chore: bump version to 0.12.13

`SwitchStep.validate()` already rejects a non-mapping `cases`, but the
engine's `execute()` path does not auto-validate (see
`WorkflowEngine.load_workflow`, whose docstring notes the definition is
"not yet validated"). On an unvalidated run, `execute` called
`cases.items()` on the raw value, so a list or scalar `cases` authoring
mistake raised `AttributeError` and took down the whole run — the engine
invokes `step_impl.execute()` with no surrounding try/except.

Guard `execute` to return a FAILED StepResult naming the type error
instead, mirroring the fan-out step's non-list `items` handling. The
expression is still evaluated first, so its value is surfaced in the
step output for downstream context.

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

.github/CODEOWNERS

@@ -5,4 +5,3 @@
 /extensions/catalog.community.json @mnriem
 /integrations/catalog.community.json @mnriem
 /presets/catalog.community.json @mnriem
-

.github/ISSUE_TEMPLATE/agent_request.yml

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

.github/ISSUE_TEMPLATE/extension_submission.yml

@@ -7,7 +7,7 @@ body:
     attributes:
       value: |
         Thanks for contributing an extension! This template helps you submit your extension to the community catalog.
-        
+
         **Before submitting:**
         - Review the [Extension Publishing Guide](https://github.com/github/spec-kit/blob/main/extensions/EXTENSION-PUBLISHING-GUIDE.md)
         - Ensure your extension has a valid `extension.yml` manifest
@@ -209,9 +209,9 @@ body:
         **Tested on:**
         - macOS 14.0 with Spec Kit v0.1.0
         - Linux Ubuntu 22.04 with Spec Kit v0.1.0
-        
+
         **Test project:** [Link or description]
-        
+
         **Test scenarios:**
         1. Installed extension
         2. Configured settings
@@ -230,7 +230,7 @@ body:
         ```bash
         # Install extension
         specify extension add <extension-name> --from https://github.com/your-org/spec-kit-your-extension/archive/refs/tags/v1.0.0.zip
-        
+
         # Use a command
         /speckit.your-extension.command-name arg1 arg2
         ```

.github/ISSUE_TEMPLATE/preset_submission.yml

@@ -7,7 +7,7 @@ body:
     attributes:
       value: |
         Thanks for contributing a preset! This template helps you submit your preset to the community catalog.
-        
+
         **Before submitting:**
         - Review the [Preset Publishing Guide](https://github.com/github/spec-kit/blob/main/presets/PUBLISHING.md)
         - Ensure your preset has a valid `preset.yml` manifest

.github/PULL_REQUEST_TEMPLATE.md

@@ -19,4 +19,3 @@
 - [ ] I **did** use AI assistance (describe below)
 
 <!-- If you used AI, briefly describe how (e.g., "Code generated by Copilot", "Consulted ChatGPT for approach"): -->
-

.github/workflows/docs.yml

@@ -35,7 +35,7 @@ jobs:
           fetch-depth: 0 # Fetch all history for git info
 
       - name: Setup .NET
-        uses: actions/setup-dotnet@9a946fdbd5fb07b82b2f5a4466058b876ab72bb2 # v5.3.0
+        uses: actions/setup-dotnet@26b0ec14cb23fa6904739307f278c14f94c95bf1 # v5.4.0
         with:
           dotnet-version: '8.x'
 

.github/workflows/lint.yml

@@ -37,7 +37,7 @@ jobs:
           fi
 
       - name: Run markdownlint-cli2
-        uses: DavidAnson/markdownlint-cli2-action@ded1f9488f68a970bc66ea5619e13e9b52e601cd # v23
+        uses: DavidAnson/markdownlint-cli2-action@8de2aa07cae85fd17c0b35642db70cf5495f1d25 # v24.0.0
         with:
           globs: |
             '**/*.md'

.github/workflows/publish-pypi.yml

@@ -32,7 +32,7 @@ jobs:
           ref: refs/tags/${{ inputs.tag }}
 
       - name: Install uv
-        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
+        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
 
       - name: Set up Python
         uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
@@ -74,7 +74,7 @@ jobs:
           path: dist/
 
       - name: Install uv
-        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
+        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
 
       - name: Publish to PyPI
         run: uv publish

.github/workflows/stale.yml

@@ -20,24 +20,24 @@ jobs:
           days-before-stale: 150
           # Days of inactivity before a stale issue or PR is closed (after being marked stale)
           days-before-close: 30
-          
+
           # Stale issue settings
           stale-issue-message: 'This issue has been automatically marked as stale because it has not had any activity for 150 days. It will be closed in 30 days if no further activity occurs.'
           close-issue-message: 'This issue has been automatically closed due to inactivity (180 days total). If you believe this issue is still relevant, please reopen it or create a new issue.'
           stale-issue-label: 'stale'
-          
+
           # Stale PR settings
           stale-pr-message: 'This pull request has been automatically marked as stale because it has not had any activity for 150 days. It will be closed in 30 days if no further activity occurs.'
           close-pr-message: 'This pull request has been automatically closed due to inactivity (180 days total). If you believe this PR is still relevant, please reopen it or create a new PR.'
           stale-pr-label: 'stale'
-          
+
           # Exempt issues and PRs with these labels from being marked as stale
           exempt-issue-labels: 'pinned,security'
           exempt-pr-labels: 'pinned,security'
-          
+
           # Only issues or PRs with all of these labels are checked
           # Leave empty to check all issues and PRs
           any-of-labels: ''
-          
+
           # Operations per run (helps avoid rate limits)
           operations-per-run: 250

.github/workflows/test.yml

@@ -16,7 +16,7 @@ jobs:
         uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
 
       - name: Install uv
-        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
+        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
 
       - name: Set up Python
         uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
@@ -37,7 +37,7 @@ jobs:
         uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
 
       - name: Install uv
-        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
+        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
 
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6

.markdownlint-cli2.jsonc

@@ -26,4 +26,4 @@
   "ignores": [
     ".genreleases/"
   ]
-}
+}

.pre-commit-config.yaml

@@ -0,0 +1,12 @@
+---
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: check-executables-have-shebangs
+      - id: check-yaml
+        exclude: \.lock\.yml$
+      - id: end-of-file-fixer
+        exclude: \.lock\.yml$
+      - id: trailing-whitespace
+        exclude: \.lock\.yml$

CHANGELOG.md

@@ -2,6 +2,156 @@
 
 <!-- insert new changelog below this comment -->
 
+## [0.12.13] - 2026-07-13
+
+### Changed
+
+- fix(workflows): fail switch step on non-mapping cases instead of crashing (#3481)
+- Cleanup agent-file-template.md (#2579)
+- fix: mark Kiro integration as multi-install safe (#3472)
+- fix: rewrite extension-relative subdir paths in generated command bodies (#3444)
+- fix(templates): point constitution sync checklist at installed command files (#3418)
+- feat(workflows): make shell step timeout configurable (#3327) (#3328)
+- docs: clarify that release tags keep the leading v prefix (#3463)
+- fix(workflows): don't crash on membership test against a non-iterable (#3448)
+- fix(workflows): if-step validate accepts falsy non-list else (#3264)
+- chore: release 0.12.12, begin 0.12.13.dev0 development (#3490)
+
+## [0.12.12] - 2026-07-13
+
+### Changed
+
+- fix(extensions): set-priority repairs corrupted boolean priority (#3268)
+- fix(presets): set-priority repairs corrupted boolean priority (#3269)
+- fix(workflows): engine loop cap ignores bool max_iterations (#3270)
+- docs(bundles): document --integration on 'bundle update' (#3271)
+- fix(workflows): harden catalog.py against mis-shaped registry & non-string fields (#3375)
+- Add Verify Review Ship extension to community catalog (#3450)
+- fix(bundle): reject file:// / local download_url — catalog URLs are HTTPS-only (#3344)
+- fix(extensions): handle prefix-colliding env vars in _get_env_config (#3350)
+- docs: document copilot skills mode (--skills) and markdown deprecation (#3313)
+- chore: release 0.12.11, begin 0.12.12.dev0 development (#3460)
+
+## [0.12.11] - 2026-07-10
+
+### Changed
+
+- fix(agent-context): discover nested plan.md in scoped layouts (#3024) (#3301)
+- fix(auth): return no matches, not raw ValueError, for a malformed URL (#3437)
+- fix(catalogs): raise catalog error, not raw ValueError, on a malformed URL (#3435)
+- fix(bundler): raise BundlerError, not raw ValueError, on a malformed catalog URL (#3433)
+- chore: add pre-commit config and fix trailing whitespace/end-of-file (#3430)
+- Add EARS Requirements Syntax extension to community catalog (#3407)
+- Add Spec Kit Figma extension to community catalog (#3408)
+- fix(workflows): report validation errors instead of crashing on non-string workflow.yml scalars (#3421)
+- fix(templates): remove self-referencing path in plan-template.md note (#3417)
+- chore: release 0.12.10, begin 0.12.11.dev0 development (#3453)
+
+## [0.12.10] - 2026-07-10
+
+### Changed
+
+- chore(deps): bump astral-sh/setup-uv from 8.2.0 to 8.3.2 (#3439)
+- chore(deps): bump DavidAnson/markdownlint-cli2-action (#3438)
+- fix(templates): correct phase numbering in plan.md (#3416)
+- fix(git-ext): honor explicit -Number 0 in PowerShell branch creation (#3412)
+- docs: add 'spectatui' entry to friends.md (#3362)
+- test: pin interpreter probe so py-template render test passes on Windows (#3428)
+- feat(workflows): make shell step timeout configurable (#3404)
+- fix: find plans in nested spec directories (#3405)
+- feat(templates): add py: lines to command templates' scripts frontmatter (#3403)
+- chore: release 0.12.9, begin 0.12.10.dev0 development (#3426)
+
+## [0.12.9] - 2026-07-09
+
+### Changed
+
+- fix(integrations): skip Windows Store python3 alias stub in resolve_python_interpreter (#3385)
+- fix(integrations): escape control characters in SKILL.md frontmatter (#3399)
+- fix(workflows): apply chained expression filters left-to-right (#3339)
+- fix(scripts): resolve invoke_separator by parse success, not python3 availability (#3304) (#3320)
+- fix(shared-infra): refresh_shared_templates preserves recovered user files (#3378)
+- fix(agents): resolve skill placeholders in Goose (yaml) command output (#3374)
+- fix(bundler): enforce version pin on bundled preset/extension installs (#3377)
+- Update Golden Demo extension to v0.3.0 (#3394)
+- test: isolate integration test home (#3144)
+- chore: release 0.12.8, begin 0.12.9.dev0 development (#3410)
+
+## [0.12.8] - 2026-07-08
+
+### Changed
+
+- [extension] Add LLM Wiki extension to community catalog (#3361)
+- Docs: Document missing CLI flags and integrations (#3182)
+- Docs: Remove Cursor from CLI check list in README (#3184)
+- feat(extensions): port update-agent-context to Python (#3387)
+- fix(scripts): fall through to grep/sed when python3 is a broken stub in feature.json parser (#3312)
+- fix(toml): escape control characters so generated command files parse (#3341)
+- fix(cli): exit cleanly on malformed IPv6 URLs in `extension`/`preset`/`workflow add` (#3369)
+- fix(github-http): return None on malformed GHES port instead of raising (#3379)
+- fix(integrations): guard _sha256 against unreadable managed files (#3376)
+- chore: release 0.12.7, begin 0.12.8.dev0 development (#3398)
+
+## [0.12.7] - 2026-07-07
+
+### Changed
+
+- fix(bundler): bundle update uninstalls components dropped by new version (#3353)
+- fix(workflows): route run/resume errors to stderr under --json (#3352)
+- fix(workflows): fan-in validate() rejects non-mapping output (#3349)
+- fix(workflows): shell step validate() rejects non-string run (#3348)
+- fix(integrations): agy honors SPECKIT_INTEGRATION_AGY_EXTRA_ARGS (#3347)
+- Add Orchestration Task Context Management extension to community catalog (#3372)
+- Update DocGuard — CDD Enforcement extension to v0.30.0 (#3371)
+- Update Ripple extension to v1.1.0 (#3370)
+- feat(integrations): generalize post-processing to all format types (#3311)
+- chore: release 0.12.6, begin 0.12.7.dev0 development (#3393)
+
+## [0.12.6] - 2026-07-07
+
+### Changed
+
+- fix(bundler): validate catalog URLs in `catalog add` (HTTPS-only, require host) (#3367)
+- Update Ralph Loop extension to v1.2.1 (#3365)
+- fix extension-local script path rewriting (#3364)
+- Add Charter extension to community catalog (#3363)
+- feat(scripts): add Python check-prerequisites PoC (#3302)
+- test: reduce registry manifest test repetition (#3146)
+- fix(integrations): hermes honors SPECKIT_INTEGRATION_HERMES_EXTRA_ARGS (#3346)
+- fix(extensions): coerce non-mapping YAML config roots to {} in ConfigManager (#3345)
+- fix(yaml): pin goose recipe prompt block-scalar indentation (#3343)
+- chore: release 0.12.5, begin 0.12.6.dev0 development (#3381)
+
+## [0.12.5] - 2026-07-06
+
+### Changed
+
+- fix(workflows): match gate reject option case-insensitively (#3335)
+- fix(bundler): reject host-less catalog URLs in adapters (use hostname, not netloc) (#3333)
+- fix(bundler): resolve catalog search at highest-precedence source before filtering (#3331)
+- fix(workflows): compare non-numeric strings lexicographically instead of returning False (#3323)
+- fix(workflows): quote-aware interpolation so a literal }} in a filter arg doesn't break multi-expression templates (#3307)
+- Support namespaced git feature branch templates (#3293)
+- chore(deps): bump actions/setup-dotnet from 5.3.0 to 5.4.0 (#3315)
+- fix(integrations): cursor-agent honors executable/extra-args env overrides (#3265)
+- docs: drop stale kimi KIMI.md->AGENTS.md migration note (#3291)
+- chore: release 0.12.4, begin 0.12.5.dev0 development (#3305)
+
+## [0.12.4] - 2026-07-02
+
+### Changed
+
+- feat(cli): add `py` script type & Python interpreter resolution (#3278) (#3285)
+- fix: resolve GitHub release asset API URL for private repo bundle downloads (#3136)
+- [extension] Add Analytics extension to community catalog (#3296)
+- fix: interpolate multi-expression templates instead of returning None (#3208) (#3228)
+- feat(cli): honor SPECIFY_INIT_DIR in the specify CLI project resolver (#3186)
+- fix(extensions): resolve core-command dirs via _assets helpers (#3274) (#3287)
+- fix: fall back to feature dir basename for empty CURRENT_BRANCH (#3026) (#3229)
+- feat(bug-fix): add label-driven bug-fix agentic workflow (#3258)
+- feat(workflows): add label-driven bug-test workflow (#3239) (#3257)
+- chore: release 0.12.3, begin 0.12.4.dev0 development (#3295)
+
 ## [0.12.3] - 2026-07-01
 
