chore: bump version to 0.4.3

* fix: unify hyphenated skills and migrate legacy kimi dotted dirs

* fix: preserve legacy kimi dotted preset skill overrides

* fix: migrate kimi legacy dotted skills without ai-skills flag

* fix: harden kimi migration and cache hook init options

* fix: apply kimi preset skill overrides without ai-skills flag

* fix: keep sequential branch numbering beyond 999

* test: align kimi scaffold skill path with hyphen naming

* chore: align hook typing and preset skill comment

* fix: restore AGENT_SKILLS_DIR_OVERRIDES compatibility export

* refactor: remove AGENT_SKILLS_DIR_OVERRIDES and update callers

* fix(ps1): support sequential branch numbers above 999

* fix: resolve preset skill placeholders for skills agents

* Fix legacy kimi migration safety and preset skill dir checks

* Harden TOML rendering and consolidate preset skill restore parsing

* Fix PowerShell overflow and hook message fallback for empty invocations

* Restore preset skills from extensions

* Refine preset skill restore helpers

* Harden skill path and preset checks

* Guard non-dict init options

* Avoid deleting unmanaged preset skill dirs

* Unify extension skill naming with hooks

* Harden extension native skill registration

* Normalize preset skill titles

.github/workflows/release-trigger.yml

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

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

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

@@ -140,8 +140,7 @@ EOF
 }
 
 # Create skills in <skills_dir>/<name>/SKILL.md format.
-# Most agents use hyphenated names (e.g. speckit-plan); Kimi is the
+# Skills use hyphenated names (e.g. speckit-plan).
-# current dotted-name exception (e.g. speckit.plan).
 #
 # Technical debt note:
 # Keep SKILL.md frontmatter aligned with `install_ai_skills()` and extension
@@ -321,7 +320,7 @@ 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

@@ -22,7 +22,10 @@
 - [🤔 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)
@@ -155,6 +158,56 @@ 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:
@@ -171,6 +224,16 @@ 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                                                                                                                                     |
@@ -229,7 +292,7 @@ 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`)                                                                                                                                                                                                                                                                                       |
+| `--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.                                                                                                                                                                                               |
 | `--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
@@ -380,7 +443,7 @@ 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, the complete community catalog, and how to build and publish your own.
+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.
 
 ### Presets — Customize Existing Workflows
 

TESTING.md

@@ -0,0 +1,79 @@
+# 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** `extensions/README.md` with your extension
+3. **Update** the Community Extensions table in `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 Extensions README
+### 3. Update Community Extensions Table
 
-Add your extension to the Available Extensions table in `extensions/README.md`:
+Add your extension to the Community Extensions table in the project root `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 extensions/README.md
+git add extensions/catalog.community.json 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 extensions/README.md Available Extensions table
+- [x] Added to Community Extensions table in README.md
 
 ### Testing
 Tested on:

extensions/EXTENSION-USER-GUIDE.md

@@ -187,6 +187,21 @@ 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

@@ -68,36 +68,9 @@ specify extension add --from https://github.com/org/spec-kit-ext/archive/refs/ta
 
 ## Available Community Extensions
 
-The following community-contributed extensions are available in [`catalog.community.json`](catalog.community.json):
+See the [Community Extensions](../README.md#-community-extensions) section in the main README for the full list of available community-contributed extensions.
 
-**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
+For the raw catalog data, see [`catalog.community.json`](catalog.community.json).
-
-**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

@@ -3,6 +3,39 @@
   "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",
@@ -73,6 +106,35 @@
       "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",
@@ -252,6 +314,37 @@
       "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",
@@ -344,6 +437,37 @@
       "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",

extensions/git/README.md

@@ -1,71 +0,0 @@
-# Git Branching Workflow Extension
-
-Feature branch creation, numbering (sequential/timestamp), validation, and Git remote detection for Spec Kit.
-
-## Overview
-
-This extension provides Git branching operations as an optional, self-contained module. It manages:
-
-- **Feature branch creation** with sequential (`001-feature-name`) or timestamp (`20260319-143022-feature-name`) numbering
-- **Branch validation** to ensure branches follow naming conventions
-- **Git remote detection** for GitHub integration (e.g., issue creation)
-
-## Commands
-
-| Command | Description |
-|---------|-------------|
-| `speckit.git.feature` | Create a feature branch with sequential or timestamp numbering |
-| `speckit.git.validate` | Validate current branch follows feature branch naming conventions |
-| `speckit.git.remote` | Detect Git remote URL for GitHub integration |
-
-## Hooks
-
-| Event | Command | Optional | Description |
-|-------|---------|----------|-------------|
-| `before_specify` | `speckit.git.feature` | No | Create feature branch before specification |
-| `after_implement` | `speckit.git.validate` | Yes | Validate branch naming after implementation |
-
-## Configuration
-
-Configuration is stored in `.specify/extensions/git/git-config.yml`:
-
-```yaml
-# Branch numbering strategy: "sequential" or "timestamp"
-branch_numbering: sequential
-```
-
-## Installation
-
-```bash
-# Install from the bundled extension directory
-specify extension add extensions/git --dev
-
-# Or it auto-installs during specify init (migration period)
-```
-
-## Disabling
-
-```bash
-# Disable the git extension (spec creation continues without branching)
-specify extension disable git
-
-# Re-enable it
-specify extension enable git
-```
-
-## Graceful Degradation
-
-When Git is not installed or the directory is not a Git repository:
-- Spec directories are still created under `specs/`
-- Branch creation is skipped with a warning
-- Branch validation is skipped with a warning
-- Remote detection returns empty results
-
-## Scripts
-
-The extension bundles cross-platform scripts:
-
-- `scripts/bash/create-new-feature.sh` — Bash implementation
-- `scripts/bash/git-common.sh` — Shared Git utilities (Bash)
-- `scripts/powershell/create-new-feature.ps1` — PowerShell implementation
-- `scripts/powershell/git-common.ps1` — Shared Git utilities (PowerShell)

extensions/git/commands/speckit.git.feature.md

@@ -1,66 +0,0 @@
----
-description: "Create a feature branch with sequential or timestamp numbering"
----
-
-# Create Feature Branch
-
-Create a new feature branch for the given specification.
-
-## User Input
-
-```text
-$ARGUMENTS
-```
-
-You **MUST** consider the user input before proceeding (if not empty).
-
-## Prerequisites
-
-- Verify Git is available by running `git rev-parse --is-inside-work-tree 2>/dev/null`
-- If Git is not available, warn the user and skip branch creation (spec directory will still be created)
-
-## Branch Numbering Mode
-
-Determine the branch numbering strategy by checking configuration in this order:
-
-1. Check `.specify/extensions/git/git-config.yml` for `branch_numbering` value
-2. Check `.specify/init-options.json` for `branch_numbering` value (backward compatibility)
-3. Default to `sequential` if neither exists
-
-## Execution
-
-Generate a concise short name (2-4 words) for the branch:
-- Analyze the feature description and extract the most meaningful keywords
-- Use action-noun format when possible (e.g., "add-user-auth", "fix-payment-bug")
-- Preserve technical terms and acronyms (OAuth2, API, JWT, etc.)
-
-Run the appropriate script based on your platform:
-
-- **Bash**: `.specify/extensions/git/scripts/bash/create-new-feature.sh --json --short-name "<short-name>" "<feature description>"`
-- **Bash (timestamp)**: `.specify/extensions/git/scripts/bash/create-new-feature.sh --json --timestamp --short-name "<short-name>" "<feature description>"`
-- **PowerShell**: `.specify/extensions/git/scripts/powershell/create-new-feature.ps1 -Json -ShortName "<short-name>" "<feature description>"`
-- **PowerShell (timestamp)**: `.specify/extensions/git/scripts/powershell/create-new-feature.ps1 -Json -Timestamp -ShortName "<short-name>" "<feature description>"`
-
-**IMPORTANT**:
-- Do NOT pass `--number` — the script determines the correct next number automatically
-- Always include the JSON flag (`--json` for Bash, `-Json` for PowerShell) so the output can be parsed reliably
-- You must only ever run this script once per feature
-- The JSON output will contain BRANCH_NAME and SPEC_FILE paths
-
-If the extension scripts are not found at the `.specify/extensions/git/` path, fall back to:
-- **Bash**: `scripts/bash/create-new-feature.sh`
-- **PowerShell**: `scripts/powershell/create-new-feature.ps1`
-
-## Graceful Degradation
-
-If Git is not installed or the current directory is not a Git repository:
-- The script will still create the spec directory under `specs/`
-- A warning will be printed: `[specify] Warning: Git repository not detected; skipped branch creation`
-- The workflow continues normally without branch creation
-
-## Output
-
-The script outputs JSON with:
-- `BRANCH_NAME`: The created branch name (e.g., `003-user-auth` or `20260319-143022-user-auth`)
-- `SPEC_FILE`: Path to the created spec file
-- `FEATURE_NUM`: The numeric or timestamp prefix used

extensions/git/commands/speckit.git.remote.md

@@ -1,45 +0,0 @@
----
-description: "Detect Git remote URL for GitHub integration"
----
-
-# Detect Git Remote URL
-
-Detect the Git remote URL for integration with GitHub services (e.g., issue creation).
-
-## Prerequisites
-
-- Check if Git is available by running `git rev-parse --is-inside-work-tree 2>/dev/null`
-- If Git is not available, output a warning and return empty:
-  ```
-  [specify] Warning: Git repository not detected; cannot determine remote URL
-  ```
-
-## Execution
-
-Run the following command to get the remote URL:
-
-```bash
-git config --get remote.origin.url
-```
-
-## Output
-
-Parse the remote URL and determine:
-
-1. **Repository owner**: Extract from the URL (e.g., `github` from `https://github.com/github/spec-kit.git`)
-2. **Repository name**: Extract from the URL (e.g., `spec-kit` from `https://github.com/github/spec-kit.git`)
-3. **Is GitHub**: Whether the remote points to a GitHub repository
-
-Supported URL formats:
-- HTTPS: `https://github.com/<owner>/<repo>.git`
-- SSH: `git@github.com:<owner>/<repo>.git`
-
-> [!CAUTION]
-> ONLY report a GitHub repository if the remote URL actually points to github.com.
-> Do NOT assume the remote is GitHub if the URL format doesn't match.
-
-## Graceful Degradation
-
-If Git is not installed, the directory is not a Git repository, or no remote is configured:
-- Return an empty result
-- Do NOT error — other workflows should continue without Git remote information

