md.is_file():
-                    continue
-                try:
-                    import yaml as _yaml
-                    raw = skill_md.read_text(encoding="utf-8")
-                    source = ""
-                    if raw.startswith("---"):
-                        parts = raw.split("---", 2)
-                        if len(parts) >= 3:
-                            fm = _yaml.safe_load(parts[1]) or {}
-                            source = (
-                                fm.get("metadata", {}).get("source", "")
-                                if isinstance(fm, dict)
-                                else ""
-                            )
-                    if source != f"extension:{extension_id}":
-                        continue
-                except (OSError, UnicodeDecodeError, Exception):
-                    continue
-                shutil.rmtree(skill_subdir)
-        else:
-            # Fallback: scan all possible agent skills directories
-            from . import AGENT_CONFIG, DEFAULT_SKILLS_DIR
-
-            candidate_dirs: set[Path] = set()
-            for cfg in AGENT_CONFIG.values():
-                folder = cfg.get("folder", "")
-                if folder:
-                    candidate_dirs.add(self.project_root / folder.rstrip("/") / "skills")
-            candidate_dirs.add(self.project_root / DEFAULT_SKILLS_DIR)
-
-            for skills_candidate in candidate_dirs:
-                if not skills_candidate.is_dir():
-                    continue
-                for skill_name in skill_names:
-                    # Same path-traversal guard as the fast path above
-                    sn_path = Path(skill_name)
-                    if sn_path.is_absolute() or len(sn_path.parts) != 1:
-                        continue
-                    try:
-                        skill_subdir = (skills_candidate / skill_name).resolve()
-                        skill_subdir.relative_to(skills_candidate.resolve())  # raises if outside
-                    except (OSError, ValueError):
-                        continue
-                    if not skill_subdir.is_dir():
-                        continue
-                    # Safety check: only delete if SKILL.md exists and its
-                    # metadata.source matches exactly this extension.  If the
-                    # file is missing or unreadable we skip to avoid deleting
-                    # unrelated user-created directories.
-                    skill_md = skill_subdir / "SKILL.md"
-                    if not skill_md.is_file():
-                        continue
-                    try:
-                        import yaml as _yaml
-                        raw = skill_md.read_text(encoding="utf-8")
-                        source = ""
-                        if raw.startswith("---"):
-                            parts = raw.split("---", 2)
-                            if len(parts) >= 3:
-                                fm = _yaml.safe_load(parts[1]) or {}
-                                source = (
-                                    fm.get("metadata", {}).get("source", "")
-                                    if isinstance(fm, dict)
-                                    else ""
-                                )
-                        # Only remove skills explicitly created by this extension
-                        if source != f"extension:{extension_id}":
-                            continue
-                    except (OSError, UnicodeDecodeError, Exception):
-                        # If we can't verify, skip to avoid accidental deletion
-                        continue
-                    shutil.rmtree(skill_subdir)
-
     def check_compatibility(
         self,
         manifest: ExtensionManifest,
@@ -878,10 +601,6 @@ class ExtensionManager:
                 manifest, dest_dir, self.project_root
             )
 
-        # Auto-register extension commands as agent skills when --ai-skills
-        # was used during project initialisation (feature parity).
-        registered_skills = self._register_extension_skills(manifest, dest_dir)
-
         # Register hooks
         hook_executor = HookExecutor(self.project_root)
         hook_executor.register_hooks(manifest)
@@ -893,8 +612,7 @@ class ExtensionManager:
             "manifest_hash": manifest.get_hash(),
             "enabled": True,
             "priority": priority,
-            "registered_commands": registered_commands,
-            "registered_skills": registered_skills,
+            "registered_commands": registered_commands
         })
 
         return manifest
@@ -972,15 +690,9 @@ class ExtensionManager:
         if not self.registry.is_installed(extension_id):
             return False
 
-        # Get registered commands and skills before removal
+        # Get registered commands before removal
         metadata = self.registry.get(extension_id)
         registered_commands = metadata.get("registered_commands", {}) if metadata else {}
-        raw_skills = metadata.get("registered_skills", []) if metadata else []
-        # Normalize: must be a list of plain strings to avoid corrupted-registry errors
-        if isinstance(raw_skills, list):
-            registered_skills = [s for s in raw_skills if isinstance(s, str)]
-        else:
-            registered_skills = []
 
         extension_dir = self.extensions_dir / extension_id
 
@@ -989,9 +701,6 @@ class ExtensionManager:
             registrar = CommandRegistrar()
             registrar.unregister_commands(registered_commands, self.project_root)
 
-        # Unregister agent skills
-        self._unregister_extension_skills(registered_skills, extension_id)
-
         if keep_config:
             # Preserve config files, only remove non-config files
             if extension_dir.exists():
@@ -1935,52 +1644,6 @@ class HookExecutor:
         self.project_root = project_root
         self.extensions_dir = project_root / ".specify" / "extensions"
         self.config_file = project_root / ".specify" / "extensions.yml"
-        self._init_options_cache: Optional[Dict[str, Any]] = None
-
-    def _load_init_options(self) -> Dict[str, Any]:
-        """Load persisted init options used to determine invocation style.
-
-        Uses the shared helper from specify_cli and caches values per executor
-        instance to avoid repeated filesystem reads during hook rendering.
-        """
-        if self._init_options_cache is None:
-            from . import load_init_options
-
-            payload = load_init_options(self.project_root)
-            self._init_options_cache = payload if isinstance(payload, dict) else {}
-        return self._init_options_cache
-
-    @staticmethod
-    def _skill_name_from_command(command: Any) -> str:
-        """Map a command id like speckit.plan to speckit-plan skill name."""
-        if not isinstance(command, str):
-            return ""
-        command_id = command.strip()
-        if not command_id.startswith("speckit."):
-            return ""
-        return f"speckit-{command_id[len('speckit.'):].replace('.', '-')}"
-
-    def _render_hook_invocation(self, command: Any) -> str:
-        """Render an agent-specific invocation string for a hook command."""
-        if not isinstance(command, str):
-            return ""
-
-        command_id = command.strip()
-        if not command_id:
-            return ""
-
-        init_options = self._load_init_options()
-        selected_ai = init_options.get("ai")
-        codex_skill_mode = selected_ai == "codex" and bool(init_options.get("ai_skills"))
-        kimi_skill_mode = selected_ai == "kimi"
-
-        skill_name = self._skill_name_from_command(command_id)
-        if codex_skill_mode and skill_name:
-            return f"${skill_name}"
-        if kimi_skill_mode and skill_name:
-            return f"/skill:{skill_name}"
-
-        return f"/{command_id}"
 
     def get_project_config(self) -> Dict[str, Any]:
         """Load project-level extension configuration.
@@ -2224,27 +1887,21 @@ class HookExecutor:
         for hook in hooks:
             extension = hook.get("extension")
             command = hook.get("command")
-            invocation = self._render_hook_invocation(command)
-            command_text = command if isinstance(command, str) and command.strip() else "<missing command>"
-            display_invocation = invocation or (
-                f"/{command_text}" if command_text != "<missing command>" else "/<missing command>"
-            )
             optional = hook.get("optional", True)
             prompt = hook.get("prompt", "")
             description = hook.get("description", "")
 
             if optional:
                 lines.append(f"\n**Optional Hook**: {extension}")
-                lines.append(f"Command: `{display_invocation}`")
+                lines.append(f"Command: `/{command}`")
                 if description:
                     lines.append(f"Description: {description}")
                 lines.append(f"\nPrompt: {prompt}")
-                lines.append(f"To execute: `{display_invocation}`")
+                lines.append(f"To execute: `/{command}`")
             else:
                 lines.append(f"\n**Automatic Hook**: {extension}")
-                lines.append(f"Executing: `{display_invocation}`")
-                lines.append(f"EXECUTE_COMMAND: {command_text}")
-                lines.append(f"EXECUTE_COMMAND_INVOCATION: {display_invocation}")
+                lines.append(f"Executing: `/{command}`")
+                lines.append(f"EXECUTE_COMMAND: {command}")
 
         return "\n".join(lines)
 
@@ -2308,7 +1965,6 @@ class HookExecutor:
         """
         return {
             "command": hook.get("command"),
-            "invocation": self._render_hook_invocation(hook.get("command")),
             "extension": hook.get("extension"),
             "optional": hook.get("optional", True),
             "description": hook.get("description", ""),
@@ -2352,3 +2008,4 @@ class HookExecutor:
                     hook["enabled"] = False
 
         self.save_project_config(config)
+

src/specify_cli/presets.py

@@ -556,31 +556,24 @@ class PresetManager:
         registrar.unregister_commands(registered_commands, self.project_root)
 
     def _get_skills_dir(self) -> Optional[Path]:
-        """Return the active skills directory for preset skill overrides.
+        """Return the skills directory if ``--ai-skills`` was used during init.
 
         Reads ``.specify/init-options.json`` to determine whether skills
         are enabled and which agent was selected, then delegates to
         the module-level ``_get_skills_dir()`` helper for the concrete path.
 
-        Kimi is treated as a native-skills agent: if ``ai == "kimi"`` and
-        ``.kimi/skills`` exists, presets should still propagate command
-        overrides to skills even when ``ai_skills`` is false.
-
         Returns:
             The skills directory ``Path``, or ``None`` if skills were not
-            enabled and no native-skills fallback applies.
+            enabled or the init-options file is missing.
         """
         from . import load_init_options, _get_skills_dir
 
         opts = load_init_options(self.project_root)
-        if not isinstance(opts, dict):
-            opts = {}
-        agent = opts.get("ai")
-        if not isinstance(agent, str) or not agent:
+        if not opts.get("ai_skills"):
             return None
 
-        ai_skills_enabled = bool(opts.get("ai_skills"))
-        if not ai_skills_enabled and agent != "kimi":
+        agent = opts.get("ai")
+        if not agent:
             return None
 
         skills_dir = _get_skills_dir(self.project_root, agent)
@@ -589,76 +582,6 @@ class PresetManager:
 
         return skills_dir
 
-    @staticmethod
-    def _skill_names_for_command(cmd_name: str) -> tuple[str, str]:
-        """Return the modern and legacy skill directory names for a command."""
-        raw_short_name = cmd_name
-        if raw_short_name.startswith("speckit."):
-            raw_short_name = raw_short_name[len("speckit."):]
-
-        modern_skill_name = f"speckit-{raw_short_name.replace('.', '-')}"
-        legacy_skill_name = f"speckit.{raw_short_name}"
-        return modern_skill_name, legacy_skill_name
-
-    @staticmethod
-    def _skill_title_from_command(cmd_name: str) -> str:
-        """Return a human-friendly title for a skill command name."""
-        title_name = cmd_name
-        if title_name.startswith("speckit."):
-            title_name = title_name[len("speckit."):]
-        return title_name.replace(".", " ").replace("-", " ").title()
-
-    def _build_extension_skill_restore_index(self) -> Dict[str, Dict[str, Any]]:
-        """Index extension-backed skill restore data by skill directory name."""
-        from .extensions import ExtensionManifest, ValidationError
-
-        resolver = PresetResolver(self.project_root)
-        extensions_dir = self.project_root / ".specify" / "extensions"
-        restore_index: Dict[str, Dict[str, Any]] = {}
-
-        for _priority, ext_id, _metadata in resolver._get_all_extensions_by_priority():
-            ext_dir = extensions_dir / ext_id
-            manifest_path = ext_dir / "extension.yml"
-            if not manifest_path.is_file():
-                continue
-
-            try:
-                manifest = ExtensionManifest(manifest_path)
-            except ValidationError:
-                continue
-
-            ext_root = ext_dir.resolve()
-            for cmd_info in manifest.commands:
-                cmd_name = cmd_info.get("name")
-                cmd_file_rel = cmd_info.get("file")
-                if not isinstance(cmd_name, str) or not isinstance(cmd_file_rel, str):
-                    continue
-
-                cmd_path = Path(cmd_file_rel)
-                if cmd_path.is_absolute():
-                    continue
-
-                try:
-                    source_file = (ext_root / cmd_path).resolve()
-                    source_file.relative_to(ext_root)
-                except (OSError, ValueError):
-                    continue
-
-                if not source_file.is_file():
-                    continue
-
-                restore_info = {
-                    "command_name": cmd_name,
-                    "source_file": source_file,
-                    "source": f"extension:{manifest.id}",
-                }
-                modern_skill_name, legacy_skill_name = self._skill_names_for_command(cmd_name)
-                restore_index.setdefault(modern_skill_name, restore_info)
-                if legacy_skill_name != modern_skill_name:
-                    restore_index.setdefault(legacy_skill_name, restore_info)
-
-        return restore_index
-
     def _register_skills(
         self,
         manifest: "PresetManifest",
@@ -706,15 +629,9 @@ class PresetManager:
             return []
 
         from . import SKILL_DESCRIPTIONS, load_init_options
-        from .agents import CommandRegistrar
 