 ### Changed

LICENSE

@@ -19,4 +19,3 @@ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
-

README.md

@@ -45,7 +45,7 @@ Spec-Driven Development **flips the script** on traditional software development
 
 ### 1. Install Specify CLI
 
-Requires **[uv](https://docs.astral.sh/uv/)** ([install uv](./docs/install/uv.md)). Replace `vX.Y.Z` with the latest tag from [Releases](https://github.com/github/spec-kit/releases):
+Requires **[uv](https://docs.astral.sh/uv/)** ([install uv](./docs/install/uv.md)). Replace `vX.Y.Z` with the latest release tag from [Releases](https://github.com/github/spec-kit/releases) — keep the leading `v` (for example, `v0.12.11`, not `0.12.11`):
 
 ```bash
 uv tool install specify-cli --from git+https://github.com/github/spec-kit.git@vX.Y.Z
@@ -406,7 +406,7 @@ specify init . --force --integration copilot
 specify init --here --force --integration copilot
 ```
 
-The CLI will check that your selected agent's CLI tool is installed (for integrations that require a CLI), such as Claude Code, Gemini CLI, Qwen Code, opencode, Codex CLI, Qoder CLI, Tabnine CLI, Kiro CLI, Pi Coding Agent, Oh My Pi, Forge, Goose, Mistral Vibe, or ZCode. If you don't have the required tool installed, or you prefer to get the templates without checking for the right tools, use `--ignore-agent-tools` with your command:
+The CLI checks that the selected integration's required CLI tool is installed on your machine when that integration has `requires_cli: True`. If you do not have the required tool installed, or you prefer to get the templates without checking for the right tools, use `--ignore-agent-tools` with your command:
 
 ```bash
 specify init <project_name> --integration copilot --ignore-agent-tools

docs/.gitignore

@@ -6,4 +6,3 @@ obj/
 # Temporary files
 *.tmp
 *.log
-

docs/community/extensions.md

@@ -42,6 +42,7 @@ The following community-contributed extensions are available in [`catalog.commun
 | Bugfix Workflow | Structured bugfix workflow — capture bugs, trace to spec artifacts, and patch specs surgically | `process` | Read+Write | [spec-kit-bugfix](https://github.com/Quratulain-bilal/spec-kit-bugfix) |
 | Canon | Adds canon-driven (baseline-driven) workflows: spec-first, code-first, spec-drift. Requires Canon Core preset installation. | `process` | Read+Write | [spec-kit-canon](https://github.com/maximiliamus/spec-kit-canon/tree/master/extension) |
 | Catalog CI | Automated validation for spec-kit community catalog entries — structure, URLs, diffs, and linting | `process` | Read-only | [spec-kit-catalog-ci](https://github.com/Quratulain-bilal/spec-kit-catalog-ci) |
+| Charter | Compose modular project constitutions from shared fragment registries. Centralize governance rules, select per-project fragments, track upstream changes, and keep multi-project setups consistent. | `process` | Read+Write | [spec-kit-charter](https://github.com/Fyloss/spec-kit-charter) |
 | CI Guard | Spec compliance gates for CI/CD — verify specs exist, check drift, and block merges on gaps | `process` | Read-only | [spec-kit-ci-guard](https://github.com/Quratulain-bilal/spec-kit-ci-guard) |
 | Checkpoint Extension | Commit the changes made during the middle of the implementation, so you don't end up with just one very large commit at the end | `code` | Read+Write | [spec-kit-checkpoint](https://github.com/aaronrsun/spec-kit-checkpoint) |
 | Cleanup Extension | Post-implementation quality gate that reviews changes, fixes small issues (scout rule), creates tasks for medium issues, and generates analysis for large issues | `code` | Read+Write | [spec-kit-cleanup](https://github.com/dsrednicki/spec-kit-cleanup) |
@@ -50,14 +51,15 @@ The following community-contributed extensions are available in [`catalog.commun
 | Confluence Extension | Create a doc in Confluence summarizing the specifications and planning files | `integration` | Read+Write | [spec-kit-confluence](https://github.com/aaronrsun/spec-kit-confluence) |
 | Cost Tracker | Track real LLM dollar cost across SDD workflows — per-feature budgets, per-integration comparison, and finance-ready exports | `visibility` | Read+Write | [spec-kit-cost](https://github.com/Quratulain-bilal/spec-kit-cost) |
 | Data Model Diagram | Generates Mermaid ER diagrams from Spec Kit data models after planning | `docs` | Read+Write | [spec-kit-data-model-diagram](https://github.com/benizzio/spec-kit-data-model-diagram) |
-| DocGuard — CDD Enforcement | Canonical-Driven Development enforcement. Validates, scores, and traces project documentation with automated checks, AI-driven workflows, and spec-kit hooks. One pinned runtime dependency; pure Node.js otherwise. | `docs` | Read+Write | [spec-kit-docguard](https://github.com/raccioly/docguard) |
+| DocGuard — CDD Enforcement | The only doc-integrity engine with an MCP server, SARIF output, and a deterministic zero-LLM core. Validates, scores, and traces documentation against code — 24 validators, stable finding codes, GitHub Action with PR annotations, spec-kit hooks. Pure Node.js, one pinned dep. | `docs` | Read+Write | [spec-kit-docguard](https://github.com/raccioly/docguard) |
+| EARS Requirements Syntax | Author, lint, and convert requirements using EARS - the five industry-standard sentence patterns for unambiguous, testable requirements | `docs` | Read+Write | [spec-kit-ears](https://github.com/dhruv-15-03/spec-kit-ears) |
 | Extensify | Create and validate extensions and extension catalogs | `process` | Read+Write | [extensify](https://github.com/mnriem/spec-kit-extensions/tree/main/extensify) |
 | Fix Findings | Automated analyze-fix-reanalyze loop that resolves spec findings until clean | `code` | Read+Write | [spec-kit-fix-findings](https://github.com/Quratulain-bilal/spec-kit-fix-findings) |
 | FixIt Extension | Spec-aware bug fixing — maps bugs to spec artifacts, proposes a plan, applies minimal changes | `code` | Read+Write | [spec-kit-fixit](https://github.com/speckit-community/spec-kit-fixit) |
 | 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) |
 | GitHub Issues Integration 1 | Generate spec artifacts from GitHub Issues - import issues, sync updates, and maintain bidirectional traceability | `integration` | Read+Write | [spec-kit-github-issues](https://github.com/Fatima367/spec-kit-github-issues) |
 | GitHub Issues Integration 2 | Creates and syncs local specs from an existing GitHub issue | `integration` | Read+Write | [spec-kit-issue](https://github.com/aaronrsun/spec-kit-issue) |
-| Golden Demo | Extracts acceptance criteria from specs, builds test vectors, and produces a behavioral drift report — complementary to Architecture Guard and CDD | `docs` | Read+Write | [spec-kit-golden-demo](https://github.com/jasstt/spec-kit-golden-demo) |
+| Golden Demo | Deterministic behavioral drift oracle. Extracts acceptance criteria, generates fuzz test vectors (seed=42), compares golden Python implementations against real code in any language. CI/CD gatekeeper with warn/strict modes. | `docs` | Read+Write | [spec-kit-golden-demo](https://github.com/jasstt/spec-kit-golden-demo) |
 | Improve Extension | Audits any codebase as a senior advisor and writes prioritized, self-contained spec prompts under specs/ that the spec-kit lifecycle can process | `process` | Read+Write | [spec-kit-improve](https://github.com/d0whc3r/spec-kit-improve) |
 | Intake | Normalize PRD, design, HTML SSOT, and test-case evidence into SDD-ready intake artifacts. | `docs` | Read+Write | [spec-kit-intake](https://github.com/bigsmartben/spec-kit-intake) |
 | Intelligent Agent Orchestrator | Cross-catalog agent discovery and intelligent prompt-to-command routing | `process` | Read+Write | [spec-kit-orchestrator](https://github.com/pragya247/spec-kit-orchestrator) |
@@ -66,6 +68,7 @@ The following community-contributed extensions are available in [`catalog.commun
 | Jira Integration (Sync Engine) | Idempotent, drift-aware, fail-closed reconcile engine mirroring spec-kit specs into Jira (Epic per repo, Story per spec, Subtask per phase) | `integration` | Read+Write | [spec-kit-jira-sync](https://github.com/ashbrener/spec-kit-jira-sync) |
 | Learning Extension | Generate educational guides from implementations and enhance clarifications with mentoring context | `docs` | Read+Write | [spec-kit-learn](https://github.com/imviancagrace/spec-kit-learn) |
 | Linear Integration | Mirror spec-kit feature directories into Linear (filesystem → Linear, reconcile-based, unidirectional). | `integration` | Read+Write | [spec-kit-linear-sync](https://github.com/ashbrener/spec-kit-linear-sync) |
+| LLM Wiki | LLM-maintained compounding project wiki: source ingestion, cited answers, and consistency linting | `docs` | Read+Write | [spec-kit-wiki](https://github.com/formin/spec-kit-wiki) |
 | Loop Engineering | Engineer safe autonomous agent loops for spec-driven development: a maker/checker split, externalized loop state, and stay-the-engineer guardrails against comprehension debt and cognitive surrender | `process` | Read+Write | [spec-kit-loop](https://github.com/formin/spec-kit-loop) |
 | MAQA — Multi-Agent & Quality Assurance | Coordinator → feature → QA agent workflow with parallel worktree-based implementation. Language-agnostic. Auto-detects installed board plugins. Optional CI gate. | `process` | Read+Write | [spec-kit-maqa-ext](https://github.com/GenieRobot/spec-kit-maqa-ext) |
 | MAQA Azure DevOps Integration | Azure DevOps Boards integration for MAQA — syncs User Stories and Task children as features progress | `integration` | Read+Write | [spec-kit-maqa-azure-devops](https://github.com/GenieRobot/spec-kit-maqa-azure-devops) |
@@ -85,6 +88,7 @@ The following community-contributed extensions are available in [`catalog.commun
 | .NET Framework to Modern .NET Migration | Orchestrate end-to-end .NET Framework to modern .NET migration across 7 phases, with SDD lifecycle integration | `process` | Read+Write | [spec-kit-fx-to-net](https://github.com/RogerBestMsft/spec-kit-FxToNet) |
 | Onboard | Contextual onboarding and progressive growth for developers new to spec-kit projects. Explains specs, maps dependencies, validates understanding, and guides the next step | `process` | Read+Write | [spec-kit-onboard](https://github.com/dmux/spec-kit-onboard) |
 | Optimize | Audit and optimize AI governance for context efficiency — token budgets, rule health, interpretability, compression, coherence, and echo detection | `process` | Read+Write | [spec-kit-optimize](https://github.com/sakitA/spec-kit-optimize) |
+| Orchestration Task Context Management | Adds subagent work-unit orchestration to generated Spec Kit task files | `process` | Read+Write | [spec-kit-orchestration-task-context-management](https://github.com/benizzio/spec-kit-orchestration-task-context-management) |
 | OWASP LLM Threat Model | OWASP Top 10 for LLM Applications 2025 threat analysis on agent artifacts | `code` | Read-only | [spec-kit-threatmodel](https://github.com/NaviaSamal/spec-kit-threatmodel) |
 | Plan Review Gate | Require spec.md and plan.md to be merged via MR/PR before allowing task generation | `process` | Read-only | [spec-kit-plan-review-gate](https://github.com/luno/spec-kit-plan-review-gate) |
 | PR Bridge | Auto-generate pull request descriptions, checklists, and summaries from spec artifacts | `process` | Read-only | [spec-kit-pr-bridge-](https://github.com/Quratulain-bilal/spec-kit-pr-bridge-) |
@@ -105,7 +109,7 @@ The following community-contributed extensions are available in [`catalog.commun
 | Retro Extension | Sprint retrospective analysis with metrics, spec accuracy assessment, and improvement suggestions | `process` | Read+Write | [spec-kit-retro](https://github.com/arunt14/spec-kit-retro) |
 | Retrospective Extension | Post-implementation retrospective with spec adherence scoring, drift analysis, and human-gated spec updates | `docs` | Read+Write | [spec-kit-retrospective](https://github.com/emi-dm/spec-kit-retrospective) |
 | Review Extension | Post-implementation comprehensive code review with specialized agents for code quality, comments, tests, error handling, type design, and simplification | `code` | Read-only | [spec-kit-review](https://github.com/ismaelJimenez/spec-kit-review) |
-| Ripple | Detect side effects that tests can't catch after implementation — delta-anchored analysis across 9 domain-agnostic categories | `code` | Read+Write | [spec-kit-ripple](https://github.com/chordpli/spec-kit-ripple) |
+| Ripple | Detect side effects that tests can't catch after implementation — surface hidden ripple effects across 9 analysis categories | `code` | Read+Write | [spec-kit-ripple](https://github.com/chordpli/spec-kit-ripple) |
 | SDD Utilities | Resume interrupted workflows, validate project health, and verify spec-to-task traceability | `process` | Read+Write | [speckit-utils](https://github.com/mvanhorn/speckit-utils) |
 | Security Review | Full-project secure-by-design security audits plus staged, branch/PR, plan, task, follow-up, and apply reviews | `code` | Read+Write | [spec-kit-security-review](https://github.com/DyanGalih/spec-kit-security-review) |
 | SFSpeckit | Enterprise Salesforce SDLC with 18 commands for the full SDD lifecycle. | `process` | Read+Write | [spec-kit-sf](https://github.com/ysumanth06/spec-kit-sf) |
@@ -114,6 +118,7 @@ The following community-contributed extensions are available in [`catalog.commun
 | Spec Critique Extension | Dual-lens critical review of spec and plan from product strategy and engineering risk perspectives | `docs` | Read-only | [spec-kit-critique](https://github.com/arunt14/spec-kit-critique) |
 | Spec Diagram | Auto-generate Mermaid diagrams of SDD workflow state, feature progress, and task dependencies | `visibility` | Read-only | [spec-kit-diagram-](https://github.com/Quratulain-bilal/spec-kit-diagram-) |
 | Spec Kit Discovery Extension | Run technical discovery commands for feasibility, technology selection, scenario-specific technical decisions, legacy codebase assessment, implementation understanding, and proof-of-concept validation | `process` | Read+Write | [spec-kit-discovery](https://github.com/bigsmartben/spec-kit-discovery) |
+| Spec Kit Figma | Agent-agnostic SpecKit extension that grounds spec, plan & task generation in Figma design context — REST + optional MCP, single/mono/multi-repo, macOS/Linux/Windows. | `integration` | Read+Write | [spec-kit-figma](https://github.com/Fyloss/spec-kit-figma) |
 | Spec Kit Preview | Generate evidence-backed low, mid, or high fidelity previews from Spec Kit artifacts as Markdown or self-contained HTML | `docs` | Read+Write | [spec-kit-preview](https://github.com/bigsmartben/spec-kit-preview) |
 | Spec Kit Schedule | Optimal multi-agent task scheduling via CP-SAT — DAG precedence, hallucination-aware caps, file-conflict avoidance, stochastic durations, replanning, and interactive HTML output | `process` | Read+Write | [spec-kit-schedule](https://github.com/jfranc38/spec-kit-schedule) |
 | Spec Kit TLDR | Render a feature's spec.md / plan.md into a review-oriented TLDR (self-contained HTML dashboard + PR-native Markdown) that surfaces risks for faster PR review. | `visibility` | Read+Write | [speckit-tldr](https://github.com/qurore/speckit-tldr) |
@@ -143,6 +148,7 @@ The following community-contributed extensions are available in [`catalog.commun
 | Token Economy | Token routing, measured savings, and context audit workflows | `process` | Read+Write | [spec-kit-token-economy](https://github.com/formin/spec-kit-token-economy) |
 | 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 Review Ship | Adds post-implementation verify, review, and ship readiness gates to Spec Kit workflows | `process` | Read-only | [spec-kit-verify-review-ship](https://github.com/cadugevaerd/spec-kit-verify-review-ship) |
 | 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) |
 | Version Guard | Verify tech stack versions against live npm registries before planning and implementation | `process` | Read-only | [spec-kit-version-guard](https://github.com/KevinBrown5280/spec-kit-version-guard) |
 | What-if Analysis | Preview the downstream impact (complexity, effort, tasks, risks) of requirement changes before committing to them | `visibility` | Read-only | [spec-kit-whatif](https://github.com/DevAbdullah90/spec-kit-whatif) |

docs/community/friends.md

@@ -14,3 +14,5 @@ Community projects that extend, visualize, or build on Spec Kit:
 - **[SpecKit Companion](https://marketplace.visualstudio.com/items?itemName=alfredoperez.speckit-companion)** — A VS Code extension that brings a visual GUI to Spec Kit. Browse specs in a rich markdown viewer with clickable file references, create specifications with image attachments, comment and refine each step inline (GitHub-style review), track your progress through the SDD workflow with a visual phase stepper, and manage steering documents like constitutions and templates.
 
 - **[cc-spec-kit](https://github.com/speckit-community/cc-spec-kit)** — Community-maintained plugin for Claude Code and GitHub Copilot CLI that installs Spec Kit skills via the plugin marketplace.
+
+- **[spectatui](https://github.com/tinesoft/spectatui)** — A terminal UI (TUI) dashboard for Spec Kit that lets you track features, manage specifications, integrations, presets, workflows, and extensions, and monitor AI agent workflows. Attach to existing AI sessions or launch new ones from your terminal. Keyboard and mouse support. Light/dark theme support. Customizable and performance-oriented. Requires the `specify` CLI in your PATH.

docs/install/one-time.md

@@ -11,7 +11,8 @@ If you want to try Spec Kit without installing it permanently, use `uvx` to run
 # Create a new project (latest from main)
 uvx --from git+https://github.com/github/spec-kit.git specify init <PROJECT_NAME>
 
-# Or target a specific release (replace vX.Y.Z with a tag from Releases)
+# Or target a specific release (replace vX.Y.Z with a tag from Releases;
+# keep the leading v, e.g. v0.12.11 not 0.12.11)
 uvx --from git+https://github.com/github/spec-kit.git@vX.Y.Z specify init <PROJECT_NAME>
 
 # Initialize in the current directory

docs/install/pipx.md

@@ -7,7 +7,8 @@
 Pin a specific release tag for stability (check [Releases](https://github.com/github/spec-kit/releases) for the latest):
 