extensions/git/commands/speckit.git.validate.md

@@ -1,49 +0,0 @@
----
-description: "Validate current branch follows feature branch naming conventions"
----
-
-# Validate Feature Branch
-
-Validate that the current Git branch follows the expected feature branch naming conventions.
-
-## Prerequisites
-
-- Check if Git is available by running `git rev-parse --is-inside-work-tree 2>/dev/null`
-- If Git is not available, output a warning and skip validation:
-  ```
-  [specify] Warning: Git repository not detected; skipped branch validation
-  ```
-
-## Validation Rules
-
-Get the current branch name:
-
-```bash
-git rev-parse --abbrev-ref HEAD
-```
-
-The branch name must match one of these patterns:
-
-1. **Sequential**: `^[0-9]{3}-` (e.g., `001-feature-name`, `042-fix-bug`)
-2. **Timestamp**: `^[0-9]{8}-[0-9]{6}-` (e.g., `20260319-143022-feature-name`)
-
-## Execution
-
-If on a feature branch (matches either pattern):
-- Output: `✓ On feature branch: <branch-name>`
-- Check if the corresponding spec directory exists under `specs/`:
-  - For sequential branches, look for `specs/<prefix>-*` where prefix matches the `###` portion
-  - For timestamp branches, look for `specs/<prefix>-*` where prefix matches the `YYYYMMDD-HHMMSS` portion
-- If spec directory exists: `✓ Spec directory found: <path>`
-- If spec directory missing: `⚠ No spec directory found for prefix <prefix>`
-
-If NOT on a feature branch:
-- Output: `✗ Not on a feature branch. Current branch: <branch-name>`
-- Output: `Feature branches should be named like: 001-feature-name or 20260319-143022-feature-name`
-
-## Graceful Degradation
-
-If Git is not installed or the directory is not a Git repository:
-- Check the `SPECIFY_FEATURE` environment variable as a fallback
-- If set, validate that value against the naming patterns
-- If not set, skip validation with a warning

extensions/git/config-template.yml

@@ -1,5 +0,0 @@
-# Git Branching Workflow Extension Configuration
-# Copy this file to .specify/extensions/git/git-config.yml to customize
-
-# Branch numbering strategy: "sequential" (001, 002, ...) or "timestamp" (YYYYMMDD-HHMMSS)
-branch_numbering: sequential

extensions/git/extension.yml

@@ -1,47 +0,0 @@
-schema_version: "1.0"
-
-extension:
-  id: git
-  name: "Git Branching Workflow"
-  version: "1.0.0"
-  description: "Feature branch creation, numbering (sequential/timestamp), validation, and Git remote detection"
-  author: spec-kit-core
-  repository: https://github.com/github/spec-kit
-  license: MIT
-
-requires:
-  speckit_version: ">=0.2.0"
-  tools:
-    - name: git
-      required: false
-
-provides:
-  commands:
-    - name: speckit.git.feature
-      file: commands/speckit.git.feature.md
-      description: "Create a feature branch with sequential or timestamp numbering"
-    - name: speckit.git.validate
-      file: commands/speckit.git.validate.md
-      description: "Validate current branch follows feature branch naming conventions"
-    - name: speckit.git.remote
-      file: commands/speckit.git.remote.md
-      description: "Detect Git remote URL for GitHub integration"
-
-hooks:
-  before_specify:
-    command: speckit.git.feature
-    optional: false
-    description: "Create feature branch before specification"
-  after_implement:
-    command: speckit.git.validate
-    optional: true
-    prompt: "Verify feature branch naming?"
-    description: "Validate branch naming after implementation"
-
-tags:
-  - "git"
-  - "branching"
-  - "workflow"
-
-defaults:
-  branch_numbering: sequential