-        init_opts = load_init_options(self.project_root)
-        if not isinstance(init_opts, dict):
-            init_opts = {}
-        selected_ai = init_opts.get("ai")
-        if not isinstance(selected_ai, str):
-            return []
-        registrar = CommandRegistrar()
+        opts = load_init_options(self.project_root)
+        selected_ai = opts.get("ai", "")
 
         written: List[str] = []
 
@@ -726,61 +643,62 @@ class PresetManager:
                 continue
 
             # Derive the short command name (e.g. "specify" from "speckit.specify")
-            raw_short_name = cmd_name
-            if raw_short_name.startswith("speckit."):
-                raw_short_name = raw_short_name[len("speckit."):]
-            short_name = raw_short_name.replace(".", "-")
-            skill_name, legacy_skill_name = self._skill_names_for_command(cmd_name)
-            skill_title = self._skill_title_from_command(cmd_name)
+            short_name = cmd_name
+            if short_name.startswith("speckit."):
+                short_name = short_name[len("speckit."):]
+            if selected_ai == "kimi":
+                skill_name = f"speckit.{short_name}"
+            else:
+                skill_name = f"speckit-{short_name}"
 
-            # Only overwrite skills that already exist under skills_dir,
-            # including Kimi native skills when ai_skills is false.
-            # If both modern and legacy directories exist, update both.
-            target_skill_names: List[str] = []
-            if (skills_dir / skill_name).is_dir():
-                target_skill_names.append(skill_name)
-            if legacy_skill_name != skill_name and (skills_dir / legacy_skill_name).is_dir():
-                target_skill_names.append(legacy_skill_name)
-            if not target_skill_names:
+            # Only overwrite if the skill already exists (i.e. --ai-skills was used)
+            skill_subdir = skills_dir / skill_name
+            if not skill_subdir.exists():
                 continue
 
             # Parse the command file
             content = source_file.read_text(encoding="utf-8")
-            frontmatter, body = registrar.parse_frontmatter(content)
+            if content.startswith("---"):
+                parts = content.split("---", 2)
+                if len(parts) >= 3:
+                    frontmatter = yaml.safe_load(parts[1])
+                    if not isinstance(frontmatter, dict):
+                        frontmatter = {}
+                    body = parts[2].strip()
+                else:
+                    frontmatter = {}
+                    body = content
+            else:
+                frontmatter = {}
+                body = content
 
             original_desc = frontmatter.get("description", "")
             enhanced_desc = SKILL_DESCRIPTIONS.get(
                 short_name,
                 original_desc or f"Spec-kit workflow command: {short_name}",
             )
-            frontmatter = dict(frontmatter)
-            frontmatter["description"] = enhanced_desc
-            body = registrar.resolve_skill_placeholders(
-                selected_ai, frontmatter, body, self.project_root
+
+            frontmatter_data = {
+                "name": skill_name,
+                "description": enhanced_desc,
+                "compatibility": "Requires spec-kit project structure with .specify/ directory",
+                "metadata": {
+                    "author": "github-spec-kit",
+                    "source": f"preset:{manifest.id}",
+                },
+            }
+            frontmatter_text = yaml.safe_dump(frontmatter_data, sort_keys=False).strip()
+            skill_content = (
+                f"---\n"
+                f"{frontmatter_text}\n"
+                f"---\n\n"
+                f"# Speckit {short_name.title()} Skill\n\n"
+                f"{body}\n"
             )
 
-            for target_skill_name in target_skill_names:
-                frontmatter_data = {
-                    "name": target_skill_name,
-                    "description": enhanced_desc,
-                    "compatibility": "Requires spec-kit project structure with .specify/ directory",
-                    "metadata": {
-                        "author": "github-spec-kit",
-                        "source": f"preset:{manifest.id}",
-                    },
-                }
-                frontmatter_text = yaml.safe_dump(frontmatter_data, sort_keys=False).strip()
-                skill_content = (
-                    f"---\n"
-                    f"{frontmatter_text}\n"
-                    f"---\n\n"
-                    f"# Speckit {skill_title} Skill\n\n"
-                    f"{body}\n"
-                )
-
-                skill_file = skills_dir / target_skill_name / "SKILL.md"
-                skill_file.write_text(skill_content, encoding="utf-8")
-                written.append(target_skill_name)
+            skill_file = skill_subdir / "SKILL.md"
+            skill_file.write_text(skill_content, encoding="utf-8")
+            written.append(skill_name)
 
         return written
 
@@ -802,17 +720,10 @@ class PresetManager:
         if not skills_dir:
             return
 
-        from . import SKILL_DESCRIPTIONS, load_init_options
-        from .agents import CommandRegistrar
+        from . import SKILL_DESCRIPTIONS
 
         # Locate core command templates from the project's installed templates
         core_templates_dir = self.project_root / ".specify" / "templates" / "commands"
-        init_opts = load_init_options(self.project_root)
-        if not isinstance(init_opts, dict):
-            init_opts = {}
-        selected_ai = init_opts.get("ai")
-        registrar = CommandRegistrar()
-        extension_restore_index = self._build_extension_skill_restore_index()
 
         for skill_name in skill_names:
             # Derive command name from skill name (speckit-specify -> specify)
@@ -824,10 +735,7 @@ class PresetManager:
 
             skill_subdir = skills_dir / skill_name
             skill_file = skill_subdir / "SKILL.md"
-            if not skill_subdir.is_dir():
-                continue
-            if not skill_file.is_file():
-                # Only manage directories that contain the expected skill entrypoint.
+            if not skill_file.exists():
                 continue
 
             # Try to find the core command template
@@ -838,11 +746,19 @@ class PresetManager:
             if core_file:
                 # Restore from core template
                 content = core_file.read_text(encoding="utf-8")
-                frontmatter, body = registrar.parse_frontmatter(content)
-                if isinstance(selected_ai, str):
-                    body = registrar.resolve_skill_placeholders(
-                        selected_ai, frontmatter, body, self.project_root
-                    )
+                if content.startswith("---"):
+                    parts = content.split("---", 2)
+                    if len(parts) >= 3:
+                        frontmatter = yaml.safe_load(parts[1])
+                        if not isinstance(frontmatter, dict):
+                            frontmatter = {}
+                        body = parts[2].strip()
+                    else:
+                        frontmatter = {}
+                        body = content
+                else:
+                    frontmatter = {}
+                    body = content
 
                 original_desc = frontmatter.get("description", "")
                 enhanced_desc = SKILL_DESCRIPTIONS.get(
@@ -860,49 +776,16 @@ class PresetManager:
                     },
                 }
                 frontmatter_text = yaml.safe_dump(frontmatter_data, sort_keys=False).strip()
-                skill_title = self._skill_title_from_command(short_name)
                 skill_content = (
                     f"---\n"
                     f"{frontmatter_text}\n"
                     f"---\n\n"
-                    f"# Speckit {skill_title} Skill\n\n"
-                    f"{body}\n"
-                )
-                skill_file.write_text(skill_content, encoding="utf-8")
-                continue
-
-            extension_restore = extension_restore_index.get(skill_name)
-            if extension_restore:
-                content = extension_restore["source_file"].read_text(encoding="utf-8")
-                frontmatter, body = registrar.parse_frontmatter(content)
-                if isinstance(selected_ai, str):
-                    body = registrar.resolve_skill_placeholders(
-                        selected_ai, frontmatter, body, self.project_root
-                    )
-
-                command_name = extension_restore["command_name"]
-                title_name = self._skill_title_from_command(command_name)
-
-                frontmatter_data = {
-                    "name": skill_name,
-                    "description": frontmatter.get("description", f"Extension command: {command_name}"),
-                    "compatibility": "Requires spec-kit project structure with .specify/ directory",
-                    "metadata": {
-                        "author": "github-spec-kit",
-                        "source": extension_restore["source"],
-                    },
-                }
-                frontmatter_text = yaml.safe_dump(frontmatter_data, sort_keys=False).strip()
-                skill_content = (
-                    f"---\n"
-                    f"{frontmatter_text}\n"
-                    f"---\n\n"
-                    f"# {title_name} Skill\n\n"
+                    f"# Speckit {short_name.title()} Skill\n\n"
                     f"{body}\n"
                 )
                 skill_file.write_text(skill_content, encoding="utf-8")
             else:
-                # No core or extension template — remove the skill entirely
+                # No core template — remove the skill entirely
                 shutil.rmtree(skill_subdir)
 
     def install_from_directory(
@@ -1032,26 +915,17 @@ class PresetManager:
         if not self.registry.is_installed(pack_id):
             return False
 
+        # Unregister commands from AI agents
         metadata = self.registry.get(pack_id)
+        registered_commands = metadata.get("registered_commands", {}) if metadata else {}
+        if registered_commands:
+            self._unregister_commands(registered_commands)
+
         # Restore original skills when preset is removed
         registered_skills = metadata.get("registered_skills", []) if metadata else []
-        registered_commands = metadata.get("registered_commands", {}) if metadata else {}
         pack_dir = self.presets_dir / pack_id
         if registered_skills:
             self._unregister_skills(registered_skills, pack_dir)
-            try:
-                from . import NATIVE_SKILLS_AGENTS
-            except ImportError:
-                NATIVE_SKILLS_AGENTS = set()
-            registered_commands = {
-                agent_name: cmd_names
-                for agent_name, cmd_names in registered_commands.items()
-                if agent_name not in NATIVE_SKILLS_AGENTS
-            }
-
-        # Unregister non-skill command files from AI agents.
-        if registered_commands:
-            self._unregister_commands(registered_commands)
 
         if pack_dir.exists():
             shutil.rmtree(pack_dir)

templates/commands/analyze.md

@@ -44,7 +44,7 @@ Load only the minimal necessary context from each artifact:
 
 - Overview/Context
 - Functional Requirements
-- Success Criteria (measurable outcomes — e.g., performance, security, availability, user success, business impact)
+- Non-Functional Requirements
 - User Stories
 - Edge Cases (if present)
 
@@ -71,7 +71,7 @@ Load only the minimal necessary context from each artifact:
 
 Create internal representations (do not include raw artifacts in output):
 
-- **Requirements inventory**: For each Functional Requirement (FR-###) and Success Criterion (SC-###), record a stable key. Use the explicit FR-/SC- identifier as the primary key when present, and optionally also derive an imperative-phrase slug for readability (e.g., "User can upload file" → `user-can-upload-file`). Include only Success Criteria items that require buildable work (e.g., load-testing infrastructure, security audit tooling), and exclude post-launch outcome metrics and business KPIs (e.g., "Reduce support tickets by 50%").
+- **Requirements inventory**: Each functional + non-functional requirement with a stable key (derive slug based on imperative phrase; e.g., "User can upload file" → `user-can-upload-file`)
 - **User story/action inventory**: Discrete user actions with acceptance criteria
 - **Task coverage mapping**: Map each task to one or more requirements or stories (inference by keyword / explicit reference patterns like IDs or key phrases)
 - **Constitution rule set**: Extract principle names and MUST/SHOULD normative statements
@@ -105,7 +105,7 @@ Focus on high-signal findings. Limit to 50 findings total; aggregate remainder i
 
 - Requirements with zero associated tasks
 - Tasks with no mapped requirement/story
-- Success Criteria requiring buildable work (performance, security, availability) not reflected in tasks
+- Non-functional requirements not reflected in tasks (e.g., performance, security)
 