 ```bash
-# Install a specific stable release (recommended — replace vX.Y.Z with the latest tag)
+# Install a specific stable release (recommended — replace vX.Y.Z with the
+# latest tag, keeping the leading v, e.g. v0.12.11 not 0.12.11)
 pipx install git+https://github.com/github/spec-kit.git@vX.Y.Z
 
 # Or install latest from main (may include unreleased changes)

docs/installation.md

@@ -15,7 +15,7 @@
 
 ### Persistent Installation (Recommended)
 
-Install once and use everywhere. Replace `vX.Y.Z` with a tag from [Releases](https://github.com/github/spec-kit/releases):
+Install once and use everywhere. Replace `vX.Y.Z` with a release tag from [Releases](https://github.com/github/spec-kit/releases) — keep the leading `v` (for example, `v0.12.11`, not `0.12.11`):
 
 > [!NOTE]
 > The command below requires **[uv](https://docs.astral.sh/uv/)**. If you see `command not found: uv`, [install uv first](./install/uv.md).

docs/reference/bundles.md

@@ -51,10 +51,11 @@ If the current directory is not yet a Spec Kit project, `install` initializes on
 specify bundle update [<bundle_id>]
 ```
 
-| Option       | Description                          |
-| ------------ | ------------------------------------ |
-| `--all`      | Update every installed bundle        |
-| `--offline`  | Do not access the network            |
+| Option           | Description                                                                                                            |
+| ---------------- | --------------------------------------------------------------------------------------------------------------------- |
+| `--all`          | Update every installed bundle                                                                                         |
+| `--integration`  | Override the integration used when refreshing components; applied only when the project's active integration can't be determined |
+| `--offline`      | Do not access the network                                                                                             |
 
 Re-resolves a bundle and **refreshes** its components through each primitive's update path, bringing already-installed components up to the bundle's newly pinned versions while preserving primitive-level overrides (such as preset priority). Provide a bundle id, or use `--all` to update everything installed.
 

docs/reference/extensions.md

@@ -26,7 +26,7 @@ specify extension add <name>
 | --------------- | -------------------------------------------------------- |
 | `--dev`         | Install from a local directory (for development)         |
 | `--from <url>`  | Install from a custom URL instead of the catalog         |
-| `--force`       | Overwrite if already installed                           |
+| `--force`       | Overwrite if the extension is already installed          |
 | `--priority <N>`| Resolution priority (default: 10; lower = higher precedence) |
 
 Installs an extension from the catalog, a URL, or a local directory. Extension commands are automatically registered with the currently installed AI coding agent integration.

docs/reference/integrations.md

@@ -18,13 +18,13 @@ The Specify CLI supports a wide range of AI coding agents. When you run `specify
 | [Firebender](https://firebender.com/)                                                | `firebender`     | IDE-based agent for Android Studio / IntelliJ                                                                                             |
 | [Forge](https://forgecode.dev/)                                                      | `forge`          |                                                                                                                                           |
 | [Gemini CLI](https://github.com/google-gemini/gemini-cli)                            | `gemini`         |                                                                                                                                           |
-| [GitHub Copilot](https://code.visualstudio.com/)                                     | `copilot`        |                                                                                                                                           |
+| [GitHub Copilot](https://code.visualstudio.com/)                                     | `copilot`        | Defaults to legacy markdown mode: `.agent.md` command files under `.github/agents/`, companion `.prompt.md` files under `.github/prompts/`, and a `.vscode/settings.json` merge. Pass `--integration-options="--skills"` to scaffold skills as `speckit-<command>/SKILL.md` under `.github/skills/` instead. Legacy markdown mode is deprecated and will stop being the default in a future release. |
 | [Goose](https://goose-docs.ai/)                                                      | `goose`          | Uses YAML recipe format in `.goose/recipes/`                                                                                              |
 | [Hermes](https://github.com/NousResearch/hermes-agent)                               | `hermes`         | Skills-based integration; installs skills globally into `~/.hermes/skills/`                                                                |
 | [IBM Bob](https://www.ibm.com/products/bob)                                          | `bob`            | IDE-based agent                                                                                                                           |
 | [Junie](https://junie.jetbrains.com/)                                                | `junie`          |                                                                                                                                           |
 | [Kilo Code](https://github.com/Kilo-Org/kilocode)                                    | `kilocode`       |                                                                                                                                           |
-| [Kimi Code](https://code.kimi.com/)                                                  | `kimi`           | Skills-based integration; installs into `.kimi-code/skills/`. `--migrate-legacy` moves old `.kimi/skills/` installs to the new paths, and (when the `agent-context` extension is enabled) migrates `KIMI.md` context into `AGENTS.md` |
+| [Kimi Code](https://code.kimi.com/)                                                  | `kimi`           | Skills-based integration; installs into `.kimi-code/skills/`. `--migrate-legacy` moves old `.kimi/skills/` installs to the new paths |
 | [Kiro CLI](https://kiro.dev/docs/cli/)                                               | `kiro-cli`       | Kiro CLI does not substitute `$ARGUMENTS` in file-based prompts, so Spec Kit ships a prose fallback at render time (see [Manage prompts](https://kiro.dev/docs/cli/chat/manage-prompts/) and issue [#1926](https://github.com/github/spec-kit/issues/1926)). Alias: `--integration kiro` |
 | [Lingma](https://lingma.aliyun.com/)                                                 | `lingma`         | Skills-based integration; skills are installed automatically                                                                               |
 | [Mistral Vibe](https://github.com/mistralai/mistral-vibe)                            | `vibe`           |                                                                                                                                           |
@@ -218,7 +218,8 @@ Some integrations accept additional options via `--integration-options`:
 | Integration | Option              | Description                                                    |
 | ----------- | ------------------- | -------------------------------------------------------------- |
 | `generic`   | `--commands-dir`    | Required. Directory for command files                          |
-| `kimi`      | `--migrate-legacy`  | Migrate legacy `.kimi/skills/` installs to `.kimi-code/skills/` (including dotted→hyphenated directory names); when the `agent-context` extension is enabled, also migrates `KIMI.md` to `AGENTS.md` |
+| `kimi`      | `--migrate-legacy`  | Migrate legacy `.kimi/skills/` installs to `.kimi-code/skills/` (including dotted→hyphenated skill naming, e.g. `speckit.xxx` → `speckit-xxx`) |
+| `copilot`   | `--skills`          | Scaffold commands as agent skills (`speckit-<command>/SKILL.md` under `.github/skills/`, invoked as `/speckit-<command>`) instead of the default legacy markdown mode (`.github/agents/*.agent.md` plus `.github/prompts/*.prompt.md` and a `.vscode/settings.json` merge). Without this flag, install warns that legacy markdown mode is deprecated. |
 
 Example:
 

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

@@ -15,7 +15,7 @@ The script reads the agent-context extension config at
 - `context_files` — optional project-relative paths for multiple coding agent context files. When non-empty, the script updates each listed file and the list takes precedence over `context_file`.
 - `context_markers.start` / `.end` — the delimiters surrounding the managed section. Defaults to `<!-- SPECKIT START -->` and `<!-- SPECKIT END -->` when the field is missing.
 
-It then creates, replaces, or appends the managed block so that the section points at the most recent plan path when one can be discovered (`specs/<feature>/plan.md`).
+It then creates, replaces, or appends the managed block so that the section points at the most recent plan path when one can be discovered (any `plan.md` under `specs/`, including nested scoped layouts such as `specs/<scope>/<feature>/plan.md`).
 
 If `context_files` and `context_file` are empty, the command reports nothing to do and exits successfully. Context file paths must stay project-relative; absolute paths, Windows drive paths, backslash separators, and `..` path segments are rejected.
 
@@ -24,4 +24,4 @@ If `context_files` and `context_file` are empty, the command reports nothing to
 - **Bash**: `.specify/extensions/agent-context/scripts/bash/update-agent-context.sh [plan_path]`
 - **PowerShell**: `.specify/extensions/agent-context/scripts/powershell/update-agent-context.ps1 [plan_path]`
 
-When `plan_path` is omitted, the script auto-detects the most recently modified `specs/*/plan.md`.
+When `plan_path` is omitted, the script auto-detects the most recently modified `specs/**/plan.md` (searched recursively, so nested scoped layouts are discovered).

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

@@ -12,7 +12,7 @@
 #
 # When `plan_path` is omitted, the script derives it from `.specify/feature.json`
 # (written by /speckit-specify). Falls back to the most recently modified
-# `specs/*/plan.md` only when feature.json is absent or its plan does not exist yet.
+# `specs/**/plan.md` only when feature.json is absent or its plan does not exist yet.
 
 set -euo pipefail
 
@@ -307,16 +307,28 @@ import sys
 from pathlib import Path
 root = Path(sys.argv[1]).resolve()
 specs = root / "specs"
-plans = sorted(
-    specs.glob("*/plan.md"),
-    key=lambda p: p.stat().st_mtime,
-    reverse=True,
-)
-if plans:
+
+def _resolved_rel(p):
+    # Resolve symlinks before checking containment: relative_to() is lexical
+    # and would otherwise accept a plan reached through a specs/ symlink that
+    # points outside the project, emitting an in-project-looking path for an
+    # out-of-project file (or picking it as "most recent").
     try:
-        print(plans[0].relative_to(root).as_posix())
-    except ValueError:
-        print("")
+        return p.resolve().relative_to(root)
+    except (OSError, ValueError):
+        return None
+
+# Recurse (rather than the old one-level specs/*/plan.md glob) so scoped layouts
+# created via SPECIFY_FEATURE_DIRECTORY, e.g. specs/<scope>/<feature>/plan.md,
+# are still discovered when feature.json is absent (#3024).
+candidates = []
+for p in specs.rglob("plan.md"):
+    rel = _resolved_rel(p)
+    if rel:
+        candidates.append((p, rel))
+candidates.sort(key=lambda pr: pr[0].stat().st_mtime, reverse=True)
+if candidates:
+    print(candidates[0][1].as_posix())
 else:
     print("")
 PY

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

@@ -12,7 +12,7 @@
 #
 # When `plan_path` is omitted, the script derives it from `.specify/feature.json`
 # (written by /speckit-specify). Falls back to the most recently modified
-# `specs/*/plan.md` only when feature.json is absent or its plan does not exist yet.
+# `specs/**/plan.md` only when feature.json is absent or its plan does not exist yet.
 
 [CmdletBinding()]
 param(
@@ -426,9 +426,11 @@ if (-not $PlanPath) {
     if (-not $PlanPath) {
         try {
             $specsDir = Join-Path $ProjectRoot 'specs'
-            $candidate = Get-ChildItem -Path $specsDir -Directory -ErrorAction SilentlyContinue |
-                ForEach-Object { Get-Item -LiteralPath (Join-Path $_.FullName 'plan.md') -ErrorAction SilentlyContinue } |
-                Where-Object { $_ } |
+            # Recurse (rather than the old one-level specs/*/plan.md scan) so scoped
+            # layouts created via SPECIFY_FEATURE_DIRECTORY, e.g.
+            # specs/<scope>/<feature>/plan.md, are still discovered when
+            # feature.json is absent (#3024).
+            $candidate = Get-ChildItem -Path $specsDir -Filter 'plan.md' -File -Recurse -ErrorAction SilentlyContinue |
                 Sort-Object LastWriteTime -Descending |
                 Select-Object -First 1
             if ($candidate) {

extensions/agent-context/scripts/python/update_agent_context.py

@@ -0,0 +1,352 @@
+#!/usr/bin/env python3
+"""Refresh the managed Spec Kit section in the coding agent's context file(s).
+
+Python port of ``update-agent-context.sh`` / ``update-agent-context.ps1``.
+
+Reads ``context_files`` or ``context_file``, plus ``context_markers.{start,end}``,
+from the agent-context extension config:
+    .specify/extensions/agent-context/agent-context-config.yml
+
+Usage: update_agent_context.py [plan_path]
+
+When ``plan_path`` is omitted, the script derives it from
+``.specify/feature.json`` (written by /speckit-specify). Falls back to the most
+recently modified ``specs/*/plan.md`` only when feature.json is absent or its
+plan does not exist yet.
+"""
+
+from __future__ import annotations
+
+import json
+import os
+import re
+import sys
+from pathlib import Path
+
+DEFAULT_START = "<!-- SPECKIT START -->"
+DEFAULT_END = "<!-- SPECKIT END -->"
+
+
+def _err(message: str) -> None:
+    print(message, file=sys.stderr)
+
+
+def _get_str(obj: object, *keys: str) -> str:
+    node = obj
+    for key in keys:
+        if isinstance(node, dict) and key in node:
+            node = node[key]
+        else:
+            return ""
+    return node if isinstance(node, str) else ""
+
+
+def _collect_context_files(data: dict, project_root: str) -> list[str]:
+    """Resolve the managed context files from config, mirroring the bash logic."""
+    context_files: list[str] = []
+    seen: set[str] = set()
+    case_insensitive = sys.platform.startswith(("win32", "cygwin", "msys"))
+
+    def add(value: object) -> None:
+        if not isinstance(value, str):
+            return
+        candidate = value.strip()
+        if not candidate:
+            return
+        key = candidate.casefold() if case_insensitive else candidate
+        if key in seen:
+            return
+        context_files.append(candidate)
+        seen.add(key)
+
+    raw_files = data.get("context_files")
+    if isinstance(raw_files, list):
+        for value in raw_files:
+            add(value)
+    if not context_files:
+        add(_get_str(data, "context_file"))
+    if not context_files:
+        # Self-seed: when the config declares no target, derive one from the
+        # active integration recorded in init-options.json, mapped through the
+        # bundled agent-context-defaults.json file. Independent of the Specify
+        # CLI by design.
+        integration_key = ""
+        try:
+            with open(
+                f"{project_root}/.specify/init-options.json", "r", encoding="utf-8"
+            ) as fh:
+                opts = json.load(fh)
+            if isinstance(opts, dict):
+                value = opts.get("integration") or opts.get("ai") or ""
+                integration_key = value if isinstance(value, str) else ""
+        except Exception:
+            integration_key = ""
+        if integration_key:
+            defaults_path = (
+                f"{project_root}/.specify/extensions/agent-context/"
+                "agent-context-defaults.json"
+            )
+            mapping = {}
+            try:
+                with open(defaults_path, "r", encoding="utf-8") as fh:
+                    loaded = json.load(fh)
+                agents = loaded.get("agents", {}) if isinstance(loaded, dict) else {}
+                mapping = agents if isinstance(agents, dict) else {}
+            except Exception:
+                _err(
+                    "agent-context: unable to read %s; cannot self-seed the context "
+                    "file. Set context_file in the extension config." % defaults_path
+                )
+                mapping = {}
+            add(mapping.get(integration_key, "") or "")
+            if not context_files:
+                _err(
+                    "agent-context: no default context file is known for integration "
+                    "%s. Set context_file in the extension config to choose one."
+                    % integration_key
+                )
+    return context_files
+
+
+def _validate_context_file(project_root: str, context_file: str) -> str | None:
+    """Return an error message when the path escapes the project root."""
+    if context_file.startswith("/") or re.match(r"^[A-Za-z]:", context_file):
+        return (
+            "agent-context: context files must be project-relative paths; "
+            f"got '{context_file}'."
+        )
+    if "\\" in context_file:
+        return (
+            "agent-context: context files must not contain backslash separators; "
+            f"got '{context_file}'."
+        )
+    if ".." in context_file.split("/"):
+        return (
+            "agent-context: context files must not contain '..' path segments; "
+            f"got '{context_file}'."
+        )
+    root = Path(project_root).resolve()
+    target = (root / context_file).resolve()
+    try:
+        target.relative_to(root)
+    except ValueError:
+        return (
+            "agent-context: context file path resolves outside the project root; "
+            f"got '{context_file}'."
+        )
+    return None
+
+
+def _resolve_plan_path(project_root: str) -> str:
+    """Derive the plan path: feature.json first, then the mtime fallback."""
+    plan_path = ""
+    feature_json = Path(project_root) / ".specify" / "feature.json"
+    if feature_json.is_file():
+        feature_dir = ""
+        try:
+            with open(feature_json, "r", encoding="utf-8") as fh:
+                data = json.load(fh)
+            value = data.get("feature_directory", "")
+            feature_dir = value if isinstance(value, str) else ""
+        except Exception:
+            feature_dir = ""
+        # Normalize backslashes (written by PS on Windows) before path ops.
+        feature_dir = feature_dir.replace("\\", "/").rstrip("/")
+        if feature_dir:
+            # feature_directory may be relative or absolute (absolute paths
+            # outside the project root are preserved as-is), including
+            # drive-qualified paths (C:/...) written by PowerShell on Windows.
+            if feature_dir.startswith("/") or re.match(r"^[A-Za-z]:/", feature_dir):
+                candidate = Path(feature_dir) / "plan.md"
+            else:
+                candidate = Path(project_root) / feature_dir / "plan.md"
+            if candidate.is_file():
+                # Resolve symlinks before comparing so paths like /var/… vs
+                # /private/var/… (macOS) are treated as equivalent.
+                root = Path(project_root).resolve()
+                resolved = candidate.resolve()
+                try:
+                    plan_path = resolved.relative_to(root).as_posix()
+                except ValueError:
+                    plan_path = resolved.as_posix()
+
+    if not plan_path:
+        root = Path(project_root).resolve()
+        plans = sorted(
+            (root / "specs").glob("*/plan.md"),
+            key=lambda p: p.stat().st_mtime,
+            reverse=True,
+        )
+        if plans:
+            try:
+                plan_path = plans[0].relative_to(root).as_posix()
+            except ValueError:
+                plan_path = ""
+    return plan_path
+
+
+def _build_section(marker_start: str, marker_end: str, plan_path: str) -> str:
+    lines = [
+        marker_start,
+        "For additional context about technologies to be used, project structure,",
+        "shell commands, and other important information, read the current plan",
+    ]
+    if plan_path:
+        lines.append(f"at {plan_path}")
+    lines.append(marker_end)
+    return "\n".join(lines) + "\n"
+
+
+def ensure_mdc_frontmatter(content: str) -> str:
+    """Ensure ``.mdc`` content has YAML frontmatter with ``alwaysApply: true``.
+
+    Cursor only auto-loads ``.mdc`` rule files that carry frontmatter with
+    ``alwaysApply: true``. Prepend it when missing, or repair the value while
+    preserving any existing frontmatter comments/formatting.
+    """
+    leading_ws = len(content) - len(content.lstrip())
+    leading = content[:leading_ws]
+    stripped = content[leading_ws:]
+
+    if not stripped.startswith("---"):
+        return "---\nalwaysApply: true\n---\n\n" + content
+
+    match = re.match(
+        r"^(---[ \t]*\r?\n)(.*?)(\r?\n---[ \t]*)(\r?\n|$)(.*)",
+        stripped,
+        re.DOTALL,
+    )
+    if not match:
+        return "---\nalwaysApply: true\n---\n\n" + content
+