extensions/git/scripts/bash/create-new-feature.sh

@@ -1,394 +0,0 @@
-#!/usr/bin/env bash
-
-set -e
-
-JSON_MODE=false
-SHORT_NAME=""
-BRANCH_NUMBER=""
-USE_TIMESTAMP=false
-ARGS=()
-i=1
-while [ $i -le $# ]; do
-    arg="${!i}"
-    case "$arg" in
-        --json)
-            JSON_MODE=true
-            ;;
-        --short-name)
-            if [ $((i + 1)) -gt $# ]; then
-                echo 'Error: --short-name requires a value' >&2
-                exit 1
-            fi
-            i=$((i + 1))
-            next_arg="${!i}"
-            # Check if the next argument is another option (starts with --)
-            if [[ "$next_arg" == --* ]]; then
-                echo 'Error: --short-name requires a value' >&2
-                exit 1
-            fi
-            SHORT_NAME="$next_arg"
-            ;;
-        --number)
-            if [ $((i + 1)) -gt $# ]; then
-                echo 'Error: --number requires a value' >&2
-                exit 1
-            fi
-            i=$((i + 1))
-            next_arg="${!i}"
-            if [[ "$next_arg" == --* ]]; then
-                echo 'Error: --number requires a value' >&2
-                exit 1
-            fi
-            BRANCH_NUMBER="$next_arg"
-            ;;
-        --timestamp)
-            USE_TIMESTAMP=true
-            ;;
-        --help|-h)
-            echo "Usage: $0 [--json] [--short-name <name>] [--number N] [--timestamp] <feature_description>"
-            echo ""
-            echo "Options:"
-            echo "  --json              Output in JSON format"
-            echo "  --short-name <name> Provide a custom short name (2-4 words) for the branch"
-            echo "  --number N          Specify branch number manually (overrides auto-detection)"
-            echo "  --timestamp         Use timestamp prefix (YYYYMMDD-HHMMSS) instead of sequential numbering"
-            echo "  --help, -h          Show this help message"
-            echo ""
-            echo "Examples:"
-            echo "  $0 'Add user authentication system' --short-name 'user-auth'"
-            echo "  $0 'Implement OAuth2 integration for API' --number 5"
-            echo "  $0 --timestamp --short-name 'user-auth' 'Add user authentication'"
-            exit 0
-            ;;
-        *)
-            ARGS+=("$arg")
-            ;;
-    esac
-    i=$((i + 1))
-done
-
-FEATURE_DESCRIPTION="${ARGS[*]}"
-if [ -z "$FEATURE_DESCRIPTION" ]; then
-    echo "Usage: $0 [--json] [--short-name <name>] [--number N] [--timestamp] <feature_description>" >&2
-    exit 1
-fi
-
-# Trim whitespace and validate description is not empty (e.g., user passed only whitespace)
-FEATURE_DESCRIPTION=$(echo "$FEATURE_DESCRIPTION" | xargs)
-if [ -z "$FEATURE_DESCRIPTION" ]; then
-    echo "Error: Feature description cannot be empty or contain only whitespace" >&2
-    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="$1"
-    local highest=0
-    
-    if [ -d "$specs_dir" ]; then
-        for dir in "$specs_dir"/*; do
-            [ -d "$dir" ] || continue
-            dirname=$(basename "$dir")
-            # 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
-                fi
-            fi
-        done
-    fi
-    
-    echo "$highest"
-}
-
-# Function to get highest number from git branches
-get_highest_from_branches() {
-    local highest=0
-    
-    # Get all branches (local and remote)
-    branches=$(git branch -a 2>/dev/null || echo "")
-    
-    if [ -n "$branches" ]; then
-        while IFS= read -r branch; do
-            # Clean branch name: remove leading markers and remote prefixes
-            clean_branch=$(echo "$branch" | sed 's/^[* ]*//; s|^remotes/[^/]*/||')
-            
-            # Extract feature number if branch matches pattern ###-*
-            if echo "$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=$number
-                fi
-            fi
-        done <<< "$branches"
-    fi
-    
-    echo "$highest"
-}
-
-# Function to check existing branches (local and remote) and return next available number
-check_existing_branches() {
-    local specs_dir="$1"
-
-    # Fetch all remotes to get latest branch info (suppress errors if no remotes)
-    git fetch --all --prune >/dev/null 2>&1 || true
-
-    # Get highest number from ALL branches (not just matching short name)
-    local highest_branch=$(get_highest_from_branches)
-
-    # Get highest number from ALL specs (not just matching short name)
-    local highest_spec=$(get_highest_from_specs "$specs_dir")
-
-    # Take the maximum of both
-    local max_num=$highest_branch
-    if [ "$highest_spec" -gt "$max_num" ]; then
-        max_num=$highest_spec
-    fi
-
-    # Return next number
-    echo $((max_num + 1))
-}
-
-# Function to clean and format a branch name
-clean_branch_name() {
-    local name="$1"
-    echo "$name" | tr '[:upper:]' '[:lower:]' | sed 's/[^a-z0-9]/-/g' | sed 's/-\+/-/g' | sed 's/^-//' | sed 's/-$//'
-}
-
-# Resolve repository root. Prefer git information when available, but fall back
-# to searching for repository markers so the workflow still functions in repositories that
-# were initialised with --no-git.
-SCRIPT_DIR="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
-
-# Source common.sh using the following priority:
-#  1. common.sh next to this script (source checkout layout)
-#  2. .specify/scripts/bash/common.sh under the project root (installed project)
-#  3. scripts/bash/common.sh under the project root (source checkout fallback)
-#  4. git-common.sh next to this script (minimal fallback)
-_common_loaded=false
-
-if [ -f "$SCRIPT_DIR/common.sh" ]; then
-    source "$SCRIPT_DIR/common.sh"
-    _common_loaded=true
-else
-    # When running from an extension install (.specify/extensions/git/scripts/bash/),
-    # resolve to .specify/ (4 levels up), then to the project root (5 levels up).
-    _dot_specify="$(cd "$SCRIPT_DIR/../../../.." 2>/dev/null && pwd)"
-    _project_root="$(cd "$SCRIPT_DIR/../../../../.." 2>/dev/null && pwd)"
-
-    if [ -n "$_dot_specify" ] && [ -f "$_dot_specify/scripts/bash/common.sh" ]; then
-        source "$_dot_specify/scripts/bash/common.sh"
-        _common_loaded=true
-    elif [ -n "$_project_root" ] && [ -f "$_project_root/scripts/bash/common.sh" ]; then
-        source "$_project_root/scripts/bash/common.sh"
-        _common_loaded=true
-    elif [ -f "$SCRIPT_DIR/git-common.sh" ]; then
-        source "$SCRIPT_DIR/git-common.sh"
-        _common_loaded=true
-    fi
-fi
-
-if [ "$_common_loaded" != "true" ]; then
-    echo "Error: Could not locate common.sh or git-common.sh. Please ensure the Specify core scripts are installed." >&2
-    exit 1
-fi
-
-# If only git-common.sh was loaded, verify that the required helpers
-# (resolve_template, json_escape) are available.  These are provided by the
-# core common.sh; git-common.sh only supplies has_git / check_feature_branch.
-if ! type resolve_template >/dev/null 2>&1 || ! type json_escape >/dev/null 2>&1; then
-    echo "Error: resolve_template/json_escape not defined.  The core common.sh is required but could not be located." >&2
-    echo "Tried: $SCRIPT_DIR/common.sh, .specify/scripts/bash/common.sh, scripts/bash/common.sh" >&2
-    exit 1
-fi
-
-if git rev-parse --show-toplevel >/dev/null 2>&1; then
-    REPO_ROOT=$(git rev-parse --show-toplevel)
-    HAS_GIT=true
-else
-    REPO_ROOT="$(find_repo_root "$SCRIPT_DIR")"
-    if [ -z "$REPO_ROOT" ]; then
-        echo "Error: Could not determine repository root. Please run this script from within the repository." >&2
-        exit 1
-    fi
-    HAS_GIT=false
-fi
-
-cd "$REPO_ROOT"
-
-SPECS_DIR="$REPO_ROOT/specs"
-mkdir -p "$SPECS_DIR"
-
-# Function to generate branch name with stop word filtering and length filtering
-generate_branch_name() {
-    local description="$1"
-    
-    # Common stop words to filter out
-    local stop_words="^(i|a|an|the|to|for|of|in|on|at|by|with|from|is|are|was|were|be|been|being|have|has|had|do|does|did|will|would|should|could|can|may|might|must|shall|this|that|these|those|my|your|our|their|want|need|add|get|set)$"
-    
-    # Convert to lowercase and split into words
-    local clean_name=$(echo "$description" | tr '[:upper:]' '[:lower:]' | sed 's/[^a-z0-9]/ /g')
-    
-    # Filter words: remove stop words and words shorter than 3 chars (unless they're uppercase acronyms in original)
-    local meaningful_words=()
-    for word in $clean_name; do
-        # Skip empty words
-        [ -z "$word" ] && continue
-        
-        # Keep words that are NOT stop words AND (length >= 3 OR are potential acronyms)
-        if ! echo "$word" | grep -qiE "$stop_words"; then
-            if [ ${#word} -ge 3 ]; then
-                meaningful_words+=("$word")
-            elif echo "$description" | grep -q "\b${word^^}\b"; then
-                # Keep short words if they appear as uppercase in original (likely acronyms)
-                meaningful_words+=("$word")
-            fi
-        fi
-    done
-    
-    # If we have meaningful words, use first 3-4 of them
-    if [ ${#meaningful_words[@]} -gt 0 ]; then
-        local max_words=3
-        if [ ${#meaningful_words[@]} -eq 4 ]; then max_words=4; fi
-        
-        local result=""
-        local count=0
-        for word in "${meaningful_words[@]}"; do
-            if [ $count -ge $max_words ]; then break; fi
-            if [ -n "$result" ]; then result="$result-"; fi
-            result="$result$word"
-            count=$((count + 1))
-        done
-        echo "$result"
-    else
-        # Fallback to original logic if no meaningful words found
-        local cleaned=$(clean_branch_name "$description")
-        echo "$cleaned" | tr '-' '\n' | grep -v '^$' | head -3 | tr '\n' '-' | sed 's/-$//'
-    fi
-}
-
-# Generate branch name
-if [ -n "$SHORT_NAME" ]; then
-    # Use provided short name, just clean it up
-    BRANCH_SUFFIX=$(clean_branch_name "$SHORT_NAME")
-else
-    # Generate from description with smart filtering
-    BRANCH_SUFFIX=$(generate_branch_name "$FEATURE_DESCRIPTION")
-fi
-
-# Warn if --number and --timestamp are both specified
-if [ "$USE_TIMESTAMP" = true ] && [ -n "$BRANCH_NUMBER" ]; then
-    >&2 echo "[specify] Warning: --number is ignored when --timestamp is used"
-    BRANCH_NUMBER=""
-fi
-
-# Determine branch prefix
-if [ "$USE_TIMESTAMP" = true ]; then
-    FEATURE_NUM=$(date +%Y%m%d-%H%M%S)
-    BRANCH_NAME="${FEATURE_NUM}-${BRANCH_SUFFIX}"
-else
-    # Determine branch number
-    if [ -z "$BRANCH_NUMBER" ]; then
-        if [ "$HAS_GIT" = true ]; then
-            # Check existing branches on remotes
-            BRANCH_NUMBER=$(check_existing_branches "$SPECS_DIR")
-        else
-            # Fall back to local directory check
-            HIGHEST=$(get_highest_from_specs "$SPECS_DIR")
-            BRANCH_NUMBER=$((HIGHEST + 1))
-        fi
-    fi
-
-    # Force base-10 interpretation to prevent octal conversion (e.g., 010 → 8 in octal, but should be 10 in decimal)
-    FEATURE_NUM=$(printf "%03d" "$((10#$BRANCH_NUMBER))")
-    BRANCH_NAME="${FEATURE_NUM}-${BRANCH_SUFFIX}"
-fi
-
-# GitHub enforces a 244-byte limit on branch names
-# Validate and truncate if necessary
-MAX_BRANCH_LENGTH=244
-if [ ${#BRANCH_NAME} -gt $MAX_BRANCH_LENGTH ]; then
-    # Calculate how much we need to trim from suffix
-    # Account for prefix length: timestamp (15) + hyphen (1) = 16, or sequential (3) + hyphen (1) = 4
-    PREFIX_LENGTH=$(( ${#FEATURE_NUM} + 1 ))
-    MAX_SUFFIX_LENGTH=$((MAX_BRANCH_LENGTH - PREFIX_LENGTH))
-    
-    # Truncate suffix at word boundary if possible
-    TRUNCATED_SUFFIX=$(echo "$BRANCH_SUFFIX" | cut -c1-$MAX_SUFFIX_LENGTH)
-    # Remove trailing hyphen if truncation created one
-    TRUNCATED_SUFFIX=$(echo "$TRUNCATED_SUFFIX" | sed 's/-$//')
-    
-    ORIGINAL_BRANCH_NAME="$BRANCH_NAME"
-    BRANCH_NAME="${FEATURE_NUM}-${TRUNCATED_SUFFIX}"
-    
-    >&2 echo "[specify] Warning: Branch name exceeded GitHub's 244-byte limit"
-    >&2 echo "[specify] Original: $ORIGINAL_BRANCH_NAME (${#ORIGINAL_BRANCH_NAME} bytes)"
-    >&2 echo "[specify] Truncated to: $BRANCH_NAME (${#BRANCH_NAME} bytes)"
-fi
-
-if [ "$HAS_GIT" = true ]; then
-    if ! git checkout -q -b "$BRANCH_NAME" >/dev/null 2>&1; then
-        # Check if branch already exists
-        if git branch --list "$BRANCH_NAME" | grep -q .; then
-            if [ "$USE_TIMESTAMP" = true ]; then
-                >&2 echo "Error: Branch '$BRANCH_NAME' already exists. Rerun to get a new timestamp or use a different --short-name."
-            else
-                >&2 echo "Error: Branch '$BRANCH_NAME' already exists. Please use a different feature name or specify a different number with --number."
-            fi
-            exit 1
-        else
-            >&2 echo "Error: Failed to create git branch '$BRANCH_NAME'. Please check your git configuration and try again."
-            exit 1
-        fi
-    fi
-else
-    >&2 echo "[specify] Warning: Git repository not detected; skipped branch creation for $BRANCH_NAME"
-fi
-
-FEATURE_DIR="$SPECS_DIR/$BRANCH_NAME"
-mkdir -p "$FEATURE_DIR"
-
-TEMPLATE=$(resolve_template "spec-template" "$REPO_ROOT") || true
-SPEC_FILE="$FEATURE_DIR/spec.md"
-if [ -n "$TEMPLATE" ] && [ -f "$TEMPLATE" ]; then
-    cp "$TEMPLATE" "$SPEC_FILE"
-else
-    echo "Warning: Spec template not found; created empty spec file" >&2
-    touch "$SPEC_FILE"
-fi
-
-# Inform the user how to persist the feature variable in their own shell
-printf '# To persist: export SPECIFY_FEATURE=%q\n' "$BRANCH_NAME" >&2
-
-if $JSON_MODE; then
-    if command -v jq >/dev/null 2>&1; then
-        jq -cn \
-            --arg branch_name "$BRANCH_NAME" \
-            --arg spec_file "$SPEC_FILE" \
-            --arg feature_num "$FEATURE_NUM" \
-            '{BRANCH_NAME:$branch_name,SPEC_FILE:$spec_file,FEATURE_NUM:$feature_num}'
-    else
-        printf '{"BRANCH_NAME":"%s","SPEC_FILE":"%s","FEATURE_NUM":"%s"}\n' "$(json_escape "$BRANCH_NAME")" "$(json_escape "$SPEC_FILE")" "$(json_escape "$FEATURE_NUM")"
-    fi
-else
-    echo "BRANCH_NAME: $BRANCH_NAME"
-    echo "SPEC_FILE: $SPEC_FILE"
-    echo "FEATURE_NUM: $FEATURE_NUM"
-    printf '# To persist in your shell: export SPECIFY_FEATURE=%q\n' "$BRANCH_NAME"
-fi

extensions/git/scripts/bash/git-common.sh

@@ -1,30 +0,0 @@
-#!/usr/bin/env bash
-# Git-specific common functions for the git extension.
-# Extracted from scripts/bash/common.sh — contains only git-specific
-# branch validation and detection logic.
-
-# Check if we have git available
-has_git() {
-    git rev-parse --show-toplevel >/dev/null 2>&1
-}
-
-# Validate that a branch name matches the expected feature branch pattern.
-# Accepts sequential (###-*) or timestamp (YYYYMMDD-HHMMSS-*) formats.
-check_feature_branch() {
-    local branch="$1"
-    local has_git_repo="$2"
-
-    # For non-git repos, we can't enforce branch naming but still provide output
-    if [[ "$has_git_repo" != "true" ]]; then
-        echo "[specify] Warning: Git repository not detected; skipped branch validation" >&2
-        return 0
-    fi
-
-    if [[ ! "$branch" =~ ^[0-9]{3}- ]] && [[ ! "$branch" =~ ^[0-9]{8}-[0-9]{6}- ]]; then
-        echo "ERROR: Not on a feature branch. Current branch: $branch" >&2
-        echo "Feature branches should be named like: 001-feature-name or 20260319-143022-feature-name" >&2
-        return 1
-    fi
-
-    return 0
-}