 #### F. Inconsistency
 

templates/commands/clarify.md

@@ -145,7 +145,7 @@ Execution steps:
        - Functional ambiguity → Update or add a bullet in Functional Requirements.
        - User interaction / actor distinction → Update User Stories or Actors subsection (if present) with clarified role, constraint, or scenario.
        - Data shape / entities → Update Data Model (add fields, types, relationships) preserving ordering; note added constraints succinctly.
-       - Non-functional constraint → Add/modify measurable criteria in Success Criteria > Measurable Outcomes (convert vague adjective to metric or explicit target).
+       - Non-functional constraint → Add/modify measurable criteria in Non-Functional / Quality Attributes section (convert vague adjective to metric or explicit target).
        - Edge case / negative flow → Add a new bullet under Edge Cases / Error Handling (or create such subsection if template provides placeholder for it).
        - Terminology conflict → Normalize term across spec; retain original only if necessary by adding `(formerly referred to as "X")` once.
     - If the clarification invalidates an earlier ambiguous statement, replace that statement instead of duplicating; leave no obsolete contradictory text.

templates/spec-template.md

@@ -113,16 +113,3 @@
 - **SC-002**: [Measurable metric, e.g., "System handles 1000 concurrent users without degradation"]
 - **SC-003**: [User satisfaction metric, e.g., "90% of users successfully complete primary task on first attempt"]
 - **SC-004**: [Business metric, e.g., "Reduce support tickets related to [X] by 50%"]
-
-## Assumptions
-
-<!--
-  ACTION REQUIRED: The content in this section represents placeholders.
-  Fill them out with the right assumptions based on reasonable defaults
-  chosen when the feature description did not specify certain details.
--->
-
-- [Assumption about target users, e.g., "Users have stable internet connectivity"]
-- [Assumption about scope boundaries, e.g., "Mobile support is out of scope for v1"]
-- [Assumption about data/environment, e.g., "Existing authentication system will be reused"]
-- [Dependency on existing system/service, e.g., "Requires access to the existing user profile API"]

tests/test_ai_skills.py

@@ -24,8 +24,8 @@ import specify_cli
 
 from specify_cli import (
     _get_skills_dir,
-    _migrate_legacy_kimi_dotted_skills,
     install_ai_skills,
+    AGENT_SKILLS_DIR_OVERRIDES,
     DEFAULT_SKILLS_DIR,
     SKILL_DESCRIPTIONS,
     AGENT_CONFIG,
@@ -169,8 +169,8 @@ class TestGetSkillsDir:
         result = _get_skills_dir(project_dir, "copilot")
         assert result == project_dir / ".github" / "skills"
 
-    def test_codex_skills_dir_from_agent_config(self, project_dir):
-        """Codex should resolve skills directory from AGENT_CONFIG folder."""
+    def test_codex_uses_override(self, project_dir):
+        """Codex should use the AGENT_SKILLS_DIR_OVERRIDES value."""
         result = _get_skills_dir(project_dir, "codex")
         assert result == project_dir / ".agents" / "skills"
 
@@ -203,71 +203,12 @@ class TestGetSkillsDir:
             # Should always end with "skills"
             assert result.name == "skills"
 
-class TestKimiLegacySkillMigration:
-    """Test temporary migration from Kimi dotted skill names to hyphenated names."""
-
-    def test_migrates_legacy_dotted_skill_directory(self, project_dir):
-        skills_dir = project_dir / ".kimi" / "skills"
-        legacy_dir = skills_dir / "speckit.plan"
-        legacy_dir.mkdir(parents=True)
-        (legacy_dir / "SKILL.md").write_text("legacy")
-
-        migrated, removed = _migrate_legacy_kimi_dotted_skills(skills_dir)
-
-        assert migrated == 1
-        assert removed == 0
-        assert not legacy_dir.exists()
-        assert (skills_dir / "speckit-plan" / "SKILL.md").exists()
-
-    def test_removes_legacy_dir_when_hyphenated_target_exists_with_same_content(self, project_dir):
-        skills_dir = project_dir / ".kimi" / "skills"
-        legacy_dir = skills_dir / "speckit.plan"
-        legacy_dir.mkdir(parents=True)
-        (legacy_dir / "SKILL.md").write_text("legacy")
-        target_dir = skills_dir / "speckit-plan"
-        target_dir.mkdir(parents=True)
-        (target_dir / "SKILL.md").write_text("legacy")
-
-        migrated, removed = _migrate_legacy_kimi_dotted_skills(skills_dir)
-
-        assert migrated == 0
-        assert removed == 1
-        assert not legacy_dir.exists()
-        assert (target_dir / "SKILL.md").read_text() == "legacy"
-
-    def test_keeps_legacy_dir_when_hyphenated_target_differs(self, project_dir):
-        skills_dir = project_dir / ".kimi" / "skills"
-        legacy_dir = skills_dir / "speckit.plan"
-        legacy_dir.mkdir(parents=True)
-        (legacy_dir / "SKILL.md").write_text("legacy")
-        target_dir = skills_dir / "speckit-plan"
-        target_dir.mkdir(parents=True)
-        (target_dir / "SKILL.md").write_text("new")
-
-        migrated, removed = _migrate_legacy_kimi_dotted_skills(skills_dir)
-
-        assert migrated == 0
-        assert removed == 0
-        assert legacy_dir.exists()
-        assert (legacy_dir / "SKILL.md").read_text() == "legacy"
-        assert (target_dir / "SKILL.md").read_text() == "new"
-
-    def test_keeps_legacy_dir_when_matching_target_but_extra_files_exist(self, project_dir):
-        skills_dir = project_dir / ".kimi" / "skills"
-        legacy_dir = skills_dir / "speckit.plan"
-        legacy_dir.mkdir(parents=True)
-        (legacy_dir / "SKILL.md").write_text("legacy")
-        (legacy_dir / "notes.txt").write_text("custom")
-        target_dir = skills_dir / "speckit-plan"
-        target_dir.mkdir(parents=True)
-        (target_dir / "SKILL.md").write_text("legacy")
-
-        migrated, removed = _migrate_legacy_kimi_dotted_skills(skills_dir)
-
-        assert migrated == 0
-        assert removed == 0
-        assert legacy_dir.exists()
-        assert (legacy_dir / "notes.txt").read_text() == "custom"
+    def test_override_takes_precedence_over_config(self, project_dir):
+        """AGENT_SKILLS_DIR_OVERRIDES should take precedence over AGENT_CONFIG."""
+        for agent_key in AGENT_SKILLS_DIR_OVERRIDES:
+            result = _get_skills_dir(project_dir, agent_key)
+            expected = project_dir / AGENT_SKILLS_DIR_OVERRIDES[agent_key]
+            assert result == expected
 
 
 # ===== install_ai_skills Tests =====
@@ -532,7 +473,8 @@ class TestInstallAiSkills:
         skills_dir = _get_skills_dir(proj, agent_key)
         assert skills_dir.exists()
         skill_dirs = [d.name for d in skills_dir.iterdir() if d.is_dir()]
-        expected_skill_name = "speckit-specify"
+        # Kimi uses dotted skill names; other agents use hyphen-separated names.
+        expected_skill_name = "speckit.specify" if agent_key == "kimi" else "speckit-specify"
         assert expected_skill_name in skill_dirs
         assert (skills_dir / expected_skill_name / "SKILL.md").exists()
 
@@ -831,32 +773,6 @@ class TestNewProjectCommandSkip:
         mock_skills.assert_called_once()
         assert mock_skills.call_args.kwargs.get("overwrite_existing") is True
 
-    def test_kimi_legacy_migration_runs_without_ai_skills_flag(self, tmp_path):
-        """Kimi init should migrate dotted legacy skills even when --ai-skills is not set."""
-        from typer.testing import CliRunner
-
-        runner = CliRunner()
-        target = tmp_path / "kimi-legacy-no-ai-skills"
-
-        def fake_download(project_path, *args, **kwargs):
-            legacy_dir = project_path / ".kimi" / "skills" / "speckit.plan"
-            legacy_dir.mkdir(parents=True, exist_ok=True)
-            (legacy_dir / "SKILL.md").write_text("---\nname: speckit.plan\n---\n\nlegacy\n")
-
-        with patch("specify_cli.download_and_extract_template", side_effect=fake_download), \
-             patch("specify_cli.ensure_executable_scripts"), \
-             patch("specify_cli.ensure_constitution_from_template"), \
-             patch("specify_cli.is_git_repo", return_value=False), \
-             patch("specify_cli.shutil.which", return_value="/usr/bin/kimi"):
-            result = runner.invoke(
-                app,
-                ["init", str(target), "--ai", "kimi", "--script", "sh", "--no-git"],
-            )
-
-        assert result.exit_code == 0
-        assert not (target / ".kimi" / "skills" / "speckit.plan").exists()
-        assert (target / ".kimi" / "skills" / "speckit-plan" / "SKILL.md").exists()
-
     def test_codex_ai_skills_here_mode_preserves_existing_codex_dir(self, tmp_path, monkeypatch):
         """Codex --here skills init should not delete a pre-existing .codex directory."""
         from typer.testing import CliRunner
@@ -1202,12 +1118,12 @@ class TestCliValidation:
             assert "Optional skills that you can use for your specs" in result.output
 
     def test_kimi_next_steps_show_skill_invocation(self, monkeypatch):
-        """Kimi next-steps guidance should display /skill:speckit-* usage."""
+        """Kimi next-steps guidance should display /skill:speckit.* usage."""
         from typer.testing import CliRunner
 
         def _fake_download(*args, **kwargs):
             project_path = Path(args[0])
-            skill_dir = project_path / ".kimi" / "skills" / "speckit-specify"
+            skill_dir = project_path / ".kimi" / "skills" / "speckit.specify"
             skill_dir.mkdir(parents=True, exist_ok=True)
             (skill_dir / "SKILL.md").write_text("---\ndescription: Test skill\n---\n\nBody.\n")
 
@@ -1221,7 +1137,7 @@ class TestCliValidation:
             )
 
             assert result.exit_code == 0
-            assert "/skill:speckit-constitution" in result.output
+            assert "/skill:speckit.constitution" in result.output
             assert "/speckit.constitution" not in result.output
             assert "Optional skills that you can use for your specs" in result.output
 

tests/test_core_pack_scaffold.py

@@ -142,7 +142,7 @@ def _expected_cmd_dir(project_path: Path, agent: str) -> Path:
 
 # Agents whose commands are laid out as <skills_dir>/<name>/SKILL.md.
 # Maps agent -> separator used in skill directory names.
-_SKILL_AGENTS: dict[str, str] = {"codex": "-", "kimi": "-"}
+_SKILL_AGENTS: dict[str, str] = {"codex": "-", "kimi": "."}
 
 
 def _expected_ext(agent: str) -> str:

tests/test_extension_skills.py

@@ -1,741 +0,0 @@
-"""
-Unit tests for extension skill auto-registration.
-
-Tests cover:
-- SKILL.md generation when --ai-skills was used during init
-- No skills created when ai_skills not active
-- SKILL.md content correctness
-- Existing user-modified skills not overwritten
-- Skill cleanup on extension removal
-- Registry metadata includes registered_skills
-"""
-
-import json
-import pytest
-import tempfile
-import shutil
-import yaml
-from pathlib import Path
-
-from specify_cli.extensions import (
-    ExtensionManifest,
-    ExtensionManager,
-    ExtensionError,
-)
-
-
-# ===== Helpers =====
-
-def _create_init_options(project_root: Path, ai: str = "claude", ai_skills: bool = True):
-    """Write a .specify/init-options.json file."""
-    opts_dir = project_root / ".specify"
-    opts_dir.mkdir(parents=True, exist_ok=True)
-    opts_file = opts_dir / "init-options.json"
-    opts_file.write_text(json.dumps({
-        "ai": ai,
-        "ai_skills": ai_skills,
-        "script": "sh",
-    }))
-
-
-def _create_skills_dir(project_root: Path, ai: str = "claude") -> Path:
-    """Create and return the expected skills directory for the given agent."""
-    # Match the logic in _get_skills_dir() from specify_cli
-    from specify_cli import AGENT_CONFIG, DEFAULT_SKILLS_DIR
-
-    agent_config = AGENT_CONFIG.get(ai, {})
-    agent_folder = agent_config.get("folder", "")
-    if agent_folder:
-        skills_dir = project_root / agent_folder.rstrip("/") / "skills"
-    else:
-        skills_dir = project_root / DEFAULT_SKILLS_DIR
-
-    skills_dir.mkdir(parents=True, exist_ok=True)
-    return skills_dir
-
-
-def _create_extension_dir(temp_dir: Path, ext_id: str = "test-ext") -> Path:
-    """Create a complete extension directory with manifest and command files."""
-    ext_dir = temp_dir / ext_id
-    ext_dir.mkdir()
-
-    manifest_data = {
-        "schema_version": "1.0",
-        "extension": {
-            "id": ext_id,
-            "name": "Test Extension",
-            "version": "1.0.0",
-            "description": "A test extension for skill registration",
-        },
-        "requires": {
-            "speckit_version": ">=0.1.0",
-        },
-        "provides": {
-            "commands": [
-                {
-                    "name": f"speckit.{ext_id}.hello",
-                    "file": "commands/hello.md",
-                    "description": "Test hello command",
-                },
-                {
-                    "name": f"speckit.{ext_id}.world",
-                    "file": "commands/world.md",
-                    "description": "Test world command",
-                },
-            ]
-        },
-    }
-
-    with open(ext_dir / "extension.yml", "w") as f:
-        yaml.dump(manifest_data, f)
-
-    commands_dir = ext_dir / "commands"
-    commands_dir.mkdir()
-
-    (commands_dir / "hello.md").write_text(
-        "---\n"
-        "description: \"Test hello command\"\n"
-        "---\n"
-        "\n"
-        "# Hello Command\n"
-        "\n"
-        "Run this to say hello.\n"
-        "$ARGUMENTS\n"
-    )
-
-    (commands_dir / "world.md").write_text(
-        "---\n"
-        "description: \"Test world command\"\n"
-        "---\n"
-        "\n"
-        "# World Command\n"
-        "\n"
-        "Run this to greet the world.\n"
-    )
-
-    return ext_dir
-
-
-# ===== Fixtures =====
-
-@pytest.fixture
-def temp_dir():
-    """Create a temporary directory for tests."""
-    tmpdir = tempfile.mkdtemp()
-    yield Path(tmpdir)
-    shutil.rmtree(tmpdir)
-
-
-@pytest.fixture
-def project_dir(temp_dir):
-    """Create a mock spec-kit project directory."""
-    proj_dir = temp_dir / "project"
-    proj_dir.mkdir()
-
-    # Create .specify directory
-    specify_dir = proj_dir / ".specify"
-    specify_dir.mkdir()
-
-    return proj_dir
-
-
-@pytest.fixture
-def extension_dir(temp_dir):
-    """Create a complete extension directory."""
-    return _create_extension_dir(temp_dir)
-
-
-@pytest.fixture
-def skills_project(project_dir):
-    """Create a project with --ai-skills enabled and skills directory."""
-    _create_init_options(project_dir, ai="claude", ai_skills=True)
-    skills_dir = _create_skills_dir(project_dir, ai="claude")
-    return project_dir, skills_dir
-
-
-@pytest.fixture
-def no_skills_project(project_dir):
-    """Create a project without --ai-skills."""
-    _create_init_options(project_dir, ai="claude", ai_skills=False)
-    return project_dir
-
-
-# ===== ExtensionManager._get_skills_dir Tests =====
-
-class TestExtensionManagerGetSkillsDir:
-    """Test _get_skills_dir() on ExtensionManager."""
-
-    def test_returns_skills_dir_when_active(self, skills_project):
-        """Should return skills dir when ai_skills is true and dir exists."""
-        project_dir, skills_dir = skills_project
-        manager = ExtensionManager(project_dir)
-        result = manager._get_skills_dir()
-        assert result == skills_dir
-
-    def test_returns_none_when_no_ai_skills(self, no_skills_project):
-        """Should return None when ai_skills is false."""
-        manager = ExtensionManager(no_skills_project)
-        result = manager._get_skills_dir()
-        assert result is None
-
-    def test_returns_none_when_no_init_options(self, project_dir):
-        """Should return None when init-options.json is missing."""
-        manager = ExtensionManager(project_dir)
-        result = manager._get_skills_dir()
-        assert result is None
-
-    def test_returns_none_when_skills_dir_missing(self, project_dir):
-        """Should return None when skills dir doesn't exist on disk."""
-        _create_init_options(project_dir, ai="claude", ai_skills=True)
-        # Don't create the skills directory
-        manager = ExtensionManager(project_dir)
-        result = manager._get_skills_dir()
-        assert result is None
-
-    def test_returns_kimi_skills_dir_when_ai_skills_disabled(self, project_dir):
-        """Kimi should still use its native skills dir when ai_skills is false."""
-        _create_init_options(project_dir, ai="kimi", ai_skills=False)
-        skills_dir = _create_skills_dir(project_dir, ai="kimi")
-        manager = ExtensionManager(project_dir)
-        result = manager._get_skills_dir()
-        assert result == skills_dir
-
-    def test_returns_none_for_non_dict_init_options(self, project_dir):
-        """Corrupted-but-parseable init-options should not crash skill-dir lookup."""
-        opts_file = project_dir / ".specify" / "init-options.json"
-        opts_file.parent.mkdir(parents=True, exist_ok=True)
-        opts_file.write_text("[]")
-        _create_skills_dir(project_dir, ai="claude")
-        manager = ExtensionManager(project_dir)
-        result = manager._get_skills_dir()
-        assert result is None
-
-
-# ===== Extension Skill Registration Tests =====
-
-class TestExtensionSkillRegistration:
-    """Test _register_extension_skills() on ExtensionManager."""
-
-    def test_skills_created_when_ai_skills_active(self, skills_project, extension_dir):
-        """Skills should be created when ai_skills is enabled."""
-        project_dir, skills_dir = skills_project
-        manager = ExtensionManager(project_dir)
-        manifest = manager.install_from_directory(
-            extension_dir, "0.1.0", register_commands=False
-        )
-
-        # Check that skill directories were created
-        skill_dirs = sorted([d.name for d in skills_dir.iterdir() if d.is_dir()])
-        assert "speckit-test-ext-hello" in skill_dirs
-        assert "speckit-test-ext-world" in skill_dirs
-
-    def test_skill_md_content_correct(self, skills_project, extension_dir):
-        """SKILL.md should have correct agentskills.io structure."""
-        project_dir, skills_dir = skills_project
-        manager = ExtensionManager(project_dir)
-        manager.install_from_directory(
-            extension_dir, "0.1.0", register_commands=False
-        )
-
-        skill_file = skills_dir / "speckit-test-ext-hello" / "SKILL.md"
-        assert skill_file.exists()
-        content = skill_file.read_text()
-
-        # Check structure
-        assert content.startswith("---\n")
-        assert "name: speckit-test-ext-hello" in content
-        assert "description:" in content
-        assert "Test hello command" in content
-        assert "source: extension:test-ext" in content
-        assert "author: github-spec-kit" in content
-        assert "compatibility:" in content
-        assert "Run this to say hello." in content
-
-    def test_skill_md_has_parseable_yaml(self, skills_project, extension_dir):
-        """Generated SKILL.md should contain valid, parseable YAML frontmatter."""
-        project_dir, skills_dir = skills_project
-        manager = ExtensionManager(project_dir)
-        manager.install_from_directory(
-            extension_dir, "0.1.0", register_commands=False
-        )
-
-        skill_file = skills_dir / "speckit-test-ext-hello" / "SKILL.md"
-        content = skill_file.read_text()
-
-        assert content.startswith("---\n")
-        parts = content.split("---", 2)
-        assert len(parts) >= 3
-        parsed = yaml.safe_load(parts[1])
-        assert isinstance(parsed, dict)
-        assert parsed["name"] == "speckit-test-ext-hello"
-        assert "description" in parsed
-
-    def test_no_skills_when_ai_skills_disabled(self, no_skills_project, extension_dir):
-        """No skills should be created when ai_skills is false."""
-        manager = ExtensionManager(no_skills_project)
-        manifest = manager.install_from_directory(
-            extension_dir, "0.1.0", register_commands=False
-        )
-
-        # Verify registry
-        metadata = manager.registry.get(manifest.id)
-        assert metadata["registered_skills"] == []
-
-    def test_no_skills_when_init_options_missing(self, project_dir, extension_dir):
-        """No skills should be created when init-options.json is absent."""
-        manager = ExtensionManager(project_dir)
-        manifest = manager.install_from_directory(
-            extension_dir, "0.1.0", register_commands=False
-        )
-
-        metadata = manager.registry.get(manifest.id)
-        assert metadata["registered_skills"] == []
-
-    def test_existing_skill_not_overwritten(self, skills_project, extension_dir):
-        """Pre-existing SKILL.md should not be overwritten."""
-        project_dir, skills_dir = skills_project
-
-        # Pre-create a custom skill
-        custom_dir = skills_dir / "speckit-test-ext-hello"
-        custom_dir.mkdir(parents=True)
-        custom_content = "# My Custom Hello Skill\nUser-modified content\n"
-        (custom_dir / "SKILL.md").write_text(custom_content)
-
-        manager = ExtensionManager(project_dir)
-        manifest = manager.install_from_directory(
-            extension_dir, "0.1.0", register_commands=False
-        )
-
-        # Custom skill should be untouched
-        assert (custom_dir / "SKILL.md").read_text() == custom_content
-
-        # But the other skill should still be created
-        metadata = manager.registry.get(manifest.id)
-        assert "speckit-test-ext-world" in metadata["registered_skills"]
-        # The pre-existing one should NOT be in registered_skills (it was skipped)
-        assert "speckit-test-ext-hello" not in metadata["registered_skills"]
-
-    def test_registered_skills_in_registry(self, skills_project, extension_dir):
-        """Registry should contain registered_skills list."""
-        project_dir, skills_dir = skills_project
-        manager = ExtensionManager(project_dir)
-        manifest = manager.install_from_directory(
-            extension_dir, "0.1.0", register_commands=False
-        )
-
-        metadata = manager.registry.get(manifest.id)
-        assert "registered_skills" in metadata
-        assert len(metadata["registered_skills"]) == 2
-        assert "speckit-test-ext-hello" in metadata["registered_skills"]
-        assert "speckit-test-ext-world" in metadata["registered_skills"]
-
-    def test_kimi_uses_hyphenated_skill_names(self, project_dir, temp_dir):
-        """Kimi agent should use the same hyphenated skill names as hooks."""
-        _create_init_options(project_dir, ai="kimi", ai_skills=True)
-        _create_skills_dir(project_dir, ai="kimi")
-        ext_dir = _create_extension_dir(temp_dir, ext_id="test-ext")
-
-        manager = ExtensionManager(project_dir)
-        manifest = manager.install_from_directory(
-            ext_dir, "0.1.0", register_commands=False
-        )
-
-        metadata = manager.registry.get(manifest.id)
-        assert "speckit-test-ext-hello" in metadata["registered_skills"]
-        assert "speckit-test-ext-world" in metadata["registered_skills"]
-
-    def test_kimi_creates_skills_when_ai_skills_disabled(self, project_dir, temp_dir):
-        """Kimi should still auto-register extension skills in native-skills mode."""
-        _create_init_options(project_dir, ai="kimi", ai_skills=False)
-        skills_dir = _create_skills_dir(project_dir, ai="kimi")
-        ext_dir = _create_extension_dir(temp_dir, ext_id="test-ext")
-
-        manager = ExtensionManager(project_dir)
-        manifest = manager.install_from_directory(
-            ext_dir, "0.1.0", register_commands=False
-        )
-
-        metadata = manager.registry.get(manifest.id)
-        assert "speckit-test-ext-hello" in metadata["registered_skills"]
-        assert "speckit-test-ext-world" in metadata["registered_skills"]
-        assert (skills_dir / "speckit-test-ext-hello" / "SKILL.md").exists()
-
-    def test_skill_registration_resolves_script_placeholders(self, project_dir, temp_dir):
-        """Auto-registered extension skills should resolve script placeholders."""
-        _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.plan",
-                        "file": "commands/plan.md",
-                        "description": "Scripted plan command",
-                    }
-                ]
-            },
-        }
-        with open(ext_dir / "extension.yml", "w") as f:
-            yaml.dump(manifest_data, f)
-
-        (ext_dir / "commands").mkdir()
-        (ext_dir / "commands" / "plan.md").write_text(
-            "---\n"