+    opening, fm_text, closing, sep, rest = match.groups()
+    newline = "\r\n" if "\r\n" in opening else "\n"
+
+    if re.search(r"(?m)^[ \t]*alwaysApply[ \t]*:[ \t]*true[ \t]*(?:#.*)?$", fm_text):
+        return content
+
+    if re.search(r"(?m)^[ \t]*alwaysApply[ \t]*:", fm_text):
+        fm_text = re.sub(
+            r"(?m)^([ \t]*)alwaysApply[ \t]*:.*?([ \t]*(?:#.*)?)$",
+            r"\1alwaysApply: true\2",
+            fm_text,
+            count=1,
+        )
+    elif fm_text.strip():
+        fm_text = fm_text + newline + "alwaysApply: true"
+    else:
+        fm_text = "alwaysApply: true"
+
+    return f"{leading}{opening}{fm_text}{closing}{sep}{rest}"
+
+
+def _upsert_section(
+    ctx_path: str, marker_start: str, marker_end: str, section: str
+) -> None:
+    """Insert or replace the managed section, then normalize and write."""
+    if os.path.exists(ctx_path):
+        with open(ctx_path, "r", encoding="utf-8-sig") as fh:
+            content = fh.read()
+        s = content.find(marker_start)
+        e = content.find(marker_end, s if s != -1 else 0)
+        if s != -1 and e != -1 and e > s:
+            end_of_marker = e + len(marker_end)
+            if end_of_marker < len(content) and content[end_of_marker] == "\r":
+                end_of_marker += 1
+            if end_of_marker < len(content) and content[end_of_marker] == "\n":
+                end_of_marker += 1
+            new_content = content[:s] + section + content[end_of_marker:]
+        elif s != -1:
+            new_content = content[:s] + section
+        elif e != -1:
+            end_of_marker = e + len(marker_end)
+            if end_of_marker < len(content) and content[end_of_marker] == "\r":
+                end_of_marker += 1
+            if end_of_marker < len(content) and content[end_of_marker] == "\n":
+                end_of_marker += 1
+            new_content = section + content[end_of_marker:]
+        else:
+            if content and not content.endswith("\n"):
+                content += "\n"
+            new_content = (content + "\n" + section) if content else section
+    else:
+        new_content = section
+
+    new_content = new_content.replace("\r\n", "\n").replace("\r", "\n")
+    if ctx_path.casefold().endswith(".mdc"):
+        new_content = ensure_mdc_frontmatter(new_content)
+    with open(ctx_path, "wb") as fh:
+        fh.write(new_content.encode("utf-8"))
+
+
+def main(argv: list[str] | None = None) -> int:
+    args = sys.argv[1:] if argv is None else argv
+    project_root = os.getcwd()
+    ext_config = (
+        f"{project_root}/.specify/extensions/agent-context/agent-context-config.yml"
+    )
+
+    if not os.path.isfile(ext_config):
+        _err(f"agent-context: {ext_config} not found; nothing to do.")
+        return 0
+
+    try:
+        import yaml
+    except ImportError:
+        _err(
+            "agent-context: PyYAML is required to parse extension config but is "
+            "not available in the current Python environment.\n"
+            "  To resolve: pip install pyyaml (or install it into the environment "
+            "used by python3).\n"
+            "  Context file will not be updated until PyYAML is importable."
+        )
+        _err("agent-context: skipping update (see above for details).")
+        return 0
+
+    try:
+        with open(ext_config, "r", encoding="utf-8") as fh:
+            data = yaml.safe_load(fh)
+    except Exception as exc:
+        _err(
+            f"agent-context: unable to parse {ext_config} ({exc}); "
+            "cannot update context."
+        )
+        _err("agent-context: skipping update (see above for details).")
+        return 0
+    if not isinstance(data, dict):
+        data = {}
+
+    context_files = _collect_context_files(data, project_root)
+    if not context_files:
+        _err(
+            "agent-context: context_files/context_file not set in extension config; "
+            "nothing to do."
+        )
+        return 0
+
+    for context_file in context_files:
+        error = _validate_context_file(project_root, context_file)
+        if error:
+            _err(error)
+            return 1
+
+    marker_start = _get_str(data, "context_markers", "start") or DEFAULT_START
+    marker_end = _get_str(data, "context_markers", "end") or DEFAULT_END
+
+    plan_path = args[0] if args else ""
+    if not plan_path:
+        plan_path = _resolve_plan_path(project_root)
+
+    section = _build_section(marker_start, marker_end, plan_path)
+
+    for context_file in context_files:
+        ctx_path = os.path.join(project_root, context_file)
+        os.makedirs(os.path.dirname(ctx_path) or ".", exist_ok=True)
+        _upsert_section(ctx_path, marker_start, marker_end, section)
+        print(f"agent-context: updated {context_file}")
+
+    return 0
+
+
+if __name__ == "__main__":
+    sys.exit(main())

extensions/catalog.community.json

@@ -1,6 +1,6 @@
 {
   "schema_version": "1.0",
-  "updated_at": "2026-07-01T00:00:00Z",
+  "updated_at": "2026-07-10T00:00:00Z",
   "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/extensions/catalog.community.json",
   "extensions": {
     "aide": {
@@ -670,6 +670,40 @@
       "created_at": "2026-04-11T18:00:00Z",
       "updated_at": "2026-04-11T18:00:00Z"
     },
+    "charter": {
+      "name": "Charter",
+      "id": "charter",
+      "description": "Compose modular project constitutions from shared fragment registries. Centralize governance rules, select per-project fragments, track upstream changes, and keep multi-project setups consistent.",
+      "author": "Fyloss",
+      "version": "0.3.1",
+      "download_url": "https://github.com/Fyloss/spec-kit-charter/archive/refs/tags/v0.3.1.zip",
+      "repository": "https://github.com/Fyloss/spec-kit-charter",
+      "homepage": "https://github.com/Fyloss/spec-kit-charter",
+      "documentation": "https://github.com/Fyloss/spec-kit-charter/tree/master/docs",
+      "changelog": "https://github.com/Fyloss/spec-kit-charter/blob/master/CHANGELOG.md",
+      "license": "MIT",
+      "category": "process",
+      "effect": "read-write",
+      "requires": {
+        "speckit_version": ">=0.11.9"
+      },
+      "provides": {
+        "commands": 5,
+        "hooks": 1
+      },
+      "tags": [
+        "constitution",
+        "governance",
+        "modular",
+        "fragments",
+        "registry"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-07-06T00:00:00Z",
+      "updated_at": "2026-07-06T00:00:00Z"
+    },
     "ci-guard": {
       "name": "CI Guard",
       "id": "ci-guard",
@@ -1072,10 +1106,10 @@
     "docguard": {
       "name": "DocGuard — CDD Enforcement",
       "id": "docguard",
-      "description": "Canonical-Driven Development enforcement. Validates, scores, and traces project documentation with automated checks, AI-driven workflows, and spec-kit hooks. One pinned runtime dependency; pure Node.js otherwise.",
+      "description": "The only doc-integrity engine with an MCP server, SARIF output, and a deterministic zero-LLM core. Validates, scores, and traces documentation against code — 24 validators, stable finding codes, GitHub Action with PR annotations, spec-kit hooks. Pure Node.js, one pinned dep.",
       "author": "raccioly",
-      "version": "0.28.0",
-      "download_url": "https://github.com/raccioly/docguard/releases/download/v0.28.0/spec-kit-docguard-v0.28.0.zip",
+      "version": "0.30.0",
+      "download_url": "https://github.com/raccioly/docguard/releases/download/v0.30.0/spec-kit-docguard-v0.30.0.zip",
       "repository": "https://github.com/raccioly/docguard",
       "homepage": "https://www.npmjs.com/package/docguard-cli",
       "documentation": "https://github.com/raccioly/docguard/blob/main/extensions/spec-kit-docguard/README.md",
@@ -1111,7 +1145,7 @@
       "downloads": 0,
       "stars": 0,
       "created_at": "2026-03-13T00:00:00Z",
-      "updated_at": "2026-06-23T00:00:00Z"
+      "updated_at": "2026-07-06T00:00:00Z"
     },
     "doctor": {
       "name": "Project Health Check",
@@ -1146,6 +1180,39 @@
       "created_at": "2026-03-13T00:00:00Z",
       "updated_at": "2026-03-13T00:00:00Z"
     },
+    "ears": {
+      "name": "EARS Requirements Syntax",
+      "id": "ears",
+      "description": "Author, lint, and convert requirements using EARS (Easy Approach to Requirements Syntax) - the five industry-standard sentence patterns for unambiguous, testable requirements.",
+      "author": "dhruv-15-03",
+      "version": "1.0.0",
+      "download_url": "https://github.com/dhruv-15-03/spec-kit-ears/archive/refs/tags/v1.0.0.zip",
+      "repository": "https://github.com/dhruv-15-03/spec-kit-ears",
+      "homepage": "https://github.com/dhruv-15-03/spec-kit-ears",
+      "documentation": "https://github.com/dhruv-15-03/spec-kit-ears/blob/main/README.md",
+      "changelog": "https://github.com/dhruv-15-03/spec-kit-ears/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "category": "docs",
+      "effect": "read-write",
+      "requires": {
+        "speckit_version": ">=0.9.0"
+      },
+      "provides": {
+        "commands": 3,
+        "hooks": 0
+      },
+      "tags": [
+        "ears",
+        "requirements",
+        "specification",
+        "quality"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-07-08T00:00:00Z",
+      "updated_at": "2026-07-08T00:00:00Z"
+    },
     "extensify": {
       "name": "Extensify",
       "id": "extensify",
@@ -1179,6 +1246,47 @@
       "created_at": "2026-03-18T00:00:00Z",
       "updated_at": "2026-04-23T00:00:00Z"
     },
+    "figma": {
+      "name": "Spec Kit Figma",
+      "id": "figma",
+      "description": "Agent-agnostic SpecKit extension that grounds spec, plan & task generation in Figma design context — REST + optional MCP, single/mono/multi-repo, macOS/Linux/Windows.",
+      "author": "Fyloss",
+      "version": "1.6.0",
+      "download_url": "https://github.com/Fyloss/spec-kit-figma/archive/refs/tags/v1.6.0.zip",
+      "repository": "https://github.com/Fyloss/spec-kit-figma",
+      "homepage": "https://github.com/Fyloss/spec-kit-figma",
+      "documentation": "https://github.com/Fyloss/spec-kit-figma/blob/main/docs/INSTALL.md",
+      "changelog": "https://github.com/Fyloss/spec-kit-figma/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "category": "integration",
+      "effect": "read-write",
+      "requires": {
+        "speckit_version": ">=0.1.0",
+        "tools": [
+          { "name": "git", "required": true },
+          { "name": "bash", "required": false },
+          { "name": "curl", "required": false },
+          { "name": "jq", "required": false },
+          { "name": "pwsh", "required": false }
+        ]
+      },
+      "provides": {
+        "commands": 5,
+        "hooks": 6
+      },
+      "tags": [
+        "figma",
+        "design",
+        "frontend",
+        "ui",
+        "design-system"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-07-08T00:00:00Z",
+      "updated_at": "2026-07-08T00:00:00Z"
+    },
     "fix-findings": {
       "name": "Fix Findings",
       "id": "fix-findings",
@@ -1364,10 +1472,10 @@
     "golden-demo": {
       "name": "Golden Demo",
       "id": "golden-demo",
-      "description": "Extracts acceptance criteria from specs, builds test vectors, and produces a behavioral drift report — complementary to Architecture Guard and CDD.",
+      "description": "Deterministic behavioral drift oracle. Extracts acceptance criteria, generates fuzz test vectors (seed=42), compares golden Python implementations against real code in any language. CI/CD gatekeeper with warn/strict modes.",
       "author": "jasstt",
-      "version": "0.1.1",
-      "download_url": "https://github.com/jasstt/spec-kit-golden-demo/archive/refs/tags/v0.1.1.zip",
+      "version": "0.3.0",
+      "download_url": "https://github.com/jasstt/spec-kit-golden-demo/archive/refs/tags/v0.3.0.zip",
       "repository": "https://github.com/jasstt/spec-kit-golden-demo",
       "homepage": "https://github.com/jasstt/spec-kit-golden-demo",
       "documentation": "https://github.com/jasstt/spec-kit-golden-demo",
@@ -1378,13 +1486,16 @@
         "speckit_version": ">=0.1.0"
       },
       "provides": {
-        "commands": 2,
+        "commands": 3,
         "hooks": 2
       },
       "tags": [
         "testing",
         "drift-detection",
         "behavioral-oracle",
+        "fuzzing",
+        "ci-cd",
+        "cross-language",
         "tdd",
         "quality"
       ],
@@ -1392,7 +1503,7 @@
       "downloads": 0,
       "stars": 0,
       "created_at": "2026-06-24T00:00:00Z",
-      "updated_at": "2026-06-24T00:00:00Z"
+      "updated_at": "2026-07-07T00:00:00Z"
     },
     "harness": {
       "name": "Research Harness",
@@ -2362,6 +2473,39 @@
       "created_at": "2026-04-03T00:00:00Z",
       "updated_at": "2026-04-03T00:00:00Z"
     },
+    "orchestration-task-context-management": {
+      "name": "Orchestration Task Context Management",
+      "id": "orchestration-task-context-management",
+      "description": "Adds subagent work-unit orchestration to generated Spec Kit task files",
+      "author": "Igor Benicio de Mesquita",
+      "version": "0.0.0",
+      "download_url": "https://github.com/benizzio/spec-kit-orchestration-task-context-management/archive/refs/tags/v0.0.0.zip",
+      "repository": "https://github.com/benizzio/spec-kit-orchestration-task-context-management",
+      "homepage": "https://github.com/benizzio/spec-kit-orchestration-task-context-management",
+      "documentation": "https://github.com/benizzio/spec-kit-orchestration-task-context-management/blob/main/README.md",
+      "changelog": "https://github.com/benizzio/spec-kit-orchestration-task-context-management/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "category": "process",
+      "effect": "read-write",
+      "requires": {
+        "speckit_version": ">=0.7.2"
+      },
+      "provides": {
+        "commands": 2,
+        "hooks": 2
+      },
+      "tags": [
+        "agent",
+        "orchestration",
+        "tasks",
+        "context"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-07-06T00:00:00Z",
+      "updated_at": "2026-07-06T00:00:00Z"
+    },
     "orchestrator": {
       "name": "Spec Orchestrator",
       "id": "orchestrator",
@@ -2679,8 +2823,8 @@
       "id": "ralph",
       "description": "Autonomous implementation loop using AI agent CLI",
       "author": "Rubiss",
-      "version": "1.1.1",
-      "download_url": "https://github.com/Rubiss-Projects/spec-kit-ralph/archive/refs/tags/v1.1.1.zip",
+      "version": "1.2.1",
+      "download_url": "https://github.com/Rubiss-Projects/spec-kit-ralph/archive/refs/tags/v1.2.1.zip",
       "repository": "https://github.com/Rubiss-Projects/spec-kit-ralph",
       "homepage": "https://github.com/Rubiss-Projects/spec-kit-ralph",
       "documentation": "https://github.com/Rubiss-Projects/spec-kit-ralph/blob/main/README.md",
@@ -2689,7 +2833,7 @@
       "category": "code",
       "effect": "read-write",
       "requires": {
-        "speckit_version": ">=0.1.0",
+        "speckit_version": ">=0.8.5",
         "tools": [
           {
             "name": "copilot",
@@ -2699,6 +2843,10 @@
             "name": "codex",
             "required": false
           },
+          {
+            "name": "claude",
+            "required": false
+          },
           {
             "name": "git",
             "required": true
@@ -2714,13 +2862,14 @@
         "automation",
         "loop",
         "copilot",
-        "codex"
+        "codex",
+        "claude"
       ],
       "verified": false,
       "downloads": 0,
       "stars": 0,
       "created_at": "2026-03-09T00:00:00Z",
-      "updated_at": "2026-06-05T03:11:06Z"
+      "updated_at": "2026-07-06T00:00:00Z"
     },
     "reconcile": {
       "name": "Reconcile Extension",
@@ -3047,10 +3196,10 @@
     "ripple": {
       "name": "Ripple",
       "id": "ripple",
-      "description": "Detect side effects that tests can't catch after implementation — delta-anchored analysis across 9 domain-agnostic categories with fix-induced side effect detection",
+      "description": "Detect side effects that tests can't catch after implementation — surface hidden ripple effects across 9 analysis categories",
       "author": "chordpli",
-      "version": "1.0.0",
-      "download_url": "https://github.com/chordpli/spec-kit-ripple/archive/refs/tags/v1.0.0.zip",
+      "version": "1.1.0",
+      "download_url": "https://github.com/chordpli/spec-kit-ripple/archive/refs/tags/v1.1.0.zip",
       "repository": "https://github.com/chordpli/spec-kit-ripple",
       "homepage": "https://github.com/chordpli/spec-kit-ripple",
       "documentation": "https://github.com/chordpli/spec-kit-ripple/blob/main/README.md",
@@ -3059,7 +3208,13 @@
       "category": "code",
       "effect": "read-write",
       "requires": {
-        "speckit_version": ">=0.2.0"
+        "speckit_version": ">=0.2.0",
+        "tools": [
+          {
+            "name": "git",
+            "required": true
+          }
+        ]
       },
       "provides": {
         "commands": 3,
@@ -3076,7 +3231,7 @@
       "downloads": 0,
       "stars": 0,
       "created_at": "2026-04-20T00:00:00Z",
-      "updated_at": "2026-04-20T00:00:00Z"
+      "updated_at": "2026-07-06T00:00:00Z"
     },
     "roadmap": {
       "name": "Spec Roadmap",
@@ -4201,6 +4356,40 @@
       "created_at": "2026-03-03T00:00:00Z",
       "updated_at": "2026-04-09T00:00:00Z"
     },
+    "verify-review-ship": {
+      "name": "Verify Review Ship",
+      "id": "verify-review-ship",
+      "description": "Adds post-implementation verify, review, and ship readiness gates to Spec Kit workflows.",
+      "author": "Carlos Eduardo Gevaerd Araujo",
+      "version": "0.1.0",
+      "download_url": "https://github.com/cadugevaerd/spec-kit-verify-review-ship/archive/refs/tags/v0.1.0.zip",
+      "repository": "https://github.com/cadugevaerd/spec-kit-verify-review-ship",
+      "homepage": "https://github.com/cadugevaerd/spec-kit-verify-review-ship",
+      "documentation": "https://github.com/cadugevaerd/spec-kit-verify-review-ship/blob/main/README.md",
+      "changelog": "https://github.com/cadugevaerd/spec-kit-verify-review-ship/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "category": "process",
+      "effect": "read-only",
+      "requires": {
+        "speckit_version": ">=0.1.0"
+      },
+      "provides": {
+        "commands": 3,
+        "hooks": 1
+      },
+      "tags": [
+        "quality",
+        "review",
+        "shipping",
+        "workflow",
+        "testing"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-07-10T00:00:00Z",
+      "updated_at": "2026-07-10T00:00:00Z"
+    },
     "verify-tasks": {
       "name": "Verify Tasks Extension",
       "id": "verify-tasks",
@@ -4297,6 +4486,40 @@
       "created_at": "2026-04-13T00:00:00Z",
       "updated_at": "2026-04-13T00:00:00Z"
     },
+    "wiki": {
+      "name": "LLM Wiki",
+      "id": "wiki",
+      "description": "LLM-maintained compounding project wiki: source ingestion, cited answers, and consistency linting",
+      "author": "formin",
+      "version": "1.0.0",
+      "download_url": "https://github.com/formin/spec-kit-wiki/archive/refs/tags/v1.0.0.zip",
+      "repository": "https://github.com/formin/spec-kit-wiki",
+      "homepage": "https://github.com/formin/spec-kit-wiki",
+      "documentation": "https://github.com/formin/spec-kit-wiki/blob/main/README.md",
+      "changelog": "https://github.com/formin/spec-kit-wiki/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "category": "docs",
+      "effect": "read-write",
+      "requires": {
+        "speckit_version": ">=0.2.0"
+      },
+      "provides": {
+        "commands": 5,
+        "hooks": 2
+      },
+      "tags": [
+        "wiki",
+        "knowledge-base",
+        "docs",
+        "memory",
+        "context-management"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-07-06T00:00:00Z",
+      "updated_at": "2026-07-06T00:00:00Z"
+    },
     "wireframe": {
       "name": "Wireframe Visual Feedback Loop",
       "id": "wireframe",

extensions/catalog.json

@@ -48,4 +48,4 @@
       ]
     }
   }
-}
+}

extensions/git/README.md

@@ -7,7 +7,7 @@ Git repository initialization, feature branch creation, numbering (sequential/ti
 This extension provides Git operations as an optional, self-contained module. It manages:
 
 - **Repository initialization** with configurable commit messages
-- **Feature branch creation** with sequential (`001-feature-name`) or timestamp (`20260319-143022-feature-name`) numbering
+- **Feature branch creation** with sequential (`001-feature-name`) or timestamp (`20260319-143022-feature-name`) numbering and optional templates for branch namespaces
 - **Branch validation** to ensure branches follow naming conventions
 - **Git remote detection** for GitHub integration (e.g., issue creation)
 - **Auto-commit** after core commands (configurable per-command with custom messages)
@@ -53,6 +53,16 @@ Configuration is stored in `.specify/extensions/git/git-config.yml`:
 # Branch numbering strategy: "sequential" or "timestamp"
 branch_numbering: sequential
 
+# Optional branch name template. Leave empty for the default "{number}-{slug}".
+# Supported tokens: {author}, {app}, {number}, {slug}; {slug} must not appear
+# before {number}, and the final path segment must start with {number}-.
+# Example for monorepos: "{author}/{app}/{number}-{slug}"
+branch_template: ""
+
+# Optional shorthand namespace. Leave empty to use branch_template/default behavior.
+# Example: "features/{app}" expands to "features/{app}/{number}-{slug}"
+branch_prefix: ""
+
 # Custom commit message for git init
 init_commit_message: "[Spec Kit] Initial commit"
 
@@ -65,6 +75,10 @@ auto_commit:
     message: "[Spec Kit] Add specification"
 ```
 