extensions/git/scripts/powershell/create-new-feature.ps1

@@ -1,368 +0,0 @@
-#!/usr/bin/env pwsh
-# Create a new feature
-[CmdletBinding()]
-param(
-    [switch]$Json,
-    [string]$ShortName,
-    [Parameter()]
-    [int]$Number = 0,
-    [switch]$Timestamp,
-    [switch]$Help,
-    [Parameter(Position = 0, ValueFromRemainingArguments = $true)]
-    [string[]]$FeatureDescription
-)
-$ErrorActionPreference = 'Stop'
-
-# Show help if requested
-if ($Help) {
-    Write-Host "Usage: ./create-new-feature.ps1 [-Json] [-ShortName <name>] [-Number N] [-Timestamp] <feature description>"
-    Write-Host ""
-    Write-Host "Options:"
-    Write-Host "  -Json               Output in JSON format"
-    Write-Host "  -ShortName <name>   Provide a custom short name (2-4 words) for the branch"
-    Write-Host "  -Number N           Specify branch number manually (overrides auto-detection)"
-    Write-Host "  -Timestamp          Use timestamp prefix (YYYYMMDD-HHMMSS) instead of sequential numbering"
-    Write-Host "  -Help               Show this help message"
-    Write-Host ""
-    Write-Host "Examples:"
-    Write-Host "  ./create-new-feature.ps1 'Add user authentication system' -ShortName 'user-auth'"
-    Write-Host "  ./create-new-feature.ps1 'Implement OAuth2 integration for API'"
-    Write-Host "  ./create-new-feature.ps1 -Timestamp -ShortName 'user-auth' 'Add user authentication'"
-    exit 0
-}
-
-# Check if feature description provided
-if (-not $FeatureDescription -or $FeatureDescription.Count -eq 0) {
-    Write-Error "Usage: ./create-new-feature.ps1 [-Json] [-ShortName <name>] [-Number N] [-Timestamp] <feature description>"
-    exit 1
-}
-
-$featureDesc = ($FeatureDescription -join ' ').Trim()
-
-# Validate description is not empty after trimming (e.g., user passed only whitespace)
-if ([string]::IsNullOrWhiteSpace($featureDesc)) {
-    Write-Error "Error: Feature description cannot be empty or contain only whitespace"
-    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)
-    
-    $highest = 0
-    if (Test-Path $SpecsDir) {
-        Get-ChildItem -Path $SpecsDir -Directory | ForEach-Object {
-            if ($_.Name -match '^(\d{3})-') {
-                $num = [int]$matches[1]
-                if ($num -gt $highest) { $highest = $num }
-            }
-        }
-    }
-    return $highest
-}
-
-function Get-HighestNumberFromBranches {
-    param()
-    
-    $highest = 0
-    try {
-        $branches = git branch -a 2>$null
-        if ($LASTEXITCODE -eq 0) {
-            foreach ($branch in $branches) {
-                # Clean branch name: remove leading markers and remote prefixes
-                $cleanBranch = $branch.Trim() -replace '^\*?\s+', '' -replace '^remotes/[^/]+/', ''
-                
-                # Extract feature number if branch matches pattern ###-*
-                if ($cleanBranch -match '^(\d{3})-') {
-                    $num = [int]$matches[1]
-                    if ($num -gt $highest) { $highest = $num }
-                }
-            }
-        }
-    } catch {
-        # If git command fails, return 0
-        Write-Verbose "Could not check Git branches: $_"
-    }
-    return $highest
-}
-
-function Get-NextBranchNumber {
-    param(
-        [string]$SpecsDir
-    )
-
-    # Fetch all remotes to get latest branch info (suppress errors if no remotes)
-    try {
-        git fetch --all --prune 2>$null | Out-Null
-    } catch {
-        # Ignore fetch errors
-    }
-
-    # Get highest number from ALL branches (not just matching short name)
-    $highestBranch = Get-HighestNumberFromBranches
-
-    # Get highest number from ALL specs (not just matching short name)
-    $highestSpec = Get-HighestNumberFromSpecs -SpecsDir $SpecsDir
-
-    # Take the maximum of both
-    $maxNum = [Math]::Max($highestBranch, $highestSpec)
-
-    # Return next number
-    return $maxNum + 1
-}
-
-function ConvertTo-CleanBranchName {
-    param([string]$Name)
-    
-    return $Name.ToLower() -replace '[^a-z0-9]', '-' -replace '-{2,}', '-' -replace '^-', '' -replace '-$', ''
-}
-$fallbackRoot = (Find-RepositoryRoot -StartDir $PSScriptRoot)
-if (-not $fallbackRoot) {
-    Write-Error "Error: Could not determine repository root. Please run this script from within the repository."
-    exit 1
-}
-
-# Load common functions (includes Resolve-Template).
-# Search locations in priority order:
-#  1. common.ps1 next to this script (source checkout layout)
-#  2. .specify/scripts/powershell/common.ps1 under the project root (installed project)
-#  3. scripts/powershell/common.ps1 under the project root (source checkout fallback)
-#  4. git-common.ps1 next to this script (minimal fallback)
-$commonLoaded = $false
-
-if (Test-Path "$PSScriptRoot/common.ps1") {
-    . "$PSScriptRoot/common.ps1"
-    $commonLoaded = $true
-} else {
-    $coreCommonCandidates = @()
-
-    if ($fallbackRoot) {
-        $coreCommonCandidates += (Join-Path $fallbackRoot ".specify/scripts/powershell/common.ps1")
-        $coreCommonCandidates += (Join-Path $fallbackRoot "scripts/powershell/common.ps1")
-    }
-
-    $coreCommonCandidates += "$PSScriptRoot/git-common.ps1"
-
-    foreach ($candidate in $coreCommonCandidates) {
-        if ($candidate -and (Test-Path $candidate)) {
-            . $candidate
-            $commonLoaded = $true
-            break
-        }
-    }
-}
-
-if (-not $commonLoaded) {
-    throw "Unable to locate common script file. Please ensure the Specify core scripts are installed."
-}
-
-# If only git-common.ps1 was loaded, verify that Resolve-Template is available.
-# Resolve-Template is provided by the core common.ps1; git-common.ps1 only
-# supplies Test-HasGit / Test-FeatureBranch.
-if (-not (Get-Command Resolve-Template -ErrorAction SilentlyContinue)) {
-    throw ("Resolve-Template not defined. The core common.ps1 is required but could not be located. " +
-           "Tried: $PSScriptRoot/common.ps1, .specify/scripts/powershell/common.ps1, scripts/powershell/common.ps1")
-}
-
-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 $repoRoot
-
-$specsDir = Join-Path $repoRoot 'specs'
-New-Item -ItemType Directory -Path $specsDir -Force | Out-Null
-
-# Function to generate branch name with stop word filtering and length filtering
-function Get-BranchName {
-    param([string]$Description)
-    
-    # Common stop words to filter out
-    $stopWords = @(
-        'i', 'a', 'an', 'the', 'to', 'for', 'of', 'in', 'on', 'at', 'by', 'with', 'from',
-        'is', 'are', 'was', 'were', 'be', 'been', 'being', 'have', 'has', 'had',
-        'do', 'does', 'did', 'will', 'would', 'should', 'could', 'can', 'may', 'might', 'must', 'shall',
-        'this', 'that', 'these', 'those', 'my', 'your', 'our', 'their',
-        'want', 'need', 'add', 'get', 'set'
-    )
-    
-    # Convert to lowercase and extract words (alphanumeric only)
-    $cleanName = $Description.ToLower() -replace '[^a-z0-9\s]', ' '
-    $words = $cleanName -split '\s+' | Where-Object { $_ }
-    
-    # Filter words: remove stop words and words shorter than 3 chars (unless they're uppercase acronyms in original)
-    $meaningfulWords = @()
-    foreach ($word in $words) {
-        # Skip stop words
-        if ($stopWords -contains $word) { continue }
-        
-        # Keep words that are length >= 3 OR appear as uppercase in original (likely acronyms)
-        if ($word.Length -ge 3) {
-            $meaningfulWords += $word
-        } elseif ($Description -match "\b$($word.ToUpper())\b") {
-            # Keep short words if they appear as uppercase in original (likely acronyms)
-            $meaningfulWords += $word
-        }
-    }
-    
-    # If we have meaningful words, use first 3-4 of them
-    if ($meaningfulWords.Count -gt 0) {
-        $maxWords = if ($meaningfulWords.Count -eq 4) { 4 } else { 3 }
-        $result = ($meaningfulWords | Select-Object -First $maxWords) -join '-'
-        return $result
-    } else {
-        # Fallback to original logic if no meaningful words found
-        $result = ConvertTo-CleanBranchName -Name $Description
-        $fallbackWords = ($result -split '-') | Where-Object { $_ } | Select-Object -First 3
-        return [string]::Join('-', $fallbackWords)
-    }
-}
-
-# Generate branch name
-if ($ShortName) {
-    # Use provided short name, just clean it up
-    $branchSuffix = ConvertTo-CleanBranchName -Name $ShortName
-} else {
-    # Generate from description with smart filtering
-    $branchSuffix = Get-BranchName -Description $featureDesc
-}
-
-# Warn if -Number and -Timestamp are both specified
-if ($Timestamp -and $Number -ne 0) {
-    Write-Warning "[specify] Warning: -Number is ignored when -Timestamp is used"
-    $Number = 0
-}
-
-# Determine branch prefix
-if ($Timestamp) {
-    $featureNum = Get-Date -Format 'yyyyMMdd-HHmmss'
-    $branchName = "$featureNum-$branchSuffix"
-} else {
-    # Determine branch number
-    if ($Number -eq 0) {
-        if ($hasGit) {
-            # Check existing branches on remotes
-            $Number = Get-NextBranchNumber -SpecsDir $specsDir
-        } else {
-            # Fall back to local directory check
-            $Number = (Get-HighestNumberFromSpecs -SpecsDir $specsDir) + 1
-        }
-    }
-
-    $featureNum = ('{0:000}' -f $Number)
-    $branchName = "$featureNum-$branchSuffix"
-}
-
-# GitHub enforces a 244-byte limit on branch names
-# Validate and truncate if necessary
-$maxBranchLength = 244
-if ($branchName.Length -gt $maxBranchLength) {
-    # Calculate how much we need to trim from suffix
-    # Account for prefix length: timestamp (15) + hyphen (1) = 16, or sequential (3) + hyphen (1) = 4
-    $prefixLength = $featureNum.Length + 1
-    $maxSuffixLength = $maxBranchLength - $prefixLength
-    
-    # Truncate suffix
-    $truncatedSuffix = $branchSuffix.Substring(0, [Math]::Min($branchSuffix.Length, $maxSuffixLength))
-    # Remove trailing hyphen if truncation created one
-    $truncatedSuffix = $truncatedSuffix -replace '-$', ''
-    
-    $originalBranchName = $branchName
-    $branchName = "$featureNum-$truncatedSuffix"
-    
-    Write-Warning "[specify] Branch name exceeded GitHub's 244-byte limit"
-    Write-Warning "[specify] Original: $originalBranchName ($($originalBranchName.Length) bytes)"
-    Write-Warning "[specify] Truncated to: $branchName ($($branchName.Length) bytes)"
-}
-
-if ($hasGit) {
-    $branchCreated = $false
-    try {
-        git checkout -q -b $branchName 2>$null | Out-Null
-        if ($LASTEXITCODE -eq 0) {
-            $branchCreated = $true
-        }
-    } catch {
-        # Exception during git command
-    }
-
-    if (-not $branchCreated) {
-        # Check if branch already exists
-        $existingBranch = git branch --list $branchName 2>$null
-        if ($existingBranch) {
-            if ($Timestamp) {
-                Write-Error "Error: Branch '$branchName' already exists. Rerun to get a new timestamp or use a different -ShortName."
-            } else {
-                Write-Error "Error: Branch '$branchName' already exists. Please use a different feature name or specify a different number with -Number."
-            }
-            exit 1
-        } else {
-            Write-Error "Error: Failed to create git branch '$branchName'. Please check your git configuration and try again."
-            exit 1
-        }
-    }
-} else {
-    Write-Warning "[specify] Warning: Git repository not detected; skipped branch creation for $branchName"
-}
-
-$featureDir = Join-Path $specsDir $branchName
-New-Item -ItemType Directory -Path $featureDir -Force | Out-Null
-
-$template = Resolve-Template -TemplateName 'spec-template' -RepoRoot $repoRoot
-$specFile = Join-Path $featureDir 'spec.md'
-if ($template -and (Test-Path $template)) { 
-    Copy-Item $template $specFile -Force 
-} else { 
-    New-Item -ItemType File -Path $specFile | Out-Null 
-}
-
-# Set the SPECIFY_FEATURE environment variable for the current session
-$env:SPECIFY_FEATURE = $branchName
-
-if ($Json) {
-    $obj = [PSCustomObject]@{ 
-        BRANCH_NAME = $branchName
-        SPEC_FILE = $specFile
-        FEATURE_NUM = $featureNum
-        HAS_GIT = $hasGit
-    }
-    $obj | ConvertTo-Json -Compress
-} else {
-    Write-Output "BRANCH_NAME: $branchName"
-    Write-Output "SPEC_FILE: $specFile"
-    Write-Output "FEATURE_NUM: $featureNum"
-    Write-Output "HAS_GIT: $hasGit"
-    Write-Output "SPECIFY_FEATURE environment variable set to: $branchName"
-}
-