-            "description: Scripted plan command\n"
-            "scripts:\n"
-            "  sh: ../../scripts/bash/setup-plan.sh --json \"{ARGS}\"\n"
-            "agent_scripts:\n"
-            "  sh: ../../scripts/bash/update-agent-context.sh __AGENT__\n"
-            "---\n\n"
-            "Run {SCRIPT}\n"
-            "Then {AGENT_SCRIPT}\n"
-            "Review templates/checklist.md and memory/constitution.md for __AGENT__.\n"
-        )
-
-        manager = ExtensionManager(project_dir)
-        manager.install_from_directory(ext_dir, "0.1.0", register_commands=False)
-
-        content = (skills_dir / "speckit-scripted-ext-plan" / "SKILL.md").read_text()
-        assert "{SCRIPT}" not in content
-        assert "{AGENT_SCRIPT}" not in content
-        assert "{ARGS}" not in content
-        assert "__AGENT__" not in content
-        assert '.specify/scripts/bash/setup-plan.sh --json "$ARGUMENTS"' in content
-        assert ".specify/scripts/bash/update-agent-context.sh claude" in content
-        assert ".specify/templates/checklist.md" in content
-        assert ".specify/memory/constitution.md" 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
-
-        ext_dir = temp_dir / "missing-cmd-ext"
-        ext_dir.mkdir()
-        manifest_data = {
-            "schema_version": "1.0",
-            "extension": {
-                "id": "missing-cmd-ext",
-                "name": "Missing Cmd Extension",
-                "version": "1.0.0",
-                "description": "Test",
-            },
-            "requires": {"speckit_version": ">=0.1.0"},
-            "provides": {
-                "commands": [
-                    {
-                        "name": "speckit.missing-cmd-ext.exists",
-                        "file": "commands/exists.md",
-                        "description": "Exists",
-                    },
-                    {
-                        "name": "speckit.missing-cmd-ext.ghost",
-                        "file": "commands/ghost.md",
-                        "description": "Does not exist",
-                    },
-                ]
-            },
-        }
-        with open(ext_dir / "extension.yml", "w") as f:
-            yaml.dump(manifest_data, f)
-
-        (ext_dir / "commands").mkdir()
-        (ext_dir / "commands" / "exists.md").write_text(
-            "---\ndescription: Exists\n---\n\n# Exists\n\nBody.\n"
-        )
-        # Intentionally do NOT create ghost.md
-
-        manager = ExtensionManager(project_dir)
-        manifest = manager.install_from_directory(
-            ext_dir, "0.1.0", register_commands=False
-        )
-
-        metadata = manager.registry.get(manifest.id)
-        assert "speckit-missing-cmd-ext-exists" in metadata["registered_skills"]
-        assert "speckit-missing-cmd-ext-ghost" not in metadata["registered_skills"]
-
-
-# ===== Extension Skill Unregistration Tests =====
-
-class TestExtensionSkillUnregistration:
-    """Test _unregister_extension_skills() on ExtensionManager."""
-
-    def test_skills_removed_on_extension_remove(self, skills_project, extension_dir):
-        """Removing an extension should clean up its skill directories."""
-        project_dir, skills_dir = skills_project
-        manager = ExtensionManager(project_dir)
-        manifest = manager.install_from_directory(
-            extension_dir, "0.1.0", register_commands=False
-        )
-
-        # Verify skills exist
-        assert (skills_dir / "speckit-test-ext-hello" / "SKILL.md").exists()
-        assert (skills_dir / "speckit-test-ext-world" / "SKILL.md").exists()
-
-        # Remove extension
-        result = manager.remove(manifest.id, keep_config=False)
-        assert result is True
-
-        # Skills should be gone
-        assert not (skills_dir / "speckit-test-ext-hello").exists()
-        assert not (skills_dir / "speckit-test-ext-world").exists()
-
-    def test_other_skills_preserved_on_remove(self, skills_project, extension_dir):
-        """Non-extension skills should not be affected by extension removal."""
-        project_dir, skills_dir = skills_project
-
-        # Pre-create a custom skill
-        custom_dir = skills_dir / "my-custom-skill"
-        custom_dir.mkdir(parents=True)
-        (custom_dir / "SKILL.md").write_text("# My Custom Skill\n")
-
-        manager = ExtensionManager(project_dir)
-        manifest = manager.install_from_directory(
-            extension_dir, "0.1.0", register_commands=False
-        )
-
-        manager.remove(manifest.id, keep_config=False)
-
-        # Custom skill should still exist
-        assert (custom_dir / "SKILL.md").exists()
-        assert (custom_dir / "SKILL.md").read_text() == "# My Custom Skill\n"
-
-    def test_remove_handles_already_deleted_skills(self, skills_project, extension_dir):
-        """Gracefully handle case where skill dirs were already deleted."""
-        project_dir, skills_dir = skills_project
-        manager = ExtensionManager(project_dir)
-        manifest = manager.install_from_directory(
-            extension_dir, "0.1.0", register_commands=False
-        )
-
-        # Manually delete skill dirs before calling remove
-        shutil.rmtree(skills_dir / "speckit-test-ext-hello")
-        shutil.rmtree(skills_dir / "speckit-test-ext-world")
-
-        # Should not raise
-        result = manager.remove(manifest.id, keep_config=False)
-        assert result is True
-
-    def test_remove_no_skills_when_not_active(self, no_skills_project, extension_dir):
-        """Removal without active skills should not attempt skill cleanup."""
-        manager = ExtensionManager(no_skills_project)
-        manifest = manager.install_from_directory(
-            extension_dir, "0.1.0", register_commands=False
-        )
-
-        # Should not raise even though no skills exist
-        result = manager.remove(manifest.id, keep_config=False)
-        assert result is True
-
-
-# ===== Command File Without Frontmatter =====
-
-class TestExtensionSkillEdgeCases:
-    """Test edge cases in extension skill registration."""
-
-    def test_install_with_non_dict_init_options_does_not_crash(self, project_dir, extension_dir):
-        """Corrupted init-options payloads should disable skill registration, not crash install."""
-        opts_file = project_dir / ".specify" / "init-options.json"
-        opts_file.parent.mkdir(parents=True, exist_ok=True)
-        opts_file.write_text("[]")
-        _create_skills_dir(project_dir, ai="claude")
-
-        manager = ExtensionManager(project_dir)
-        manifest = manager.install_from_directory(
-            extension_dir, "0.1.0", register_commands=False
-        )
-
-        metadata = manager.registry.get(manifest.id)
-        assert metadata["registered_skills"] == []
-
-    def test_command_without_frontmatter(self, skills_project, temp_dir):
-        """Commands without YAML frontmatter should still produce valid skills."""
-        project_dir, skills_dir = skills_project
-
-        ext_dir = temp_dir / "nofm-ext"
-        ext_dir.mkdir()
-        manifest_data = {
-            "schema_version": "1.0",
-            "extension": {
-                "id": "nofm-ext",
-                "name": "No Frontmatter Extension",
-                "version": "1.0.0",
-                "description": "Test",
-            },
-            "requires": {"speckit_version": ">=0.1.0"},
-            "provides": {
-                "commands": [
-                    {
-                        "name": "speckit.nofm-ext.plain",
-                        "file": "commands/plain.md",
-                        "description": "Plain command",
-                    }
-                ]
-            },
-        }
-        with open(ext_dir / "extension.yml", "w") as f:
-            yaml.dump(manifest_data, f)
-
-        (ext_dir / "commands").mkdir()
-        (ext_dir / "commands" / "plain.md").write_text(
-            "# Plain Command\n\nBody without frontmatter.\n"
-        )
-
-        manager = ExtensionManager(project_dir)
-        manifest = manager.install_from_directory(
-            ext_dir, "0.1.0", register_commands=False
-        )
-
-        skill_file = skills_dir / "speckit-nofm-ext-plain" / "SKILL.md"
-        assert skill_file.exists()
-        content = skill_file.read_text()
-        assert "name: speckit-nofm-ext-plain" in content
-        # Fallback description when no frontmatter description
-        assert "Extension command: speckit.nofm-ext.plain" in content
-        assert "Body without frontmatter." in content
-
-    def test_gemini_agent_skills(self, project_dir, temp_dir):
-        """Gemini agent should use .gemini/skills/ for skill directory."""
-        _create_init_options(project_dir, ai="gemini", ai_skills=True)
-        _create_skills_dir(project_dir, ai="gemini")
-        ext_dir = _create_extension_dir(temp_dir, ext_id="test-ext")
-
-        manager = ExtensionManager(project_dir)
-        manifest = manager.install_from_directory(
-            ext_dir, "0.1.0", register_commands=False
-        )
-
-        skills_dir = project_dir / ".gemini" / "skills"
-        assert (skills_dir / "speckit-test-ext-hello" / "SKILL.md").exists()
-        assert (skills_dir / "speckit-test-ext-world" / "SKILL.md").exists()
-
-    def test_multiple_extensions_independent_skills(self, skills_project, temp_dir):
-        """Installing and removing different extensions should be independent."""
-        project_dir, skills_dir = skills_project
-
-        ext_dir_a = _create_extension_dir(temp_dir, ext_id="ext-a")
-        ext_dir_b = _create_extension_dir(temp_dir, ext_id="ext-b")
-
-        manager = ExtensionManager(project_dir)
-        manifest_a = manager.install_from_directory(
-            ext_dir_a, "0.1.0", register_commands=False
-        )
-        manifest_b = manager.install_from_directory(
-            ext_dir_b, "0.1.0", register_commands=False
-        )
-
-        # Both should have skills
-        assert (skills_dir / "speckit-ext-a-hello" / "SKILL.md").exists()
-        assert (skills_dir / "speckit-ext-b-hello" / "SKILL.md").exists()
-
-        # Remove ext-a
-        manager.remove("ext-a", keep_config=False)
-
-        # ext-a skills gone, ext-b skills preserved
-        assert not (skills_dir / "speckit-ext-a-hello").exists()
-        assert (skills_dir / "speckit-ext-b-hello" / "SKILL.md").exists()
-
-    def test_malformed_frontmatter_handled(self, skills_project, temp_dir):
-        """Commands with invalid YAML frontmatter should still produce valid skills."""
-        project_dir, skills_dir = skills_project
-
-        ext_dir = temp_dir / "badfm-ext"
-        ext_dir.mkdir()
-        manifest_data = {
-            "schema_version": "1.0",
-            "extension": {
-                "id": "badfm-ext",
-                "name": "Bad Frontmatter Extension",
-                "version": "1.0.0",
-                "description": "Test",
-            },
-            "requires": {"speckit_version": ">=0.1.0"},
-            "provides": {
-                "commands": [
-                    {
-                        "name": "speckit.badfm-ext.broken",
-                        "file": "commands/broken.md",
-                        "description": "Broken frontmatter",
-                    }
-                ]
-            },
-        }
-        with open(ext_dir / "extension.yml", "w") as f:
-            yaml.dump(manifest_data, f)
-
-        (ext_dir / "commands").mkdir()
-        # Malformed YAML: invalid key-value syntax
-        (ext_dir / "commands" / "broken.md").write_text(
-            "---\n"
-            "description: [invalid yaml\n"
-            "  unclosed: bracket\n"
-            "---\n"
-            "\n"
-            "# Broken Command\n"
-            "\n"
-            "This body should still be used.\n"
-        )
-
-        manager = ExtensionManager(project_dir)
-        # Should not raise
-        manifest = manager.install_from_directory(
-            ext_dir, "0.1.0", register_commands=False
-        )
-
-        skill_file = skills_dir / "speckit-badfm-ext-broken" / "SKILL.md"
-        assert skill_file.exists()
-        content = skill_file.read_text()
-        # Fallback description since frontmatter was invalid
-        assert "Extension command: speckit.badfm-ext.broken" in content
-        assert "This body should still be used." in content
-
-    def test_remove_cleans_up_when_init_options_deleted(self, skills_project, extension_dir):
-        """Skills should be cleaned up even if init-options.json is deleted after install."""
-        project_dir, skills_dir = skills_project
-        manager = ExtensionManager(project_dir)
-        manifest = manager.install_from_directory(
-            extension_dir, "0.1.0", register_commands=False
-        )
-
-        # Verify skills exist
-        assert (skills_dir / "speckit-test-ext-hello" / "SKILL.md").exists()
-
-        # Delete init-options.json to simulate user change
-        init_opts = project_dir / ".specify" / "init-options.json"
-        init_opts.unlink()
-
-        # Remove should still clean up via fallback scan
-        result = manager.remove(manifest.id, keep_config=False)
-        assert result is True
-        assert not (skills_dir / "speckit-test-ext-hello").exists()
-        assert not (skills_dir / "speckit-test-ext-world").exists()
-
-    def test_remove_cleans_up_when_ai_skills_toggled(self, skills_project, extension_dir):
-        """Skills should be cleaned up even if ai_skills is toggled to false after install."""
-        project_dir, skills_dir = skills_project
-        manager = ExtensionManager(project_dir)
-        manifest = manager.install_from_directory(
-            extension_dir, "0.1.0", register_commands=False
-        )
-
-        # Verify skills exist
-        assert (skills_dir / "speckit-test-ext-hello" / "SKILL.md").exists()
-
-        # Toggle ai_skills to false
-        _create_init_options(project_dir, ai="claude", ai_skills=False)
-
-        # Remove should still clean up via fallback scan
-        result = manager.remove(manifest.id, keep_config=False)
-        assert result is True
-        assert not (skills_dir / "speckit-test-ext-hello").exists()
-        assert not (skills_dir / "speckit-test-ext-world").exists()