+`{author}` is derived from Git config and sanitized for branch names. `{app}` is derived from the Spec Kit init directory name. Custom templates must not put `{slug}` before `{number}`, and must put `{number}-` at the start of the final path segment so generated names remain valid feature branches. For a monorepo project at `apps/web/.specify/`, a template such as `{author}/{app}/{number}-{slug}` produces branches like `jdoe/web/008-guided-tour`.
+
+For simple namespace-only customization, `branch_prefix` is also accepted as a shorthand and expands to `<branch_prefix>/{number}-{slug}`.
+
 ## Installation
 
 ```bash

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

@@ -19,7 +19,7 @@ You **MUST** consider the user input before proceeding (if not empty).
 If the user explicitly provided `GIT_BRANCH_NAME` (e.g., via environment variable, argument, or in their request), pass it through to the script by setting the `GIT_BRANCH_NAME` environment variable before invoking the script. When `GIT_BRANCH_NAME` is set:
 - The script uses the exact value as the branch name, bypassing all prefix/suffix generation
 - `--short-name`, `--number`, and `--timestamp` flags are ignored
-- `FEATURE_NUM` is extracted from the name if it starts with a numeric prefix, otherwise set to the full branch name
+- `FEATURE_NUM` is extracted when the final path segment starts with a numeric or timestamp feature marker (for example `042-name`, `feat/042-name`, or `jdoe/app/042-name`), otherwise set to the full branch name
 
 ## Prerequisites
 
@@ -35,6 +35,19 @@ Determine the branch numbering strategy by checking configuration in this order:
 3. Check `.specify/init-options.json` for `branch_numbering` value (deprecated, backward compatibility — will be removed in a future release)
 4. Default to `sequential` if none of the above exist
 
+## Branch Name Template
+
+Check `.specify/extensions/git/git-config.yml` for an optional `branch_template` value. If it is empty or missing, use the default branch shape `{number}-{slug}`. If it is set, `{slug}` must not appear before `{number}`, its final path segment must start with `{number}-`, and the script expands these tokens:
+
+- `{author}`: sanitized Git config author (`user.name`, falling back to the email local part)
+- `{app}`: sanitized Spec Kit init directory name
+- `{number}`: sequential number or timestamp
+- `{slug}`: generated short branch slug
+
+For monorepos, a template such as `{author}/{app}/{number}-{slug}` creates names like `jdoe/web/008-guided-tour` while preserving per-project feature numbering.
+
+The script also accepts `branch_prefix` as a shorthand for simple namespaces; it expands to `<branch_prefix>/{number}-{slug}`.
+
 ## Execution
 
 Generate a concise short name (2-4 words) for the branch:
@@ -54,6 +67,7 @@ Run the appropriate script based on your platform:
 - Always include the JSON flag (`--json` for Bash, `-Json` for PowerShell) so the output can be parsed reliably
 - You must only ever run this script once per feature
 - The JSON output will contain `BRANCH_NAME` and `FEATURE_NUM`
+- Do not manually expand `branch_template`; the script reads the git extension config and applies it consistently
 
 ## Graceful Degradation
 
@@ -64,5 +78,5 @@ If Git is not installed or the current directory is not a Git repository:
 ## Output
 
 The script outputs JSON with:
-- `BRANCH_NAME`: The branch name (e.g., `003-user-auth` or `20260319-143022-user-auth`)
+- `BRANCH_NAME`: The branch name (e.g., `003-user-auth`, `20260319-143022-user-auth`, or `jdoe/web/003-user-auth`)
 - `FEATURE_NUM`: The numeric or timestamp prefix used

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

@@ -22,24 +22,24 @@ Get the current branch name:
 git rev-parse --abbrev-ref HEAD
 ```
 