extensions/git/scripts/powershell/git-common.ps1

@@ -1,33 +0,0 @@
-#!/usr/bin/env pwsh
-# Git-specific common functions for the git extension.
-# Extracted from scripts/powershell/common.ps1 — contains only git-specific
-# branch validation and detection logic.
-
-function Test-HasGit {
-    try {
-        git rev-parse --show-toplevel 2>$null | Out-Null
-        return ($LASTEXITCODE -eq 0)
-    } catch {
-        return $false
-    }
-}
-
-function Test-FeatureBranch {
-    param(
-        [string]$Branch,
-        [bool]$HasGit = $true
-    )
-    
-    # For non-git repos, we can't enforce branch naming but still provide output
-    if (-not $HasGit) {
-        Write-Warning "[specify] Warning: Git repository not detected; skipped branch validation"
-        return $true
-    }
-    
-    if ($Branch -notmatch '^[0-9]{3}-' -and $Branch -notmatch '^\d{8}-\d{6}-') {
-        Write-Output "ERROR: Not on a feature branch. Current branch: $Branch"
-        Write-Output "Feature branches should be named like: 001-feature-name or 20260319-143022-feature-name"
-        return $false
-    }
-    return $true
-}

presets/catalog.community.json

@@ -1,6 +1,58 @@
 {
   "schema_version": "1.0",
-  "updated_at": "2026-03-09T00:00:00Z",
+  "updated_at": "2026-03-24T00:00:00Z",
   "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/presets/catalog.community.json",
-  "presets": {}
+  "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"
+      ]
+    }
+  }
 }

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "specify-cli"
-version = "0.4.0"
+version = "0.4.3"
 description = "Specify CLI, part of GitHub Spec Kit. A tool to bootstrap your projects for Spec-Driven Development (SDD)."
 requires-python = ">=3.11"
 dependencies = [
@@ -41,7 +41,6 @@ packages = ["src/specify_cli"]
 "templates/commands" = "specify_cli/core_pack/commands"
 "scripts/bash" = "specify_cli/core_pack/scripts/bash"
 "scripts/powershell" = "specify_cli/core_pack/scripts/powershell"
-"extensions/git" = "specify_cli/core_pack/extensions/git"
 ".github/workflows/scripts/create-release-packages.sh" = "specify_cli/core_pack/release_scripts/create-release-packages.sh"
 ".github/workflows/scripts/create-release-packages.ps1" = "specify_cli/core_pack/release_scripts/create-release-packages.ps1"
 

scripts/bash/common.sh

@@ -1,15 +1,48 @@
 #!/usr/bin/env bash
 # Common functions and variables for all scripts
 
-# Get repository root, with fallback for non-git repositories
+# 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_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
-    else
+        return
-        # Fall back to script location for non-git repos
+    fi
+
+    # Final fallback to script location for non-git repos
     local script_dir="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
     (cd "$script_dir/../../.." && pwd)
-    fi
 }
 
 # Get current branch, with fallback for non-git repositories
@@ -20,14 +53,14 @@ get_current_branch() {
         return
     fi
 
-    # Then check git if available
+    # Then check git if available at the spec-kit root (not parent)
-    if git rev-parse --abbrev-ref HEAD >/dev/null 2>&1; then
+    local repo_root=$(get_repo_root)
-        git rev-parse --abbrev-ref HEAD
+    if has_git; then
+        git -C "$repo_root" 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
@@ -68,9 +101,17 @@ get_current_branch() {
     echo "main"  # Final fallback
 }
 
-# Check if we have git available
+# 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)
 has_git() {
-    git rev-parse --show-toplevel >/dev/null 2>&1
+    # 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
 }
 
 check_feature_branch() {

scripts/bash/create-new-feature.sh

@@ -80,19 +80,6 @@ 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="$1"
@@ -102,9 +89,9 @@ get_highest_from_specs() {
         for dir in "$specs_dir"/*; do
             [ -d "$dir" ] || continue
             dirname=$(basename "$dir")
-            # Only match sequential prefixes (###-*), skip timestamp dirs
+            # Match sequential prefixes (>=3 digits), but skip timestamp dirs.
-            if echo "$dirname" | grep -q '^[0-9]\{3\}-'; then
+            if echo "$dirname" | grep -Eq '^[0-9]{3,}-' && ! echo "$dirname" | grep -Eq '^[0-9]{8}-[0-9]{6}-'; then
-                number=$(echo "$dirname" | grep -o '^[0-9]\{3\}')
+                number=$(echo "$dirname" | grep -Eo '^[0-9]+')
                 number=$((10#$number))
                 if [ "$number" -gt "$highest" ]; then
                     highest=$number
@@ -128,9 +115,9 @@ get_highest_from_branches() {
             # Clean branch name: remove leading markers and remote prefixes
             clean_branch=$(echo "$branch" | sed 's/^[* ]*//; s|^remotes/[^/]*/||')
             
-            # Extract feature number if branch matches pattern ###-*
+            # Extract sequential feature number (>=3 digits), skip timestamp branches.
-            if echo "$clean_branch" | grep -q '^[0-9]\{3\}-'; then
+            if echo "$clean_branch" | grep -Eq '^[0-9]{3,}-' && ! echo "$clean_branch" | grep -Eq '^[0-9]{8}-[0-9]{6}-'; then
-                number=$(echo "$clean_branch" | grep -o '^[0-9]\{3\}' || echo "0")
+                number=$(echo "$clean_branch" | grep -Eo '^[0-9]+' || echo "0")
                 number=$((10#$number))
                 if [ "$number" -gt "$highest" ]; then
                     highest=$number
@@ -171,21 +158,16 @@ clean_branch_name() {
     echo "$name" | tr '[:upper:]' '[:lower:]' | sed 's/[^a-z0-9]/-/g' | sed 's/-\+/-/g' | sed 's/^-//' | sed 's/-$//'
 }
 
-# Resolve repository root. Prefer git information when available, but fall back
+# Resolve repository root using common.sh functions which prioritize .specify over git
-# 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"
 
-if git rev-parse --show-toplevel >/dev/null 2>&1; then
+REPO_ROOT=$(get_repo_root)
-    REPO_ROOT=$(git rev-parse --show-toplevel)
+
+# Check if git is available at this repo root (not a parent)
+if has_git; then
     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

@@ -1,7 +1,39 @@
 #!/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) {
@@ -11,8 +43,9 @@ function Get-RepoRoot {
         # Git command failed
     }
 
-    # Fall back to script location for non-git repos
+    # Final fallback to script location for non-git repos
-    return (Resolve-Path (Join-Path $PSScriptRoot "../../..")).Path
+    # Use -LiteralPath to handle paths with wildcard characters
+    return (Resolve-Path -LiteralPath (Join-Path $PSScriptRoot "../../..")).Path
 }
 
 function Get-CurrentBranch {
@@ -21,18 +54,20 @@ function Get-CurrentBranch {
         return $env:SPECIFY_FEATURE
     }
 