tests/test_extensions.py

@@ -22,7 +22,6 @@ from specify_cli.extensions import (
     ExtensionRegistry,
     ExtensionManager,
     CommandRegistrar,
-    HookExecutor,
     ExtensionCatalog,
     ExtensionError,
     ValidationError,
@@ -760,81 +759,6 @@ $ARGUMENTS
         assert "Prüfe Konformität" in output
         assert "\\u" not in output
 
-    def test_adjust_script_paths_does_not_mutate_input(self):
-        """Path adjustments should not mutate caller-owned frontmatter dicts."""
-        from specify_cli.agents import CommandRegistrar as AgentCommandRegistrar
-        registrar = AgentCommandRegistrar()
-        original = {
-            "scripts": {
-                "sh": "../../scripts/bash/setup-plan.sh {ARGS}",
-                "ps": "../../scripts/powershell/setup-plan.ps1 {ARGS}",
-            }
-        }
-        before = json.loads(json.dumps(original))
-
-        adjusted = registrar._adjust_script_paths(original)
-
-        assert original == before
-        assert adjusted["scripts"]["sh"] == ".specify/scripts/bash/setup-plan.sh {ARGS}"
-        assert adjusted["scripts"]["ps"] == ".specify/scripts/powershell/setup-plan.ps1 {ARGS}"
-
-    def test_adjust_script_paths_preserves_extension_local_paths(self):
-        """Extension-local script paths should not be rewritten into .specify/.specify."""
-        from specify_cli.agents import CommandRegistrar as AgentCommandRegistrar
-        registrar = AgentCommandRegistrar()
-        original = {
-            "scripts": {
-                "sh": ".specify/extensions/test-ext/scripts/setup.sh {ARGS}",
-                "ps": "scripts/powershell/setup-plan.ps1 {ARGS}",
-            }
-        }
-
-        adjusted = registrar._adjust_script_paths(original)
-
-        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_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
-
-        body = (
-            "Read `.specify/extensions/test-ext/templates/spec.md`\n"
-            "Run scripts/bash/setup-plan.sh\n"
-        )
-
-        rewritten = AgentCommandRegistrar._rewrite_project_relative_paths(body)
-
-        assert ".specify/extensions/test-ext/templates/spec.md" in rewritten
-        assert ".specify/scripts/bash/setup-plan.sh" 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
-        registrar = AgentCommandRegistrar()
-        output = registrar.render_toml_command(
-            {"description": "x"},
-            'line1\n"""danger"""\nline2',
-            "extension:test-ext",
-        )
-
-        assert "prompt = '''" in output
-        assert '"""danger"""' in output
-
-    def test_render_toml_command_escapes_when_both_triple_quote_styles_exist(self):
-        """If body has both triple quote styles, fall back to escaped basic string."""
-        from specify_cli.agents import CommandRegistrar as AgentCommandRegistrar
-        registrar = AgentCommandRegistrar()
-        output = registrar.render_toml_command(
-            {"description": "x"},
-            'a """ b\nc \'\'\' d',
-            "extension:test-ext",
-        )
-
-        assert 'prompt = "' in output
-        assert "\\n" in output
-        assert "\\\"\\\"\\\"" in output
-
     def test_register_commands_for_claude(self, extension_dir, project_dir):
         """Test registering commands for Claude agent."""
         # Create .claude directory
@@ -951,11 +875,11 @@ $ARGUMENTS
         registrar = CommandRegistrar()
         registrar.register_commands_for_agent("codex", manifest, extension_dir, project_dir)
 
-        skill_file = skills_dir / "speckit-test-hello" / "SKILL.md"
+        skill_file = skills_dir / "speckit-test.hello" / "SKILL.md"
         assert skill_file.exists()
 
         content = skill_file.read_text()
-        assert "name: speckit-test-hello" in content
+        assert "name: speckit-test.hello" in content
         assert "description: Test hello command" in content
         assert "compatibility:" in content
         assert "metadata:" in content
@@ -1020,7 +944,7 @@ Agent __AGENT__
         registrar = CommandRegistrar()
         registrar.register_commands_for_agent("codex", manifest, ext_dir, project_dir)
 
-        skill_file = skills_dir / "speckit-test-plan" / "SKILL.md"
+        skill_file = skills_dir / "speckit-test.plan" / "SKILL.md"
         assert skill_file.exists()
 
         content = skill_file.read_text()
@@ -1070,12 +994,12 @@ Agent __AGENT__
         registrar = CommandRegistrar()
         registrar.register_commands_for_agent("codex", manifest, ext_dir, project_dir)
 
-        primary = skills_dir / "speckit-alias-cmd" / "SKILL.md"
+        primary = skills_dir / "speckit-alias.cmd" / "SKILL.md"
         alias = skills_dir / "speckit-shortcut" / "SKILL.md"
 
         assert primary.exists()
         assert alias.exists()
-        assert "name: speckit-alias-cmd" in primary.read_text()
+        assert "name: speckit-alias.cmd" in primary.read_text()
         assert "name: speckit-shortcut" in alias.read_text()
 
     def test_codex_skill_registration_uses_fallback_script_variant_without_init_options(
@@ -1132,7 +1056,7 @@ Then {AGENT_SCRIPT}
         registrar = CommandRegistrar()
         registrar.register_commands_for_agent("codex", manifest, ext_dir, project_dir)
 
-        skill_file = skills_dir / "speckit-fallback-plan" / "SKILL.md"
+        skill_file = skills_dir / "speckit-fallback.plan" / "SKILL.md"
         assert skill_file.exists()
 
         content = skill_file.read_text()
@@ -1141,62 +1065,6 @@ Then {AGENT_SCRIPT}
         assert '.specify/scripts/bash/setup-plan.sh --json "$ARGUMENTS"' in content
         assert ".specify/scripts/bash/update-agent-context.sh codex" in content
 
-    def test_codex_skill_registration_handles_non_dict_init_options(
-        self, project_dir, temp_dir
-    ):
-        """Non-dict init-options payloads should not crash skill placeholder resolution."""
-        import yaml
-
-        ext_dir = temp_dir / "ext-script-list-init"
-        ext_dir.mkdir()
-        (ext_dir / "commands").mkdir()
-
-        manifest_data = {
-            "schema_version": "1.0",
-            "extension": {
-                "id": "ext-script-list-init",
-                "name": "List init options",
-                "version": "1.0.0",
-                "description": "Test",
-            },
-            "requires": {"speckit_version": ">=0.1.0"},
-            "provides": {
-                "commands": [
-                    {
-                        "name": "speckit.list.plan",
-                        "file": "commands/plan.md",
-                    }
-                ]
-            },
-        }
-        with open(ext_dir / "extension.yml", "w") as f:
-            yaml.dump(manifest_data, f)
-
-        (ext_dir / "commands" / "plan.md").write_text(
-            """---
-description: "List init scripted command"
-scripts:
-  sh: ../../scripts/bash/setup-plan.sh --json "{ARGS}"
----
-
-Run {SCRIPT}
-"""
-        )
-
-        init_options = project_dir / ".specify" / "init-options.json"
-        init_options.parent.mkdir(parents=True, exist_ok=True)
-        init_options.write_text("[]")
-
-        skills_dir = project_dir / ".agents" / "skills"
-        skills_dir.mkdir(parents=True)
-
-        manifest = ExtensionManifest(ext_dir / "extension.yml")
-        registrar = CommandRegistrar()
-        registrar.register_commands_for_agent("codex", manifest, ext_dir, project_dir)
-
-        content = (skills_dir / "speckit-list-plan" / "SKILL.md").read_text()
-        assert '.specify/scripts/bash/setup-plan.sh --json "$ARGUMENTS"' in content
-
     def test_codex_skill_registration_fallback_prefers_powershell_on_windows(
         self, project_dir, temp_dir, monkeypatch
     ):
@@ -1253,7 +1121,7 @@ Then {AGENT_SCRIPT}
         registrar = CommandRegistrar()
         registrar.register_commands_for_agent("codex", manifest, ext_dir, project_dir)
 
-        skill_file = skills_dir / "speckit-windows-plan" / "SKILL.md"
+        skill_file = skills_dir / "speckit-windows.plan" / "SKILL.md"
         assert skill_file.exists()
 