-The branch name must match one of these patterns:
+The branch name's final path segment must start with one of these feature markers:
 
-1. **Sequential**: `^[0-9]{3,}-` (e.g., `001-feature-name`, `042-fix-bug`, `1000-big-feature`)
-2. **Timestamp**: `^[0-9]{8}-[0-9]{6}-` (e.g., `20260319-143022-feature-name`)
+1. **Sequential**: `[0-9]{3,}-` (e.g., `001-feature-name`, `042-fix-bug`, `1000-big-feature`, `jdoe/web/008-guided-tour`)
+2. **Timestamp**: `[0-9]{8}-[0-9]{6}-` (e.g., `20260319-143022-feature-name`, `jdoe/web/20260319-143022-feature-name`)
 
 ## Execution
 
 If on a feature branch (matches either pattern):
 - Output: `✓ On feature branch: <branch-name>`
 - Check if the corresponding spec directory exists under `specs/`:
-  - For sequential branches, look for `specs/<prefix>-*` where prefix matches the numeric portion
-  - For timestamp branches, look for `specs/<prefix>-*` where prefix matches the `YYYYMMDD-HHMMSS` portion
+  - For sequential branches, look for `specs/<prefix>-*` where prefix matches the numeric portion, regardless of branch namespace prefixes
+  - For timestamp branches, look for `specs/<prefix>-*` where prefix matches the `YYYYMMDD-HHMMSS` portion, regardless of branch namespace prefixes
 - 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`
+- Output: `Feature branches should be named like: 001-feature-name, 20260319-143022-feature-name, or <namespace>/001-feature-name`
 
 ## Graceful Degradation
 

extensions/git/config-template.yml

@@ -4,6 +4,16 @@
 # Branch numbering strategy: "sequential" (001, 002, ...) or "timestamp" (YYYYMMDD-HHMMSS)
 branch_numbering: sequential
 
+# Optional branch name template. Leave empty for the default "{number}-{slug}".
+# Supported tokens: {author}, {app}, {number}, {slug}
+# {slug} must not appear before {number}; final path segment must start with {number}-.
+# Example for monorepos: "{author}/{app}/{number}-{slug}"
+branch_template: ""
+
+# Optional shorthand namespace. Leave empty to use branch_template/default behavior.
+# Example: "features/{app}" expands to "features/{app}/{number}-{slug}"
+branch_prefix: ""
+
 # Commit message used by `git commit` during repository initialization
 init_commit_message: "[Spec Kit] Initial commit"
 

extensions/git/extension.yml

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

extensions/git/git-config.yml

@@ -4,6 +4,16 @@
 # Branch numbering strategy: "sequential" (001, 002, ...) or "timestamp" (YYYYMMDD-HHMMSS)
 branch_numbering: sequential
 
+# Optional branch name template. Leave empty for the default "{number}-{slug}".
+# Supported tokens: {author}, {app}, {number}, {slug}
+# {slug} must not appear before {number}; final path segment must start with {number}-.
+# Example for monorepos: "{author}/{app}/{number}-{slug}"
+branch_template: ""
+
+# Optional shorthand namespace. Leave empty to use branch_template/default behavior.
+# Example: "features/{app}" expands to "features/{app}/{number}-{slug}"
+branch_prefix: ""
+
 # Commit message used by `git commit` during repository initialization
 init_commit_message: "[Spec Kit] Initial commit"
 

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

@@ -75,6 +75,10 @@ while [ $i -le $# ]; do
             echo "Environment variables:"
             echo "  GIT_BRANCH_NAME     Use this exact branch name, bypassing all prefix/suffix generation"
             echo ""
+            echo "Configuration:"
+            echo "  branch_template     Optional git-config.yml template with {author}, {app}, {number}, {slug}"
+            echo "  branch_prefix       Optional shorthand namespace expanded before {number}-{slug}"
+            echo ""
             echo "Examples:"
             echo "  $0 'Add user authentication system' --short-name 'user-auth'"
             echo "  $0 'Implement OAuth2 integration for API' --number 5"
@@ -127,16 +131,28 @@ get_highest_from_specs() {
 
 # Function to get highest number from git branches
 get_highest_from_branches() {
-    git branch -a 2>/dev/null | sed -E 's/^[+*][[:space:]]+//; s/^[[:space:]]+//; s|^remotes/[^/]*/||' | _extract_highest_number
+    local scope_prefix="${1:-}"
+    git branch -a 2>/dev/null | sed -E 's/^[+*][[:space:]]+//; s/^[[:space:]]+//; s|^remotes/[^/]*/||' | _extract_highest_number "$scope_prefix"
 }
 