-    # Then check git if available
+    # Then check git if available at the spec-kit root (not parent)
+    $repoRoot = Get-RepoRoot
+    if (Test-HasGit) {
         try {
-        $result = git rev-parse --abbrev-ref HEAD 2>$null
+            $result = git -C $repoRoot rev-parse --abbrev-ref HEAD 2>$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) {
@@ -69,9 +104,23 @@ 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 $false
+    }
+    # Verify it's actually a valid git work tree
     try {
-        git rev-parse --show-toplevel 2>$null | Out-Null
+        $null = git -C $repoRoot rev-parse --is-inside-work-tree 2>$null
         return ($LASTEXITCODE -eq 0)
     } catch {
         return $false

scripts/powershell/create-new-feature.ps1

@@ -5,7 +5,7 @@ param(
     [switch]$Json,
     [string]$ShortName,
     [Parameter()]
-    [int]$Number = 0,
+    [long]$Number = 0,
     [switch]$Timestamp,
     [switch]$Help,
     [Parameter(Position = 0, ValueFromRemainingArguments = $true)]
@@ -45,39 +45,18 @@ if ([string]::IsNullOrWhiteSpace($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)
     
-    $highest = 0
+    [long]$highest = 0
     if (Test-Path $SpecsDir) {
         Get-ChildItem -Path $SpecsDir -Directory | ForEach-Object {
-            if ($_.Name -match '^(\d{3})-') {
+            # Match sequential prefixes (>=3 digits), but skip timestamp dirs.
-                $num = [int]$matches[1]
+            if ($_.Name -match '^(\d{3,})-' -and $_.Name -notmatch '^\d{8}-\d{6}-') {
-                if ($num -gt $highest) { $highest = $num }
+                [long]$num = 0
+                if ([long]::TryParse($matches[1], [ref]$num) -and $num -gt $highest) {
+                    $highest = $num
+                }
             }
         }
     }
@@ -87,7 +66,7 @@ function Get-HighestNumberFromSpecs {
 function Get-HighestNumberFromBranches {
     param()
     
-    $highest = 0
+    [long]$highest = 0
     try {
         $branches = git branch -a 2>$null
         if ($LASTEXITCODE -eq 0) {
@@ -95,10 +74,12 @@ function Get-HighestNumberFromBranches {
                 # Clean branch name: remove leading markers and remote prefixes
                 $cleanBranch = $branch.Trim() -replace '^\*?\s+', '' -replace '^remotes/[^/]+/', ''
                 
-                # Extract feature number if branch matches pattern ###-*
+                # Extract sequential feature number (>=3 digits), skip timestamp branches.
-                if ($cleanBranch -match '^(\d{3})-') {
+                if ($cleanBranch -match '^(\d{3,})-' -and $cleanBranch -notmatch '^\d{8}-\d{6}-') {
-                    $num = [int]$matches[1]
+                    [long]$num = 0
-                    if ($num -gt $highest) { $highest = $num }
+                    if ([long]::TryParse($matches[1], [ref]$num) -and $num -gt $highest) {
+                        $highest = $num
+                    }
                 }
             }
         }
@@ -139,26 +120,14 @@ function ConvertTo-CleanBranchName {
     
     return $Name.ToLower() -replace '[^a-z0-9]', '-' -replace '-{2,}', '-' -replace '^-', '' -replace '-$', ''
 }
-$fallbackRoot = (Find-RepositoryRoot -StartDir $PSScriptRoot)
+# Load common functions (includes Get-RepoRoot, Test-HasGit, Resolve-Template)
-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"
 
-try {
+# Use common.ps1 functions which prioritize .specify over git
-    $repoRoot = git rev-parse --show-toplevel 2>$null
+$repoRoot = Get-RepoRoot
-    if ($LASTEXITCODE -eq 0) {
+
-        $hasGit = $true
+# Check if git is available at this repo root (not a parent)
-    } else {
+$hasGit = Test-HasGit
-        throw "Git not available"
-    }
-} catch {
-    $repoRoot = $fallbackRoot
-    $hasGit = $false
-}
 
 Set-Location $repoRoot
 
@@ -326,4 +295,3 @@ if ($Json) {
     Write-Output "HAS_GIT: $hasGit"
     Write-Output "SPECIFY_FEATURE environment variable set to: $branchName"
 }
-

src/specify_cli/__init__.py

@@ -1159,70 +1159,6 @@ def _locate_core_pack() -> Path | None:
     return None
 
 
-def _locate_bundled_git_extension() -> Path | None:
-    """Return the path to the bundled git extension, or None.
-
-    Checks the wheel's core_pack first, then falls back to the
-    source-checkout ``extensions/git/`` directory.
-    """
-    core = _locate_core_pack()
-    if core is not None:
-        candidate = core / "extensions" / "git"
-        if (candidate / "extension.yml").is_file():
-            return candidate
-
-    # Source-checkout / editable install: look relative to repo root
-    repo_root = Path(__file__).parent.parent.parent
-    candidate = repo_root / "extensions" / "git"
-    if (candidate / "extension.yml").is_file():
-        return candidate
-
-    return None
-
-
-def _install_bundled_git_extension(project_path: Path) -> bool:
-    """Auto-install the bundled git extension during ``specify init``.
-
-    This is a migration-period mechanism (pre-1.0.0) that auto-enables
-    the git extension so that existing branching workflows continue to work.
-    Before 1.0.0, this auto-install will be removed and the extension will
-    become opt-in.
-
-    Returns True if the extension was installed or already present,
-    False otherwise.
-    """
-    ext_source = _locate_bundled_git_extension()
-    if ext_source is None:
-        return False
-
-    try:
-        from .extensions import ExtensionManager
-        manager = ExtensionManager(project_path)
-
-        # Skip if already installed (e.g. via preset), but only if the
-        # on-disk extension manifest still exists. This guards against
-        # stale/corrupted registry entries.
-        if manager.registry.is_installed("git"):
-            ext_manifest = project_path / ".specify" / "extensions" / "git" / "extension.yml"
-            if ext_manifest.is_file():
-                return True
-            # Registry is stale — remove entry so reinstall can proceed
-            manager.registry.remove("git")
-
-        speckit_ver = get_speckit_version()
-        manager.install_from_directory(ext_source, speckit_ver)
-        return True
-    except Exception as exc:
-        # Non-fatal: branching still works via core scripts during migration,
-        # but log a warning so users can tell the auto-install did not happen.
-        console.print(
-            "[dim yellow]Warning: failed to auto-install bundled git extension; "
-            "branching via the git extension may be unavailable. "
-            f"Details: {exc}[/dim yellow]"
-        )
-        return False
-
-
 def _locate_release_script() -> tuple[Path, str]:
     """Return (script_path, shell_cmd) for the platform-appropriate release script.
 
@@ -1554,12 +1490,6 @@ 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"
 
@@ -1592,13 +1522,9 @@ 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_SKILLS_DIR_OVERRIDES`` first, then falls back to
+    Uses ``AGENT_CONFIG[agent]["folder"] + "skills"`` and falls back to
-    ``AGENT_CONFIG[agent]["folder"] + "skills"``, and finally to
+    ``DEFAULT_SKILLS_DIR`` for unknown agents.
-    ``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:
@@ -1712,10 +1638,7 @@ def install_ai_skills(
                 command_name = command_name[len("speckit."):]
             if command_name.endswith(".agent"):
                 command_name = command_name[:-len(".agent")]
-            if selected_ai == "kimi":
+            skill_name = f"speckit-{command_name.replace('.', '-')}"
-                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
@@ -1794,8 +1717,64 @@ def _has_bundled_skills(project_path: Path, selected_ai: str) -> bool:
     if not skills_dir.is_dir():
         return False
 
-    pattern = "speckit.*/SKILL.md" if selected_ai == "kimi" else "speckit-*/SKILL.md"
+    return any(skills_dir.glob("speckit-*/SKILL.md"))
-    return any(skills_dir.glob(pattern))
+
+
+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)
 
 
 AGENT_SKILLS_MIGRATIONS = {
@@ -2158,16 +2137,33 @@ def init(
 
             ensure_constitution_from_template(project_path, tracker=tracker)
 
-            if ai_skills:
+            # 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:
                     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", f"bundled skills → {skills_dir.relative_to(project_path)}")
+                            tracker.complete("ai-skills", detail)
                         else:
-                            console.print(f"[green]✓[/green] Using bundled agent skills in {skills_dir.relative_to(project_path)}/")
+                            console.print(f"[green]✓[/green] Using {detail}")
                     else:
                         # Compatibility fallback: convert command templates to skills
                         # when an older template archive does not include native skills.
@@ -2240,11 +2236,6 @@ def init(
                 "speckit_version": get_speckit_version(),
             })
 
-            # Auto-install the bundled git extension (migration period, pre-1.0.0).
-            # This preserves backward compatibility for existing branching workflows.
-            # Before 1.0.0, this will be removed and git becomes opt-in.
-            _install_bundled_git_extension(project_path)
-
             # Install preset if specified
             if preset:
                 try:
@@ -2357,7 +2348,7 @@ 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:")
@@ -3663,6 +3654,15 @@ 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}/")
 
@@ -3701,14 +3701,19 @@ def extension_remove(
     installed = manager.list_installed()
     extension_id, display_name = _resolve_installed_extension(extension, installed, "remove")
 
-    # Get extension info for command count
+    # Get extension info for command and skill counts
     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

@@ -10,6 +10,8 @@ from pathlib import Path
 from typing import Dict, List, Any
 
 import platform
+import re
+from copy import deepcopy
 import yaml
 
 
@@ -211,24 +213,52 @@ class CommandRegistrar:
         return f"---\n{yaml_str}---\n"
 
     def _adjust_script_paths(self, frontmatter: dict) -> dict:
-        """Adjust script paths from extension-relative to repo-relative.
+        """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.
 