         content = skill_file.read_text()
@@ -3363,128 +3231,3 @@ class TestExtensionPriorityBackwardsCompatibility:
         assert result[0][0] == "ext-with-priority"
         assert result[1][0] == "legacy-ext"
         assert result[2][0] == "ext-low-priority"
-
-
-class TestHookInvocationRendering:
-    """Test hook invocation formatting for different agent modes."""
-
-    def test_kimi_hooks_render_skill_invocation(self, project_dir):
-        """Kimi projects should render /skill:speckit-* invocations."""
-        init_options = project_dir / ".specify" / "init-options.json"
-        init_options.parent.mkdir(parents=True, exist_ok=True)
-        init_options.write_text(json.dumps({"ai": "kimi", "ai_skills": False}))
-
-        hook_executor = HookExecutor(project_dir)
-        message = hook_executor.format_hook_message(
-            "before_plan",
-            [
-                {
-                    "extension": "test-ext",
-                    "command": "speckit.plan",
-                    "optional": False,
-                }
-            ],
-        )
-
-        assert "Executing: `/skill:speckit-plan`" in message
-        assert "EXECUTE_COMMAND: speckit.plan" in message
-        assert "EXECUTE_COMMAND_INVOCATION: /skill:speckit-plan" in message
-
-    def test_codex_hooks_render_dollar_skill_invocation(self, project_dir):
-        """Codex projects with --ai-skills should render $speckit-* invocations."""
-        init_options = project_dir / ".specify" / "init-options.json"
-        init_options.parent.mkdir(parents=True, exist_ok=True)
-        init_options.write_text(json.dumps({"ai": "codex", "ai_skills": True}))
-
-        hook_executor = HookExecutor(project_dir)
-        execution = hook_executor.execute_hook(
-            {
-                "extension": "test-ext",
-                "command": "speckit.tasks",
-                "optional": False,
-            }
-        )
-
-        assert execution["command"] == "speckit.tasks"
-        assert execution["invocation"] == "$speckit-tasks"
-
-    def test_non_skill_command_keeps_slash_invocation(self, project_dir):
-        """Custom hook commands should keep slash invocation style."""
-        init_options = project_dir / ".specify" / "init-options.json"
-        init_options.parent.mkdir(parents=True, exist_ok=True)
-        init_options.write_text(json.dumps({"ai": "kimi", "ai_skills": False}))
-
-        hook_executor = HookExecutor(project_dir)
-        message = hook_executor.format_hook_message(
-            "before_tasks",
-            [
-                {
-                    "extension": "test-ext",
-                    "command": "pre_tasks_test",
-                    "optional": False,
-                }
-            ],
-        )
-
-        assert "Executing: `/pre_tasks_test`" in message
-        assert "EXECUTE_COMMAND: pre_tasks_test" in message
-        assert "EXECUTE_COMMAND_INVOCATION: /pre_tasks_test" in message
-
-    def test_extension_command_uses_hyphenated_skill_invocation(self, project_dir):
-        """Multi-segment extension command ids should map to hyphenated skills."""
-        init_options = project_dir / ".specify" / "init-options.json"
-        init_options.parent.mkdir(parents=True, exist_ok=True)
-        init_options.write_text(json.dumps({"ai": "kimi", "ai_skills": False}))
-
-        hook_executor = HookExecutor(project_dir)
-        message = hook_executor.format_hook_message(
-            "after_tasks",
-            [
-                {
-                    "extension": "test-ext",
-                    "command": "speckit.test.hello",
-                    "optional": False,
-                }
-            ],
-        )
-
-        assert "Executing: `/skill:speckit-test-hello`" in message
-        assert "EXECUTE_COMMAND: speckit.test.hello" in message
-        assert "EXECUTE_COMMAND_INVOCATION: /skill:speckit-test-hello" in message
-
-    def test_hook_executor_caches_init_options_lookup(self, project_dir, monkeypatch):
-        """Init options should be loaded once per executor instance."""
-        calls = {"count": 0}
-
-        def fake_load_init_options(_project_root):
-            calls["count"] += 1
-            return {"ai": "kimi", "ai_skills": False}
-
-        monkeypatch.setattr("specify_cli.load_init_options", fake_load_init_options)
-
-        hook_executor = HookExecutor(project_dir)
-        assert hook_executor._render_hook_invocation("speckit.plan") == "/skill:speckit-plan"
-        assert hook_executor._render_hook_invocation("speckit.tasks") == "/skill:speckit-tasks"
-        assert calls["count"] == 1
-
-    def test_hook_message_falls_back_when_invocation_is_empty(self, project_dir):
-        """Hook messages should still render actionable command placeholders."""
-        init_options = project_dir / ".specify" / "init-options.json"
-        init_options.parent.mkdir(parents=True, exist_ok=True)
-        init_options.write_text(json.dumps({"ai": "kimi", "ai_skills": False}))
-
-        hook_executor = HookExecutor(project_dir)
-        message = hook_executor.format_hook_message(
-            "after_tasks",
-            [
-                {
-                    "extension": "test-ext",
-                    "command": None,
-                    "optional": False,
-                }
-            ],
-        )
-
-        assert "Executing: `/<missing command>`" in message
-        assert "EXECUTE_COMMAND: <missing command>" in message
-        assert "EXECUTE_COMMAND_INVOCATION: /<missing command>" in message

tests/test_presets.py

@@ -1170,12 +1170,8 @@ class TestPresetCatalog:
         assert not catalog.cache_file.exists()
         assert not catalog.cache_metadata_file.exists()
 
-    def test_search_with_cached_data(self, project_dir, monkeypatch):
+    def test_search_with_cached_data(self, project_dir):
         """Test search with cached catalog data."""
-        from unittest.mock import patch
-
-        # Only use the default catalog to prevent fetching the community catalog from the network
-        monkeypatch.setenv("SPECKIT_PRESET_CATALOG_URL", PresetCatalog.DEFAULT_CATALOG_URL)
         catalog = PresetCatalog(project_dir)
         catalog.cache_dir.mkdir(parents=True, exist_ok=True)
 
@@ -1204,26 +1200,23 @@ class TestPresetCatalog:
             "cached_at": datetime.now(timezone.utc).isoformat(),
         }))
 
-        # Isolate from community catalog so results are deterministic
-        default_only = [PresetCatalogEntry(url=catalog.DEFAULT_CATALOG_URL, name="default", priority=1, install_allowed=True)]
-        with patch.object(catalog, "get_active_catalogs", return_value=default_only):
-            # Search by query
-            results = catalog.search(query="agile")
-            assert len(results) == 1
-            assert results[0]["id"] == "safe-agile"
+        # Search by query
+        results = catalog.search(query="agile")
+        assert len(results) == 1
+        assert results[0]["id"] == "safe-agile"
 
-            # Search by tag
-            results = catalog.search(tag="hipaa")
-            assert len(results) == 1
-            assert results[0]["id"] == "healthcare"
+        # Search by tag
+        results = catalog.search(tag="hipaa")
+        assert len(results) == 1
+        assert results[0]["id"] == "healthcare"
 
-            # Search by author
-            results = catalog.search(author="agile-community")
-            assert len(results) == 1
+        # Search by author
+        results = catalog.search(author="agile-community")
+        assert len(results) == 1
 
-            # Search all
-            results = catalog.search()
-            assert len(results) == 2
+        # Search all
+        results = catalog.search()
+        assert len(results) == 2
 
     def test_get_pack_info(self, project_dir):
         """Test getting info for a specific pack."""
@@ -1942,10 +1935,10 @@ class TestInitOptions:
 class TestPresetSkills:
     """Tests for preset skill registration and unregistration."""
 
-    def _write_init_options(self, project_dir, ai="claude", ai_skills=True, script="sh"):
+    def _write_init_options(self, project_dir, ai="claude", ai_skills=True):
         from specify_cli import save_init_options
 
-        save_init_options(project_dir, {"ai": ai, "ai_skills": ai_skills, "script": script})
+        save_init_options(project_dir, {"ai": ai, "ai_skills": ai_skills})
 
     def _create_skill(self, skills_dir, skill_name, body="original body"):
         skill_dir = skills_dir / skill_name
@@ -1995,26 +1988,6 @@ class TestPresetSkills:
         content = skill_file.read_text()
         assert "untouched" in content, "Skill should not be modified when ai_skills=False"
 
-    def test_get_skills_dir_returns_none_for_non_string_ai(self, project_dir):
-        """Corrupted init-options ai values should not crash preset skill resolution."""
-        init_options = project_dir / ".specify" / "init-options.json"
-        init_options.parent.mkdir(parents=True, exist_ok=True)
-        init_options.write_text('{"ai":["codex"],"ai_skills":true,"script":"sh"}')
-
-        manager = PresetManager(project_dir)
-
-        assert manager._get_skills_dir() is None
-
-    def test_get_skills_dir_returns_none_for_non_dict_init_options(self, project_dir):
-        """Corrupted non-dict init-options payloads should fail closed."""
-        init_options = project_dir / ".specify" / "init-options.json"
-        init_options.parent.mkdir(parents=True, exist_ok=True)
-        init_options.write_text("[]")
-
-        manager = PresetManager(project_dir)
-
-        assert manager._get_skills_dir() is None
-
     def test_skill_not_updated_without_init_options(self, project_dir, temp_dir):
         """When no init-options.json exists, preset install should not touch skills."""
         skills_dir = project_dir / ".claude" / "skills"
@@ -2060,52 +2033,6 @@ class TestPresetSkills:
         assert "preset:self-test" not in content, "Preset content should be gone"
         assert "templates/commands/specify.md" in content, "Should reference core template"
 
-    def test_skill_restored_on_remove_resolves_script_placeholders(self, project_dir):
-        """Core restore should resolve {SCRIPT}/{ARGS} placeholders like other skill paths."""
-        self._write_init_options(project_dir, ai="claude", ai_skills=True, script="sh")
-        skills_dir = project_dir / ".claude" / "skills"
-        self._create_skill(skills_dir, "speckit-specify", body="old")
-        (project_dir / ".claude" / "commands").mkdir(parents=True, exist_ok=True)
-
-        core_cmds = project_dir / ".specify" / "templates" / "commands"
-        core_cmds.mkdir(parents=True, exist_ok=True)
-        (core_cmds / "specify.md").write_text(
-            "---\n"
-            "description: Core specify command\n"
-            "scripts:\n"
-            "  sh: .specify/scripts/bash/create-new-feature.sh --json \"{ARGS}\"\n"
-            "---\n\n"
-            "Run:\n"
-            "{SCRIPT}\n"
-        )
-
-        manager = PresetManager(project_dir)
-        SELF_TEST_DIR = Path(__file__).parent.parent / "presets" / "self-test"
-        manager.install_from_directory(SELF_TEST_DIR, "0.1.5")
-        manager.remove("self-test")
-
-        content = (skills_dir / "speckit-specify" / "SKILL.md").read_text()
-        assert "{SCRIPT}" not in content
-        assert "{ARGS}" not in content
-        assert ".specify/scripts/bash/create-new-feature.sh --json \"$ARGUMENTS\"" in content
-
-    def test_skill_not_overridden_when_skill_path_is_file(self, project_dir):
-        """Preset install should skip non-directory skill targets."""
-        self._write_init_options(project_dir, ai="claude")
-        skills_dir = project_dir / ".claude" / "skills"
-        skills_dir.mkdir(parents=True, exist_ok=True)
-        (skills_dir / "speckit-specify").write_text("not-a-directory")
-
-        (project_dir / ".claude" / "commands").mkdir(parents=True, exist_ok=True)
-
-        manager = PresetManager(project_dir)
-        SELF_TEST_DIR = Path(__file__).parent.parent / "presets" / "self-test"
-        manager.install_from_directory(SELF_TEST_DIR, "0.1.5")
-
-        assert (skills_dir / "speckit-specify").is_file()
-        metadata = manager.registry.get("self-test")
-        assert "speckit-specify" not in metadata.get("registered_skills", [])
-
     def test_no_skills_registered_when_no_skill_dir_exists(self, project_dir, temp_dir):
         """Skills should not be created when no existing skill dir is found."""
         self._write_init_options(project_dir, ai="claude")
@@ -2120,304 +2047,6 @@ class TestPresetSkills:
         metadata = manager.registry.get("self-test")
         assert metadata.get("registered_skills", []) == []
 