 # Extract the highest sequential feature number from a list of ref names (one per line).
 _extract_highest_number() {
+    local scope_prefix="${1:-}"
     local highest=0
     while IFS= read -r name; do
         [ -z "$name" ] && continue
-        if echo "$name" | grep -Eq '^[0-9]{3,}-' && ! echo "$name" | grep -Eq '^[0-9]{8}-[0-9]{6}-'; then
-            number=$(echo "$name" | grep -Eo '^[0-9]+' || echo "0")
+        if [ -n "$scope_prefix" ]; then
+            case "$name" in
+                "$scope_prefix"*) name="${name#"$scope_prefix"}" ;;
+                *) continue ;;
+            esac
+        fi
+        name="${name##*/}"
+        if echo "$name" | grep -Eq '^[0-9]{3,}-' \
+            && ! echo "$name" | grep -Eq '^[0-9]{8}-[0-9]{6}-' \
+            && ! echo "$name" | grep -Eq '^[0-9]{7}-[0-9]{6}-' \
+            && ! echo "$name" | grep -Eq '^[0-9]{7,8}-[0-9]{6}$'; then
+            number=$(echo "$name" | grep -Eo '^[0-9]{3,}-' | sed -E 's/-$//' || echo "0")
             number=$((10#$number))
             if [ "$number" -gt "$highest" ]; then
                 highest=$number
@@ -148,11 +164,12 @@ _extract_highest_number() {
 
 # Function to get highest number from remote branches without fetching (side-effect-free)
 get_highest_from_remote_refs() {
+    local scope_prefix="${1:-}"
     local highest=0
 
     for remote in $(git remote 2>/dev/null); do
         local remote_highest
-        remote_highest=$(GIT_TERMINAL_PROMPT=0 git ls-remote --heads "$remote" 2>/dev/null | sed 's|.*refs/heads/||' | _extract_highest_number)
+        remote_highest=$(GIT_TERMINAL_PROMPT=0 git ls-remote --heads "$remote" 2>/dev/null | sed 's|.*refs/heads/||' | _extract_highest_number "$scope_prefix")
         if [ "$remote_highest" -gt "$highest" ]; then
             highest=$remote_highest
         fi
@@ -165,16 +182,17 @@ get_highest_from_remote_refs() {
 check_existing_branches() {
     local specs_dir="$1"
     local skip_fetch="${2:-false}"
+    local scope_prefix="${3:-}"
 
     if [ "$skip_fetch" = true ]; then
-        local highest_remote=$(get_highest_from_remote_refs)
-        local highest_branch=$(get_highest_from_branches)
+        local highest_remote=$(get_highest_from_remote_refs "$scope_prefix")
+        local highest_branch=$(get_highest_from_branches "$scope_prefix")
         if [ "$highest_remote" -gt "$highest_branch" ]; then
             highest_branch=$highest_remote
         fi
     else
         git fetch --all --prune >/dev/null 2>&1 || true
-        local highest_branch=$(get_highest_from_branches)
+        local highest_branch=$(get_highest_from_branches "$scope_prefix")
     fi
 
     local highest_spec=$(get_highest_from_specs "$specs_dir")
@@ -273,6 +291,152 @@ fi
 cd "$REPO_ROOT"
 
 SPECS_DIR="$REPO_ROOT/specs"
+CONFIG_FILE="$REPO_ROOT/.specify/extensions/git/git-config.yml"
+
+read_git_config_value() {
+    local key="$1"
+    [ -f "$CONFIG_FILE" ] || return 0
+    grep -E "^[[:space:]]*${key}:" "$CONFIG_FILE" 2>/dev/null \
+        | head -n 1 \
+        | sed -E "s/^[[:space:]]*${key}:[[:space:]]*//" \
+        | sed -E 's/[[:space:]]+#.*$//' \
+        | sed -E 's/^[[:space:]]+|[[:space:]]+$//g' \
+        | sed -E 's/^"//; s/"$//' \
+        | sed -E "s/^'//; s/'$//"
+}
+
+branch_token() {
+    local value="$1"
+    local fallback="$2"
+    local cleaned
+    cleaned=$(clean_branch_name "$value")
+    if [ -n "$cleaned" ]; then
+        printf '%s\n' "$cleaned"
+    else
+        printf '%s\n' "$fallback"
+    fi
+}
+
+get_author_token() {
+    local author=""
+    if command -v git >/dev/null 2>&1; then
+        author=$(git config user.name 2>/dev/null || true)
+        if [ -z "$author" ]; then
+            author=$(git config user.email 2>/dev/null | sed 's/@.*$//' || true)
+        fi
+    fi
+    if [ -z "$author" ]; then
+        author="${USER:-unknown}"
+    fi
+    branch_token "$author" "unknown"
+}
+
+get_app_token() {
+    branch_token "$(basename "$REPO_ROOT")" "app"
+}
+
+resolve_branch_template() {
+    local template
+    local prefix
+    template=$(read_git_config_value "branch_template")
+    if [ -n "$template" ]; then
+        printf '%s\n' "$template"
+        return
+    fi
+
+    prefix=$(read_git_config_value "branch_prefix")
+    if [ -z "$prefix" ]; then
+        printf '%s\n' ""
+        return
+    fi
+    case "$prefix" in
+        */) printf '%s%s\n' "$prefix" "{number}-{slug}" ;;
+        *) printf '%s/%s\n' "$prefix" "{number}-{slug}" ;;
+    esac
+}
+
+render_branch_template() {
+    local template="$1"
+    local feature_num="$2"
+    local branch_suffix="$3"
+    local rendered="$template"
+    rendered=${rendered//\{author\}/$AUTHOR_TOKEN}
+    rendered=${rendered//\{app\}/$APP_TOKEN}
+    rendered=${rendered//\{number\}/$feature_num}
+    rendered=${rendered//\{slug\}/$branch_suffix}
+    printf '%s\n' "$rendered"
+}
+
+validate_branch_template() {
+    local template="$1"
+    [ -n "$template" ] || return 0
+    local feature_segment
+    feature_segment="${template##*/}"
+    case "$template" in
+        *"{number}"*) ;;
+        *)
+            >&2 echo "Error: branch_template must include the {number} token so generated branches remain valid feature branches."
+            exit 1
+            ;;
+    esac
+    case "$template" in
+        *"{slug}"*"{number}"*)
+            >&2 echo "Error: branch_template must not place {slug} before {number}; use {slug} only in the final feature segment."
+            exit 1
+            ;;
+    esac
+    case "$feature_segment" in
+        "{number}-"*) ;;
+        *)
+            >&2 echo "Error: branch_template must put {number}- at the start of the final path segment so generated branches remain valid feature branches."
+            exit 1
+            ;;
+    esac
+}
+
+build_branch_name() {
+    local feature_num="$1"
+    local branch_suffix="$2"
+    if [ -n "$BRANCH_TEMPLATE" ]; then
+        render_branch_template "$BRANCH_TEMPLATE" "$feature_num" "$branch_suffix"
+    else
+        printf '%s-%s\n' "$feature_num" "$branch_suffix"
+    fi
+}
+
+branch_scope_prefix() {
+    local template="$1"
+    local prefix="$template"
+    [ -n "$prefix" ] || return 0
+    case "$prefix" in
+        *"{number}"*) prefix="${prefix%%\{number\}*}" ;;
+        *"{slug}"*) prefix="${prefix%%\{slug\}*}" ;;
+        *) return 0 ;;
+    esac
+    render_branch_template "$prefix" "" "$BRANCH_SUFFIX"
+}
+
+extract_feature_num_from_branch() {
+    local branch_name="$1"
+    local feature_segment="${branch_name##*/}"
+    local match
+    match=$(printf '%s\n' "$feature_segment" | grep -Eo '^[0-9]{8}-[0-9]{6}-' | head -n 1 || true)
+    if [ -n "$match" ]; then
+        printf '%s\n' "$match" | sed -E 's/-$//'
+        return
+    fi
+    match=$(printf '%s\n' "$feature_segment" | grep -Eo '^[0-9]+-' | head -n 1 || true)
+    if [ -n "$match" ]; then
+        printf '%s\n' "$match" | sed -E 's/-$//'
+        return
+    fi
+    printf '%s\n' "$branch_name"
+}
+
+AUTHOR_TOKEN=$(get_author_token)
+APP_TOKEN=$(get_app_token)
+BRANCH_TEMPLATE=$(resolve_branch_template)
+validate_branch_template "$BRANCH_TEMPLATE"
 
 # Function to generate branch name with stop word filtering
 generate_branch_name() {
@@ -318,18 +482,8 @@ generate_branch_name() {
 # Check for GIT_BRANCH_NAME env var override (exact branch name, no prefix/suffix)
 if [ -n "${GIT_BRANCH_NAME:-}" ]; then
     BRANCH_NAME="$GIT_BRANCH_NAME"
-    # Extract FEATURE_NUM from the branch name if it starts with a numeric prefix
-    # Check timestamp pattern first (YYYYMMDD-HHMMSS-) since it also matches the simpler ^[0-9]+ pattern
-    if echo "$BRANCH_NAME" | grep -Eq '^[0-9]{8}-[0-9]{6}-'; then
-        FEATURE_NUM=$(echo "$BRANCH_NAME" | grep -Eo '^[0-9]{8}-[0-9]{6}')
-        BRANCH_SUFFIX="${BRANCH_NAME#${FEATURE_NUM}-}"
-    elif echo "$BRANCH_NAME" | grep -Eq '^[0-9]+-'; then
-        FEATURE_NUM=$(echo "$BRANCH_NAME" | grep -Eo '^[0-9]+')
-        BRANCH_SUFFIX="${BRANCH_NAME#${FEATURE_NUM}-}"
-    else
-        FEATURE_NUM="$BRANCH_NAME"
-        BRANCH_SUFFIX="$BRANCH_NAME"
-    fi
+    FEATURE_NUM=$(extract_feature_num_from_branch "$BRANCH_NAME")
+    BRANCH_SUFFIX="$BRANCH_NAME"
 else
     # Generate branch name
     if [ -n "$SHORT_NAME" ]; then
@@ -347,16 +501,17 @@ else
     # Determine branch prefix
     if [ "$USE_TIMESTAMP" = true ]; then
         FEATURE_NUM=$(date +%Y%m%d-%H%M%S)
-        BRANCH_NAME="${FEATURE_NUM}-${BRANCH_SUFFIX}"
+        BRANCH_NAME=$(build_branch_name "$FEATURE_NUM" "$BRANCH_SUFFIX")
     else
+        BRANCH_SCOPE_PREFIX=$(branch_scope_prefix "$BRANCH_TEMPLATE")
         if [ -z "$BRANCH_NUMBER" ]; then
             if [ "$DRY_RUN" = true ] && [ "$HAS_GIT" = true ]; then
-                BRANCH_NUMBER=$(check_existing_branches "$SPECS_DIR" true)
+                BRANCH_NUMBER=$(check_existing_branches "$SPECS_DIR" true "$BRANCH_SCOPE_PREFIX")
             elif [ "$DRY_RUN" = true ]; then
                 HIGHEST=$(get_highest_from_specs "$SPECS_DIR")
                 BRANCH_NUMBER=$((HIGHEST + 1))
             elif [ "$HAS_GIT" = true ]; then
-                BRANCH_NUMBER=$(check_existing_branches "$SPECS_DIR")
+                BRANCH_NUMBER=$(check_existing_branches "$SPECS_DIR" false "$BRANCH_SCOPE_PREFIX")
             else
                 HIGHEST=$(get_highest_from_specs "$SPECS_DIR")
                 BRANCH_NUMBER=$((HIGHEST + 1))
@@ -364,7 +519,7 @@ else
         fi
 
         FEATURE_NUM=$(printf "%03d" "$((10#$BRANCH_NUMBER))")
-        BRANCH_NAME="${FEATURE_NUM}-${BRANCH_SUFFIX}"
+        BRANCH_NAME=$(build_branch_name "$FEATURE_NUM" "$BRANCH_SUFFIX")
     fi
 fi
 
@@ -376,18 +531,23 @@ if [ -n "${GIT_BRANCH_NAME:-}" ] && [ "$BRANCH_BYTE_LEN" -gt $MAX_BRANCH_LENGTH
     >&2 echo "Error: GIT_BRANCH_NAME must be 244 bytes or fewer in UTF-8. Provided value is ${BRANCH_BYTE_LEN} bytes."
     exit 1
 elif [ "$BRANCH_BYTE_LEN" -gt $MAX_BRANCH_LENGTH ]; then
-    PREFIX_LENGTH=$(( ${#FEATURE_NUM} + 1 ))
-    MAX_SUFFIX_LENGTH=$((MAX_BRANCH_LENGTH - PREFIX_LENGTH))
-
-    TRUNCATED_SUFFIX=$(echo "$BRANCH_SUFFIX" | cut -c1-$MAX_SUFFIX_LENGTH)
-    TRUNCATED_SUFFIX=$(echo "$TRUNCATED_SUFFIX" | sed 's/-$//')
-
     ORIGINAL_BRANCH_NAME="$BRANCH_NAME"
-    BRANCH_NAME="${FEATURE_NUM}-${TRUNCATED_SUFFIX}"
+    TRUNCATED_SUFFIX="$BRANCH_SUFFIX"
+    while [ "$(_byte_length "$BRANCH_NAME")" -gt "$MAX_BRANCH_LENGTH" ] && [ -n "$TRUNCATED_SUFFIX" ]; do
+        TRUNCATED_SUFFIX="${TRUNCATED_SUFFIX%?}"
+        TRUNCATED_SUFFIX="${TRUNCATED_SUFFIX%-}"
+        BRANCH_NAME=$(build_branch_name "$FEATURE_NUM" "$TRUNCATED_SUFFIX")
+    done
+    if [ "$(_byte_length "$BRANCH_NAME")" -gt "$MAX_BRANCH_LENGTH" ]; then
+        >&2 echo "Error: Branch template prefix exceeds GitHub's 244-byte branch name limit."
+        exit 1
+    fi
 