         Args:
             frontmatter: Frontmatter dictionary
 
         Returns:
-            Modified frontmatter with adjusted paths
+            Modified frontmatter with normalized project 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) and script_path.startswith("../../scripts/"):
+                if isinstance(script_path, str):
-                    scripts[key] = f".specify/scripts/{script_path[14:]}"
+                    scripts[key] = self._rewrite_project_relative_paths(script_path)
         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,
@@ -277,9 +307,25 @@ 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}"')
 
         return "\n".join(toml_lines)
 
@@ -308,8 +354,8 @@ class CommandRegistrar:
         if not isinstance(frontmatter, dict):
             frontmatter = {}
 
-        if agent_name == "codex":
+        if agent_name in {"codex", "kimi"}:
-            body = self._resolve_codex_skill_placeholders(frontmatter, body, project_root)
+            body = self.resolve_skill_placeholders(agent_name, frontmatter, body, project_root)
 
         description = frontmatter.get("description", f"Spec-kit workflow command: {skill_name}")
         skill_frontmatter = {
@@ -324,13 +370,8 @@ class CommandRegistrar:
         return self.render_frontmatter(skill_frontmatter) + "\n" + body
 
     @staticmethod
-    def _resolve_codex_skill_placeholders(frontmatter: dict, body: str, project_root: Path) -> str:
+    def resolve_skill_placeholders(agent_name: str, frontmatter: dict, body: str, project_root: Path) -> str:
-        """Resolve script placeholders for Codex skill overrides.
+        """Resolve script placeholders for skills-backed agents."""
-
-        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:
@@ -346,7 +387,11 @@ class CommandRegistrar:
         if not isinstance(agent_scripts, dict):
             agent_scripts = {}
 
-        script_variant = load_init_options(project_root).get("script")
+        init_opts = load_init_options(project_root)
+        if not isinstance(init_opts, dict):
+            init_opts = {}
+
+        script_variant = init_opts.get("script")
         if script_variant not in {"sh", "ps"}:
             fallback_order = []
             default_variant = "ps" if platform.system().lower().startswith("win") else "sh"
@@ -376,7 +421,8 @@ class CommandRegistrar:
             agent_script_command = agent_script_command.replace("{ARGS}", "$ARGUMENTS")
             body = body.replace("{AGENT_SCRIPT}", agent_script_command)
 
-        return body.replace("{ARGS}", "$ARGUMENTS").replace("__AGENT__", "codex")
+        body = body.replace("{ARGS}", "$ARGUMENTS").replace("__AGENT__", agent_name)
+        return CommandRegistrar._rewrite_project_relative_paths(body)
 
     def _convert_argument_placeholder(self, content: str, from_placeholder: str, to_placeholder: str) -> str:
         """Convert argument placeholder format.
@@ -400,8 +446,9 @@ 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}" if agent_name == "kimi" else f"speckit-{short_name}"
+        return f"speckit-{short_name}"
 
     def register_commands(
         self,

src/specify_cli/extensions.py

@@ -510,6 +510,283 @@ 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,
@@ -601,6 +878,10 @@ 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)
@@ -612,7 +893,8 @@ class ExtensionManager:
             "manifest_hash": manifest.get_hash(),
             "enabled": True,
             "priority": priority,
-            "registered_commands": registered_commands
+            "registered_commands": registered_commands,
+            "registered_skills": registered_skills,
         })
 
         return manifest
@@ -690,9 +972,15 @@ class ExtensionManager:
         if not self.registry.is_installed(extension_id):
             return False
 
-        # Get registered commands before removal
+        # Get registered commands and skills 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
 
@@ -701,6 +989,9 @@ 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():
@@ -1644,6 +1935,52 @@ 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.
@@ -1887,21 +2224,27 @@ 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: `/{command}`")
+                lines.append(f"Command: `{display_invocation}`")
                 if description:
                     lines.append(f"Description: {description}")
                 lines.append(f"\nPrompt: {prompt}")
-                lines.append(f"To execute: `/{command}`")
+                lines.append(f"To execute: `{display_invocation}`")
             else:
                 lines.append(f"\n**Automatic Hook**: {extension}")
-                lines.append(f"Executing: `/{command}`")
+                lines.append(f"Executing: `{display_invocation}`")
-                lines.append(f"EXECUTE_COMMAND: {command}")
+                lines.append(f"EXECUTE_COMMAND: {command_text}")
+                lines.append(f"EXECUTE_COMMAND_INVOCATION: {display_invocation}")
 
         return "\n".join(lines)
 
@@ -1965,6 +2308,7 @@ 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", ""),
@@ -2008,4 +2352,3 @@ class HookExecutor:
                     hook["enabled"] = False
 
         self.save_project_config(config)
-

src/specify_cli/presets.py

@@ -556,24 +556,31 @@ class PresetManager:
         registrar.unregister_commands(registered_commands, self.project_root)
 
     def _get_skills_dir(self) -> Optional[Path]:
-        """Return the skills directory if ``--ai-skills`` was used during init.
+        """Return the active skills directory for preset skill overrides.
 
         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 or the init-options file is missing.
+            enabled and no native-skills fallback applies.
         """
         from . import load_init_options, _get_skills_dir
 
         opts = load_init_options(self.project_root)
-        if not opts.get("ai_skills"):
+        if not isinstance(opts, dict):
+            opts = {}
+        agent = opts.get("ai")
+        if not isinstance(agent, str) or not agent:
             return None
 
-        agent = opts.get("ai")
+        ai_skills_enabled = bool(opts.get("ai_skills"))
-        if not agent:
+        if not ai_skills_enabled and agent != "kimi":
             return None
 
         skills_dir = _get_skills_dir(self.project_root, agent)
@@ -582,6 +589,76 @@ 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",
@@ -629,9 +706,15 @@ class PresetManager:
             return []
 
         from . import SKILL_DESCRIPTIONS, load_init_options
+        from .agents import CommandRegistrar
 
-        opts = load_init_options(self.project_root)
+        init_opts = load_init_options(self.project_root)
-        selected_ai = opts.get("ai", "")
+        if not isinstance(init_opts, dict):
+            init_opts = {}
+        selected_ai = init_opts.get("ai")
+        if not isinstance(selected_ai, str):
+            return []
+        registrar = CommandRegistrar()
 
         written: List[str] = []
 
@@ -643,43 +726,42 @@ class PresetManager:
                 continue
 
             # Derive the short command name (e.g. "specify" from "speckit.specify")
-            short_name = cmd_name
+            raw_short_name = cmd_name
-            if short_name.startswith("speckit."):
+            if raw_short_name.startswith("speckit."):
-                short_name = short_name[len("speckit."):]
+                raw_short_name = raw_short_name[len("speckit."):]
-            if selected_ai == "kimi":
+            short_name = raw_short_name.replace(".", "-")
-                skill_name = f"speckit.{short_name}"
+            skill_name, legacy_skill_name = self._skill_names_for_command(cmd_name)
-            else:
+            skill_title = self._skill_title_from_command(cmd_name)
-                skill_name = f"speckit-{short_name}"
 
-            # Only overwrite if the skill already exists (i.e. --ai-skills was used)
+            # Only overwrite skills that already exist under skills_dir,
-            skill_subdir = skills_dir / skill_name
+            # including Kimi native skills when ai_skills is false.
-            if not skill_subdir.exists():
+            # 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:
                 continue
 
             # Parse the command file
             content = source_file.read_text(encoding="utf-8")
-            if content.startswith("---"):
+            frontmatter, body = registrar.parse_frontmatter(content)
-                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
+            )
 
+            for target_skill_name in target_skill_names:
                 frontmatter_data = {
-                "name": skill_name,
+                    "name": target_skill_name,
                     "description": enhanced_desc,
                     "compatibility": "Requires spec-kit project structure with .specify/ directory",
                     "metadata": {
@@ -692,13 +774,13 @@ class PresetManager:
                     f"---\n"
                     f"{frontmatter_text}\n"
                     f"---\n\n"
-                f"# Speckit {short_name.title()} Skill\n\n"
+                    f"# Speckit {skill_title} Skill\n\n"
                     f"{body}\n"
                 )
 
-            skill_file = skill_subdir / "SKILL.md"
+                skill_file = skills_dir / target_skill_name / "SKILL.md"
                 skill_file.write_text(skill_content, encoding="utf-8")
-            written.append(skill_name)
+                written.append(target_skill_name)
 
         return written
 
@@ -720,10 +802,17 @@ class PresetManager:
         if not skills_dir:
             return
 
-        from . import SKILL_DESCRIPTIONS
+        from . import SKILL_DESCRIPTIONS, load_init_options
+        from .agents import CommandRegistrar
 
         # 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)
@@ -735,7 +824,10 @@ class PresetManager:
 
             skill_subdir = skills_dir / skill_name
             skill_file = skill_subdir / "SKILL.md"
-            if not skill_file.exists():
+            if not skill_subdir.is_dir():
+                continue
+            if not skill_file.is_file():
+                # Only manage directories that contain the expected skill entrypoint.
                 continue
 
             # Try to find the core command template
@@ -746,19 +838,11 @@ class PresetManager:
             if core_file:
                 # Restore from core template
                 content = core_file.read_text(encoding="utf-8")
-                if content.startswith("---"):
+                frontmatter, body = registrar.parse_frontmatter(content)
-                    parts = content.split("---", 2)
+                if isinstance(selected_ai, str):
-                    if len(parts) >= 3:
+                    body = registrar.resolve_skill_placeholders(
-                        frontmatter = yaml.safe_load(parts[1])
+                        selected_ai, frontmatter, body, self.project_root
-                        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(
@@ -776,16 +860,49 @@ 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 {short_name.title()} Skill\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"{body}\n"
                 )
                 skill_file.write_text(skill_content, encoding="utf-8")
             else:
-                # No core template — remove the skill entirely
+                # No core or extension template — remove the skill entirely
                 shutil.rmtree(skill_subdir)
 
     def install_from_directory(
@@ -915,17 +1032,26 @@ 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
-- Non-Functional Requirements
+- Success Criteria (measurable outcomes — e.g., performance, security, availability, user success, business impact)
 - 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**: 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`)
+- **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%").
 - **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
-- Non-functional requirements not reflected in tasks (e.g., performance, security)
+- Success Criteria requiring buildable work (performance, security, availability) not reflected in tasks
 
 #### 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 Non-Functional / Quality Attributes section (convert vague adjective to metric or explicit target).
+       - Non-functional constraint → Add/modify measurable criteria in Success Criteria > Measurable Outcomes (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/commands/specify.md

@@ -73,40 +73,12 @@ Given that feature description, do this:
      - "Create a dashboard for analytics" → "analytics-dashboard"
      - "Fix payment processing timeout bug" → "fix-payment-timeout"
 
-2. **Create the feature branch** (unless already handled by a `before_specify` hook — see Pre-Execution Checks above). If a mandatory `before_specify` hook for `speckit.git.feature` already executed and created the branch, **skip this step entirely** and use the branch/spec information from the hook result. Otherwise:
+2. **Create the feature branch** by running the script with `--short-name` (and `--json`). In sequential mode, do NOT pass `--number` — the script auto-detects the next available number. In timestamp mode, the script generates a `YYYYMMDD-HHMMSS` prefix automatically:
 