-    def test_extension_skill_override_matches_hyphenated_multisegment_name(self, project_dir, temp_dir):
-        """Preset overrides for speckit.<ext>.<cmd> should target speckit-<ext>-<cmd> skills."""
-        self._write_init_options(project_dir, ai="codex")
-        skills_dir = project_dir / ".agents" / "skills"
-        self._create_skill(skills_dir, "speckit-fakeext-cmd", body="untouched")
-        (project_dir / ".specify" / "extensions" / "fakeext").mkdir(parents=True, exist_ok=True)
-
-        preset_dir = temp_dir / "ext-skill-override"
-        preset_dir.mkdir()
-        (preset_dir / "commands").mkdir()
-        (preset_dir / "commands" / "speckit.fakeext.cmd.md").write_text(
-            "---\ndescription: Override fakeext cmd\n---\n\npreset:ext-skill-override\n"
-        )
-        manifest_data = {
-            "schema_version": "1.0",
-            "preset": {
-                "id": "ext-skill-override",
-                "name": "Ext Skill Override",
-                "version": "1.0.0",
-                "description": "Test",
-            },
-            "requires": {"speckit_version": ">=0.1.0"},
-            "provides": {
-                "templates": [
-                    {
-                        "type": "command",
-                        "name": "speckit.fakeext.cmd",
-                        "file": "commands/speckit.fakeext.cmd.md",
-                    }
-                ]
-            },
-        }
-        with open(preset_dir / "preset.yml", "w") as f:
-            yaml.dump(manifest_data, f)
-
-        manager = PresetManager(project_dir)
-        manager.install_from_directory(preset_dir, "0.1.5")
-
-        skill_file = skills_dir / "speckit-fakeext-cmd" / "SKILL.md"
-        assert skill_file.exists()
-        content = skill_file.read_text()
-        assert "preset:ext-skill-override" in content
-        assert "name: speckit-fakeext-cmd" in content
-        assert "# Speckit Fakeext Cmd Skill" in content
-
-        metadata = manager.registry.get("ext-skill-override")
-        assert "speckit-fakeext-cmd" in metadata.get("registered_skills", [])
-
-    def test_extension_skill_restored_on_preset_remove(self, project_dir, temp_dir):
-        """Preset removal should restore an extension-backed skill instead of deleting it."""
-        self._write_init_options(project_dir, ai="codex")
-        skills_dir = project_dir / ".agents" / "skills"
-        self._create_skill(skills_dir, "speckit-fakeext-cmd", body="original extension skill")
-
-        extension_dir = project_dir / ".specify" / "extensions" / "fakeext"
-        (extension_dir / "commands").mkdir(parents=True, exist_ok=True)
-        (extension_dir / "commands" / "cmd.md").write_text(
-            "---\n"
-            "description: Extension fakeext cmd\n"
-            "scripts:\n"
-            "  sh: ../../scripts/bash/setup-plan.sh --json \"{ARGS}\"\n"
-            "---\n\n"
-            "extension:fakeext\n"
-            "Run {SCRIPT}\n"
-        )
-        extension_manifest = {
-            "schema_version": "1.0",
-            "extension": {
-                "id": "fakeext",
-                "name": "Fake Extension",
-                "version": "1.0.0",
-                "description": "Test",
-            },
-            "requires": {"speckit_version": ">=0.1.0"},
-            "provides": {
-                "commands": [
-                    {
-                        "name": "speckit.fakeext.cmd",
-                        "file": "commands/cmd.md",
-                        "description": "Fake extension command",
-                    }
-                ]
-            },
-        }
-        with open(extension_dir / "extension.yml", "w") as f:
-            yaml.dump(extension_manifest, f)
-
-        preset_dir = temp_dir / "ext-skill-restore"
-        preset_dir.mkdir()
-        (preset_dir / "commands").mkdir()
-        (preset_dir / "commands" / "speckit.fakeext.cmd.md").write_text(
-            "---\ndescription: Override fakeext cmd\n---\n\npreset:ext-skill-restore\n"
-        )
-        preset_manifest = {
-            "schema_version": "1.0",
-            "preset": {
-                "id": "ext-skill-restore",
-                "name": "Ext Skill Restore",
-                "version": "1.0.0",
-                "description": "Test",
-            },
-            "requires": {"speckit_version": ">=0.1.0"},
-            "provides": {
-                "templates": [
-                    {
-                        "type": "command",
-                        "name": "speckit.fakeext.cmd",
-                        "file": "commands/speckit.fakeext.cmd.md",
-                    }
-                ]
-            },
-        }
-        with open(preset_dir / "preset.yml", "w") as f:
-            yaml.dump(preset_manifest, f)
-
-        manager = PresetManager(project_dir)
-        manager.install_from_directory(preset_dir, "0.1.5")
-
-        skill_file = skills_dir / "speckit-fakeext-cmd" / "SKILL.md"
-        assert "preset:ext-skill-restore" in skill_file.read_text()
-
-        manager.remove("ext-skill-restore")
-
-        assert skill_file.exists()
-        content = skill_file.read_text()
-        assert "preset:ext-skill-restore" not in content
-        assert "source: extension:fakeext" in content
-        assert "extension:fakeext" in content
-        assert '.specify/scripts/bash/setup-plan.sh --json "$ARGUMENTS"' in content
-        assert "# Fakeext Cmd Skill" in content
-
-    def test_preset_remove_skips_skill_dir_without_skill_file(self, project_dir, temp_dir):
-        """Preset removal should not delete arbitrary directories missing SKILL.md."""
-        self._write_init_options(project_dir, ai="codex")
-        skills_dir = project_dir / ".agents" / "skills"
-        stray_skill_dir = skills_dir / "speckit-fakeext-cmd"
-        stray_skill_dir.mkdir(parents=True, exist_ok=True)
-        note_file = stray_skill_dir / "notes.txt"
-        note_file.write_text("user content", encoding="utf-8")
-
-        preset_dir = temp_dir / "ext-skill-missing-file"
-        preset_dir.mkdir()
-        (preset_dir / "commands").mkdir()
-        (preset_dir / "commands" / "speckit.fakeext.cmd.md").write_text(
-            "---\ndescription: Override fakeext cmd\n---\n\npreset:ext-skill-missing-file\n"
-        )
-        preset_manifest = {
-            "schema_version": "1.0",
-            "preset": {
-                "id": "ext-skill-missing-file",
-                "name": "Ext Skill Missing File",
-                "version": "1.0.0",
-                "description": "Test",
-            },
-            "requires": {"speckit_version": ">=0.1.0"},
-            "provides": {
-                "templates": [
-                    {
-                        "type": "command",
-                        "name": "speckit.fakeext.cmd",
-                        "file": "commands/speckit.fakeext.cmd.md",
-                    }
-                ]
-            },
-        }
-        with open(preset_dir / "preset.yml", "w") as f:
-            yaml.dump(preset_manifest, f)
-
-        manager = PresetManager(project_dir)
-        installed_preset_dir = manager.presets_dir / "ext-skill-missing-file"
-        shutil.copytree(preset_dir, installed_preset_dir)
-        manager.registry.add(
-            "ext-skill-missing-file",
-            {
-                "version": "1.0.0",
-                "source": str(preset_dir),
-                "provides_templates": ["speckit.fakeext.cmd"],
-                "registered_skills": ["speckit-fakeext-cmd"],
-                "priority": 10,
-            },
-        )
-
-        manager.remove("ext-skill-missing-file")
-
-        assert stray_skill_dir.is_dir()
-        assert note_file.read_text(encoding="utf-8") == "user content"
-
-    def test_kimi_legacy_dotted_skill_override_still_applies(self, project_dir, temp_dir):
-        """Preset overrides should still target legacy dotted Kimi skill directories."""
-        self._write_init_options(project_dir, ai="kimi")
-        skills_dir = project_dir / ".kimi" / "skills"
-        self._create_skill(skills_dir, "speckit.specify", body="untouched")
-
-        (project_dir / ".kimi" / "commands").mkdir(parents=True, exist_ok=True)
-
-        manager = PresetManager(project_dir)
-        self_test_dir = Path(__file__).parent.parent / "presets" / "self-test"
-        manager.install_from_directory(self_test_dir, "0.1.5")
-
-        skill_file = skills_dir / "speckit.specify" / "SKILL.md"
-        assert skill_file.exists()
-        content = skill_file.read_text()
-        assert "preset:self-test" in content
-        assert "name: speckit.specify" in content
-
-        metadata = manager.registry.get("self-test")
-        assert "speckit.specify" in metadata.get("registered_skills", [])
-
-    def test_kimi_skill_updated_even_when_ai_skills_disabled(self, project_dir, temp_dir):
-        """Kimi presets should still propagate command overrides to existing skills."""
-        self._write_init_options(project_dir, ai="kimi", ai_skills=False)
-        skills_dir = project_dir / ".kimi" / "skills"
-        self._create_skill(skills_dir, "speckit-specify", body="untouched")
-
-        (project_dir / ".kimi" / "commands").mkdir(parents=True, exist_ok=True)
-
-        manager = PresetManager(project_dir)
-        self_test_dir = Path(__file__).parent.parent / "presets" / "self-test"
-        manager.install_from_directory(self_test_dir, "0.1.5")
-
-        skill_file = skills_dir / "speckit-specify" / "SKILL.md"
-        assert skill_file.exists()
-        content = skill_file.read_text()
-        assert "preset:self-test" in content
-        assert "name: speckit-specify" in content
-
-        metadata = manager.registry.get("self-test")
-        assert "speckit-specify" in metadata.get("registered_skills", [])
-
-    def test_kimi_preset_skill_override_resolves_script_placeholders(self, project_dir, temp_dir):
-        """Kimi preset skill overrides should resolve placeholders and rewrite project paths."""
-        self._write_init_options(project_dir, ai="kimi", ai_skills=False, script="sh")
-        skills_dir = project_dir / ".kimi" / "skills"
-        self._create_skill(skills_dir, "speckit-specify", body="untouched")
-        (project_dir / ".kimi" / "commands").mkdir(parents=True, exist_ok=True)
-
-        preset_dir = temp_dir / "kimi-placeholder-override"
-        preset_dir.mkdir()
-        (preset_dir / "commands").mkdir()
-        (preset_dir / "commands" / "speckit.specify.md").write_text(
-            "---\n"
-            "description: Kimi placeholder override\n"
-            "scripts:\n"
-            "  sh: scripts/bash/create-new-feature.sh --json \"{ARGS}\"\n"
-            "---\n\n"
-            "Execute `{SCRIPT}` for __AGENT__\n"
-            "Review templates/checklist.md and memory/constitution.md\n"
-        )
-        manifest_data = {
-            "schema_version": "1.0",
-            "preset": {
-                "id": "kimi-placeholder-override",
-                "name": "Kimi Placeholder Override",
-                "version": "1.0.0",
-                "description": "Test",
-            },
-            "requires": {"speckit_version": ">=0.1.0"},
-            "provides": {
-                "templates": [
-                    {
-                        "type": "command",
-                        "name": "speckit.specify",
-                        "file": "commands/speckit.specify.md",
-                    }
-                ]
-            },
-        }
-        with open(preset_dir / "preset.yml", "w") as f:
-            yaml.dump(manifest_data, f)
-
-        manager = PresetManager(project_dir)
-        manager.install_from_directory(preset_dir, "0.1.5")
-
-        content = (skills_dir / "speckit-specify" / "SKILL.md").read_text()
-        assert "{SCRIPT}" not in content
-        assert "__AGENT__" not in content
-        assert ".specify/scripts/bash/create-new-feature.sh --json \"$ARGUMENTS\"" in content
-        assert ".specify/templates/checklist.md" in content
-        assert ".specify/memory/constitution.md" in content
-        assert "for kimi" in content
-
-    def test_preset_skill_registration_handles_non_dict_init_options(self, project_dir, temp_dir):
-        """Non-dict init-options payloads should not crash preset install/remove flows."""
-        init_options = project_dir / ".specify" / "init-options.json"
-        init_options.parent.mkdir(parents=True, exist_ok=True)
-        init_options.write_text("[]")
-
-        skills_dir = project_dir / ".claude" / "skills"
-        self._create_skill(skills_dir, "speckit-specify", body="untouched")
-        (project_dir / ".claude" / "commands").mkdir(parents=True, exist_ok=True)
-
-        manager = PresetManager(project_dir)
-        self_test_dir = Path(__file__).parent.parent / "presets" / "self-test"
-        manager.install_from_directory(self_test_dir, "0.1.5")
-
-        content = (skills_dir / "speckit-specify" / "SKILL.md").read_text()
-        assert "untouched" in content
-
 
 class TestPresetSetPriority:
     """Test preset set-priority CLI command."""

tests/test_timestamp_branches.py

@@ -14,7 +14,6 @@ import pytest
 
 PROJECT_ROOT = Path(__file__).resolve().parent.parent
 CREATE_FEATURE = PROJECT_ROOT / "scripts" / "bash" / "create-new-feature.sh"
-CREATE_FEATURE_PS = PROJECT_ROOT / "scripts" / "powershell" / "create-new-feature.ps1"
 COMMON_SH = PROJECT_ROOT / "scripts" / "bash" / "common.sh"
 
 
@@ -148,24 +147,6 @@ class TestSequentialBranch:
                 branch = line.split(":", 1)[1].strip()
         assert branch == "003-next-feat", f"expected 003-next-feat, got: {branch}"
 
-    def test_sequential_supports_four_digit_prefixes(self, git_repo: Path):
-        """Sequential numbering should continue past 999 without truncation."""
-        (git_repo / "specs" / "999-last-3digit").mkdir(parents=True)
-        (git_repo / "specs" / "1000-first-4digit").mkdir(parents=True)
-        result = run_script(git_repo, "--short-name", "next-feat", "Next feature")
-        assert result.returncode == 0, result.stderr
-        branch = None
-        for line in result.stdout.splitlines():
-            if line.startswith("BRANCH_NAME:"):
-                branch = line.split(":", 1)[1].strip()
-        assert branch == "1001-next-feat", f"expected 1001-next-feat, got: {branch}"
-
-    def test_powershell_scanner_uses_long_tryparse_for_large_prefixes(self):
-        """PowerShell scanner should parse large prefixes without [int] casts."""
-        content = CREATE_FEATURE_PS.read_text(encoding="utf-8")
-        assert "[long]::TryParse($matches[1], [ref]$num)" in content
-        assert "$num = [int]$matches[1]" not in content
-
 
 # ── check_feature_branch Tests ───────────────────────────────────────────────