-   **Git extension check**: Before running the branch creation script, check if the git extension is enabled:
+   **Branch numbering mode**: Before running the script, check if `.specify/init-options.json` exists and read the `branch_numbering` value.
-   - Check if `.specify/extensions/.registry` exists (a single JSON file tracking all extensions)
-   - If it exists, read the JSON and look for an `extensions.git` entry
-   - **Only skip branching** when `extensions.git.enabled` is **present and explicitly `false`**. In all other cases — including when the registry file is missing, when `extensions.git` has no entry, or when `"enabled"` is `true` or absent — proceed with normal branch creation (extension script if present, else core `{SCRIPT}` fallback)
-   - If the git extension is **disabled** (explicitly `"enabled": false`), **skip branch creation entirely** — do **not** run the branch creation script. Instead:
-     - Derive a spec directory name from the short name, e.g. `specs/<short-name>/`
-     - Explicitly set the following variables so later steps can use them:
-       - `FEATURE_DIR="specs/<short-name>"`
-       - `SPEC_FILE="$FEATURE_DIR/spec.md"`
-     - Ensure the directory and spec file exist:
-       - Bash:
-         - `mkdir -p "$FEATURE_DIR"`
-         - `touch "$SPEC_FILE"`
-       - PowerShell:
-         - `New-Item -ItemType Directory -Path $FEATURE_DIR -Force | Out-Null`
-         - `New-Item -ItemType File -Path $SPEC_FILE -Force | Out-Null`
-     - Then proceed directly to step 3 using `FEATURE_DIR` and `SPEC_FILE`
-   - If the registry file does not exist, proceed with branch creation using the default behavior (backward compatibility)
-
-   Run the script with `--short-name` (and `--json`). In sequential mode, do NOT pass `--number` — the script auto-detects the next available number. In timestamp mode, the script generates a `YYYYMMDD-HHMMSS` prefix automatically:
-
-   **Branch numbering mode**: Before running the script, determine the branch numbering strategy:
-   1. Check `.specify/extensions/git/git-config.yml` for `branch_numbering` value (extension config takes precedence)
-   2. If not found, check `.specify/init-options.json` for `branch_numbering` value (backward compatibility)
-   3. Default to `sequential` if neither exists
    - If `"timestamp"`, add `--timestamp` (Bash) or `-Timestamp` (PowerShell) to the script invocation
    - If `"sequential"` or absent, do not add any extra flag (default behavior)
 
-   **Script resolution**: Use the extension's bundled scripts when available, falling back to core scripts:
-   - **Bash**: If `.specify/extensions/git/scripts/bash/create-new-feature.sh` exists, use it; otherwise, fall back to `{SCRIPT}`
-   - **PowerShell**: If `.specify/extensions/git/scripts/powershell/create-new-feature.ps1` exists, use it; otherwise, fall back to `{SCRIPT}`
-
    - Bash example: `{SCRIPT} --json --short-name "user-auth" "Add user authentication"`
    - Bash (timestamp): `{SCRIPT} --json --timestamp --short-name "user-auth" "Add user authentication"`
    - PowerShell example: `{SCRIPT} -Json -ShortName "user-auth" "Add user authentication"`

templates/spec-template.md

@@ -113,3 +113,16 @@
 - **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_uses_override(self, project_dir):
+    def test_codex_skills_dir_from_agent_config(self, project_dir):
-        """Codex should use the AGENT_SKILLS_DIR_OVERRIDES value."""
+        """Codex should resolve skills directory from AGENT_CONFIG folder."""
         result = _get_skills_dir(project_dir, "codex")
         assert result == project_dir / ".agents" / "skills"
 
@@ -203,12 +203,71 @@ class TestGetSkillsDir:
             # Should always end with "skills"
             assert result.name == "skills"
 
-    def test_override_takes_precedence_over_config(self, project_dir):
+class TestKimiLegacySkillMigration:
-        """AGENT_SKILLS_DIR_OVERRIDES should take precedence over AGENT_CONFIG."""
+    """Test temporary migration from Kimi dotted skill names to hyphenated names."""
-        for agent_key in AGENT_SKILLS_DIR_OVERRIDES:
+
-            result = _get_skills_dir(project_dir, agent_key)
+    def test_migrates_legacy_dotted_skill_directory(self, project_dir):
-            expected = project_dir / AGENT_SKILLS_DIR_OVERRIDES[agent_key]
+        skills_dir = project_dir / ".kimi" / "skills"
-            assert result == expected
+        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"
 
 
 # ===== install_ai_skills Tests =====
@@ -473,8 +532,7 @@ 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()]
-        # Kimi uses dotted skill names; other agents use hyphen-separated names.
+        expected_skill_name = "speckit-specify"
-        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()
 
@@ -773,6 +831,32 @@ 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
@@ -1118,12 +1202,12 @@ 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")
 
@@ -1137,7 +1221,7 @@ 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_branch_numbering.py

@@ -87,84 +87,3 @@ class TestBranchNumberingValidation:
         result = runner.invoke(app, ["init", str(tmp_path / "proj"), "--ai", "claude", "--branch-numbering", "timestamp", "--ignore-agent-tools"])
         assert result.exit_code == 0
         assert "Invalid --branch-numbering" not in (result.output or "")
-
-
-class TestGitExtensionAutoInstall:
-    """Tests for bundled git extension auto-install during specify init."""
-
-    def test_git_extension_installed_during_init(self, tmp_path: Path, monkeypatch):
-        """Verify that `specify init` auto-installs the bundled git extension."""
-        from typer.testing import CliRunner
-        from specify_cli import app
-
-        def _fake_download(project_path, *args, **kwargs):
-            Path(project_path).mkdir(parents=True, exist_ok=True)
-
-        monkeypatch.setattr("specify_cli.download_and_extract_template", _fake_download)
-
-        project_dir = tmp_path / "proj"
-        runner = CliRunner()
-        result = runner.invoke(app, ["init", str(project_dir), "--ai", "claude", "--ignore-agent-tools"])
-        assert result.exit_code == 0
-
-        # Extension files should exist
-        ext_dir = project_dir / ".specify" / "extensions" / "git"
-        assert ext_dir.is_dir(), "git extension directory not created"
-        assert (ext_dir / "extension.yml").is_file(), "extension.yml not installed"
-
-        # Registry should contain the git extension
-        registry_file = project_dir / ".specify" / "extensions" / ".registry"
-        assert registry_file.is_file(), "extension registry not created"
-        registry = json.loads(registry_file.read_text())
-        assert "git" in registry.get("extensions", {}), "git not in registry"
-        assert registry["extensions"]["git"]["enabled"] is True
-
-    def test_git_extension_noop_when_already_installed(self, tmp_path: Path):
-        """_install_bundled_git_extension should no-op if git is already installed."""
-        from specify_cli import _install_bundled_git_extension
-        from specify_cli.extensions import ExtensionManager
-
-        project_dir = tmp_path / "proj"
-        (project_dir / ".specify").mkdir(parents=True)
-
-        # First install
-        result1 = _install_bundled_git_extension(project_dir)
-        assert result1 is True
-
-        # Second install should also succeed (no-op)
-        result2 = _install_bundled_git_extension(project_dir)
-        assert result2 is True
-
-        # Only one entry in registry
-        manager = ExtensionManager(project_dir)
-        assert manager.registry.is_installed("git")
-
-    def test_git_extension_reinstalls_when_directory_missing(self, tmp_path: Path):
-        """_install_bundled_git_extension should reinstall if registry says installed but directory is gone."""
-        import shutil
-        from specify_cli import _install_bundled_git_extension
-        from specify_cli.extensions import ExtensionManager
-
-        project_dir = tmp_path / "proj"
-        (project_dir / ".specify").mkdir(parents=True)
-
-        # First install
-        result1 = _install_bundled_git_extension(project_dir)
-        assert result1 is True
-
-        ext_dir = project_dir / ".specify" / "extensions" / "git"
-        assert ext_dir.is_dir()
-
-        # Simulate stale registry: delete extension directory but keep registry
-        shutil.rmtree(ext_dir)
-        assert not ext_dir.exists()
-
-        # Registry still says installed
-        manager = ExtensionManager(project_dir)
-        assert manager.registry.is_installed("git")
-
-        # Re-install should detect missing directory and reinstall
-        result2 = _install_bundled_git_extension(project_dir)
-        assert result2 is True
-        assert ext_dir.is_dir(), "extension directory should be reinstalled"
-        assert (ext_dir / "extension.yml").is_file(), "extension.yml should be reinstalled"

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

@@ -0,0 +1,741 @@
+"""
+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

@@ -22,6 +22,7 @@ from specify_cli.extensions import (
     ExtensionRegistry,
     ExtensionManager,
     CommandRegistrar,
+    HookExecutor,
     ExtensionCatalog,
     ExtensionError,
     ValidationError,
@@ -759,6 +760,81 @@ $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
@@ -875,11 +951,11 @@ $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
@@ -944,7 +1020,7 @@ 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()
@@ -994,12 +1070,12 @@ 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(
@@ -1056,7 +1132,7 @@ 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()
@@ -1065,6 +1141,62 @@ 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
     ):
@@ -1121,7 +1253,7 @@ 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()
@@ -3231,3 +3363,128 @@ 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

@@ -1170,8 +1170,12 @@ class TestPresetCatalog:
         assert not catalog.cache_file.exists()
         assert not catalog.cache_metadata_file.exists()
 
-    def test_search_with_cached_data(self, project_dir):
+    def test_search_with_cached_data(self, project_dir, monkeypatch):
         """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)
 
@@ -1200,6 +1204,9 @@ 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
@@ -1935,10 +1942,10 @@ class TestInitOptions:
 class TestPresetSkills:
     """Tests for preset skill registration and unregistration."""
 
-    def _write_init_options(self, project_dir, ai="claude", ai_skills=True):
+    def _write_init_options(self, project_dir, ai="claude", ai_skills=True, script="sh"):
         from specify_cli import save_init_options
 
-        save_init_options(project_dir, {"ai": ai, "ai_skills": ai_skills})
+        save_init_options(project_dir, {"ai": ai, "ai_skills": ai_skills, "script": script})
 
     def _create_skill(self, skills_dir, skill_name, body="original body"):
         skill_dir = skills_dir / skill_name
@@ -1988,6 +1995,26 @@ 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"
@@ -2033,6 +2060,52 @@ 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")
@@ -2047,6 +2120,304 @@ 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

@@ -14,6 +14,7 @@ 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"
 
 
@@ -147,6 +148,24 @@ 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 ───────────────────────────────────────────────