     >&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)"
+    ORIGINAL_BRANCH_BYTE_LEN=$(_byte_length "$ORIGINAL_BRANCH_NAME")
+    TRUNCATED_BRANCH_BYTE_LEN=$(_byte_length "$BRANCH_NAME")
+    >&2 echo "[specify] Original: $ORIGINAL_BRANCH_NAME (${ORIGINAL_BRANCH_BYTE_LEN} bytes)"
+    >&2 echo "[specify] Truncated to: $BRANCH_NAME (${TRUNCATED_BRANCH_BYTE_LEN} bytes)"
 fi
 
 if [ "$DRY_RUN" != true ]; then

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

@@ -23,8 +23,9 @@ spec_kit_effective_branch_name() {
 }
 
 # Validate that a branch name matches the expected feature branch pattern.
-# Accepts sequential (###-* with >=3 digits) or timestamp (YYYYMMDD-HHMMSS-*) formats.
-# Logic aligned with scripts/bash/common.sh check_feature_branch after effective-name normalization.
+# Accepts sequential (###-* with >=3 digits) or timestamp (YYYYMMDD-HHMMSS-*) formats,
+# either at the start of the branch or after path-style namespace prefixes.
+# Logic aligned with the git extension's PowerShell Test-FeatureBranch twin.
 check_feature_branch() {
     local raw="$1"
     local has_git_repo="$2"
@@ -37,16 +38,17 @@ check_feature_branch() {
 
     local branch
     branch=$(spec_kit_effective_branch_name "$raw")
+    local feature_segment="${branch##*/}"
 
     # Accept sequential prefix (3+ digits) but exclude malformed timestamps
     # Malformed: 7-or-8 digit date + 6-digit time with no trailing slug (e.g. "2026031-143022" or "20260319-143022")
     local is_sequential=false
-    if [[ "$branch" =~ ^[0-9]{3,}- ]] && [[ ! "$branch" =~ ^[0-9]{7}-[0-9]{6}- ]] && [[ ! "$branch" =~ ^[0-9]{7,8}-[0-9]{6}$ ]]; then
+    if [[ "$feature_segment" =~ ^[0-9]{3,}- ]] && [[ ! "$feature_segment" =~ ^[0-9]{7}-[0-9]{6}- ]] && [[ ! "$feature_segment" =~ ^[0-9]{7,8}-[0-9]{6}$ ]]; then
         is_sequential=true
     fi
-    if [[ "$is_sequential" != "true" ]] && [[ ! "$branch" =~ ^[0-9]{8}-[0-9]{6}- ]]; then
+    if [[ "$is_sequential" != "true" ]] && [[ ! "$feature_segment" =~ ^[0-9]{8}-[0-9]{6}- ]]; then
         echo "ERROR: Not on a feature branch. Current branch: $raw" >&2
-        echo "Feature branches should be named like: 001-feature-name, 1234-feature-name, or 20260319-143022-feature-name" >&2
+        echo "Feature branches should be named like: 001-feature-name, 1234-feature-name, 20260319-143022-feature-name, or <prefix>/001-feature-name" >&2
         return 1
     fi
 

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

@@ -34,6 +34,10 @@ if ($Help) {
     Write-Host "Environment variables:"
     Write-Host "  GIT_BRANCH_NAME     Use this exact branch name, bypassing all prefix/suffix generation"
     Write-Host ""
+    Write-Host "Configuration:"
+    Write-Host "  branch_template     Optional git-config.yml template with {author}, {app}, {number}, {slug}"
+    Write-Host "  branch_prefix       Optional shorthand namespace expanded before {number}-{slug}"
+    Write-Host ""
     exit 0
 }
 
@@ -67,11 +71,23 @@ function Get-HighestNumberFromSpecs {
 }
 
 function Get-HighestNumberFromNames {
-    param([string[]]$Names)
+    param(
+        [string[]]$Names,
+        [string]$ScopePrefix = ''
+    )
 
     [long]$highest = 0
     foreach ($name in $Names) {
-        if ($name -match '^(\d{3,})-' -and $name -notmatch '^\d{8}-\d{6}-') {
+        if ($ScopePrefix -and -not $name.StartsWith($ScopePrefix, [System.StringComparison]::Ordinal)) {
+            continue
+        }
+        if ($ScopePrefix) {
+            $name = $name.Substring($ScopePrefix.Length)
+        }
+        $name = ($name -split '/')[-1]
+        $hasTimestampPrefix = $name -match '^\d{8}-\d{6}-'
+        $hasMalformedTimestamp = ($name -match '^\d{7}-\d{6}-') -or ($name -match '^(?:\d{7}|\d{8})-\d{6}$')
+        if ($name -match '^(\d{3,})-' -and -not $hasTimestampPrefix -and -not $hasMalformedTimestamp) {
             [long]$num = 0
             if ([long]::TryParse($matches[1], [ref]$num) -and $num -gt $highest) {
                 $highest = $num
@@ -82,7 +98,7 @@ function Get-HighestNumberFromNames {
 }
 
 function Get-HighestNumberFromBranches {
-    param()
+    param([string]$ScopePrefix = '')
 
     try {
         $branches = git branch -a 2>$null
@@ -90,7 +106,7 @@ function Get-HighestNumberFromBranches {
             $cleanNames = $branches | ForEach-Object {
                 $_.Trim() -replace '^[+*]?\s+', '' -replace '^remotes/[^/]+/', ''
             }
-            return Get-HighestNumberFromNames -Names $cleanNames
+            return Get-HighestNumberFromNames -Names $cleanNames -ScopePrefix $ScopePrefix
         }
     } catch {
         Write-Verbose "Could not check Git branches: $_"
@@ -99,6 +115,8 @@ function Get-HighestNumberFromBranches {
 }
 
 function Get-HighestNumberFromRemoteRefs {
+    param([string]$ScopePrefix = '')
+
     [long]$highest = 0
     try {
         $remotes = git remote 2>$null
@@ -111,7 +129,7 @@ function Get-HighestNumberFromRemoteRefs {
                     $refNames = $refs | ForEach-Object {
                         if ($_ -match 'refs/heads/(.+)$') { $matches[1] }
                     } | Where-Object { $_ }
-                    $remoteHighest = Get-HighestNumberFromNames -Names $refNames
+                    $remoteHighest = Get-HighestNumberFromNames -Names $refNames -ScopePrefix $ScopePrefix
                     if ($remoteHighest -gt $highest) { $highest = $remoteHighest }
                 }
             }
@@ -125,18 +143,19 @@ function Get-HighestNumberFromRemoteRefs {
 function Get-NextBranchNumber {
     param(
         [string]$SpecsDir,
-        [switch]$SkipFetch
+        [switch]$SkipFetch,
+        [string]$ScopePrefix = ''
     )
 
     if ($SkipFetch) {
-        $highestBranch = Get-HighestNumberFromBranches
-        $highestRemote = Get-HighestNumberFromRemoteRefs
+        $highestBranch = Get-HighestNumberFromBranches -ScopePrefix $ScopePrefix
+        $highestRemote = Get-HighestNumberFromRemoteRefs -ScopePrefix $ScopePrefix
         $highestBranch = [Math]::Max($highestBranch, $highestRemote)
     } else {
         try {
             git fetch --all --prune 2>$null | Out-Null
         } catch { }
-        $highestBranch = Get-HighestNumberFromBranches
+        $highestBranch = Get-HighestNumberFromBranches -ScopePrefix $ScopePrefix
     }
 
     $highestSpec = Get-HighestNumberFromSpecs -SpecsDir $SpecsDir
@@ -232,6 +251,145 @@ if (Get-Command Test-HasGit -ErrorAction SilentlyContinue) {
 Set-Location $repoRoot
 
 $specsDir = Join-Path $repoRoot 'specs'
+$configFile = Join-Path $repoRoot ".specify/extensions/git/git-config.yml"
+
+function Read-GitConfigValue {
+    param([string]$Key)
+
+    if (-not (Test-Path -LiteralPath $configFile -PathType Leaf)) { return '' }
+    $escapedKey = [regex]::Escape($Key)
+    foreach ($line in Get-Content -LiteralPath $configFile) {
+        if ($line -match "^\s*$escapedKey\s*:\s*(.*)$") {
+            $val = ($matches[1] -replace '\s+#.*$', '').Trim()
+            $val = $val -replace '^["'']', '' -replace '["'']$', ''
+            return $val
+        }
+    }
+    return ''
+}
+
+function ConvertTo-BranchToken {
+    param(
+        [string]$Value,
+        [string]$Fallback
+    )
+
+    $cleaned = ConvertTo-CleanBranchName -Name $Value
+    if ($cleaned) { return $cleaned }
+    return $Fallback
+}
+
+function Get-GitAuthorToken {
+    $author = ''
+    if (Get-Command git -ErrorAction SilentlyContinue) {
+        try { $author = (git config user.name 2>$null | Out-String).Trim() } catch {}
+        if (-not $author) {
+            try {
+                $email = (git config user.email 2>$null | Out-String).Trim()
+                if ($email) { $author = ($email -split '@')[0] }
+            } catch {}
+        }
+    }
+    if (-not $author) { $author = if ($env:USER) { $env:USER } elseif ($env:USERNAME) { $env:USERNAME } else { 'unknown' } }
+    return ConvertTo-BranchToken -Value $author -Fallback 'unknown'
+}
+
+function Get-AppToken {
+    return ConvertTo-BranchToken -Value (Split-Path $repoRoot -Leaf) -Fallback 'app'
+}
+
+function Resolve-BranchTemplate {
+    $template = Read-GitConfigValue -Key 'branch_template'
+    if ($template) { return $template }
+
+    $prefix = Read-GitConfigValue -Key 'branch_prefix'
+    if (-not $prefix) { return '' }
+    if ($prefix.EndsWith('/')) { return "${prefix}{number}-{slug}" }
+    return "$prefix/{number}-{slug}"
+}
+
+function Expand-BranchTemplate {
+    param(
+        [string]$Template,
+        [string]$FeatureNum,
+        [string]$BranchSuffix
+    )
+
+    $rendered = $Template.Replace('{author}', $authorToken)
+    $rendered = $rendered.Replace('{app}', $appToken)
+    $rendered = $rendered.Replace('{number}', $FeatureNum)
+    $rendered = $rendered.Replace('{slug}', $BranchSuffix)
+    return $rendered
+}
+
+function Assert-BranchTemplateValid {
+    param([string]$Template)
+
+    if ($Template -and -not $Template.Contains('{number}')) {
+        throw "branch_template must include the {number} token so generated branches remain valid feature branches."
+    }
+    if ($Template) {
+        $numberIndex = $Template.IndexOf('{number}', [System.StringComparison]::Ordinal)
+        $slugIndex = $Template.IndexOf('{slug}', [System.StringComparison]::Ordinal)
+        if ($slugIndex -ge 0 -and $slugIndex -lt $numberIndex) {
+            throw "branch_template must not place {slug} before {number}; use {slug} only in the final feature segment."
+        }
+        $featureSegment = ($Template -split '/')[-1]
+        if (-not $featureSegment.StartsWith('{number}-', [System.StringComparison]::Ordinal)) {
+            throw "branch_template must put {number}- at the start of the final path segment so generated branches remain valid feature branches."
+        }
+    }
+}
+
+function New-BranchName {
+    param(
+        [string]$FeatureNum,
+        [string]$BranchSuffix
+    )
+
+    if ($branchTemplate) {
+        return Expand-BranchTemplate -Template $branchTemplate -FeatureNum $FeatureNum -BranchSuffix $BranchSuffix
+    }
+    return "$FeatureNum-$BranchSuffix"
+}
+
+function Get-BranchScopePrefix {
+    param(
+        [string]$Template,
+        [string]$BranchSuffix
+    )
+
+    if (-not $Template) { return '' }
+    $numberIndex = $Template.IndexOf('{number}', [System.StringComparison]::Ordinal)
+    $slugIndex = $Template.IndexOf('{slug}', [System.StringComparison]::Ordinal)
+    $indexes = @($numberIndex, $slugIndex) | Where-Object { $_ -ge 0 } | Sort-Object
+    if (-not $indexes) { return '' }
+    $prefix = $Template.Substring(0, $indexes[0])
+    return Expand-BranchTemplate -Template $prefix -FeatureNum '' -BranchSuffix $BranchSuffix
+}
+
+function Get-FeatureNumberFromBranchName {
+    param([string]$BranchName)
+
+    $featureSegment = ($BranchName -split '/')[-1]
+    if ($featureSegment -match '^(\d{8}-\d{6})-') {
+        return $matches[1]
+    }
+    if ($featureSegment -match '^(\d+)-') {
+        return $matches[1]
+    }
+    return $BranchName
+}
+
+function Get-Utf8ByteCount {
+    param([string]$Value)
+    return [System.Text.Encoding]::UTF8.GetByteCount($Value)
+}
+
+$authorToken = Get-GitAuthorToken
+$appToken = Get-AppToken
+$branchTemplate = Resolve-BranchTemplate
+Assert-BranchTemplateValid -Template $branchTemplate
 
 function Get-BranchName {
     param([string]$Description)
@@ -276,19 +434,11 @@ function Get-BranchName {
 if ($env:GIT_BRANCH_NAME) {
     $branchName = $env:GIT_BRANCH_NAME
     # Check 244-byte limit (UTF-8) for override names
-    $branchNameUtf8ByteCount = [System.Text.Encoding]::UTF8.GetByteCount($branchName)
+    $branchNameUtf8ByteCount = Get-Utf8ByteCount -Value $branchName
     if ($branchNameUtf8ByteCount -gt 244) {
         throw "GIT_BRANCH_NAME must be 244 bytes or fewer in UTF-8. Provided value is $branchNameUtf8ByteCount bytes; please supply a shorter override branch name."
     }
-    # Extract FEATURE_NUM from the branch name if it starts with a numeric prefix
-    # Check timestamp pattern first (YYYYMMDD-HHMMSS-) since it also matches the simpler ^\d+ pattern
-    if ($branchName -match '^(\d{8}-\d{6})-') {
-        $featureNum = $matches[1]
-    } elseif ($branchName -match '^(\d+)-') {
-        $featureNum = $matches[1]
-    } else {
-        $featureNum = $branchName
-    }
+    $featureNum = Get-FeatureNumberFromBranchName -BranchName $branchName
 } else {
     if ($ShortName) {
         $branchSuffix = ConvertTo-CleanBranchName -Name $ShortName
@@ -296,46 +446,54 @@ if ($env:GIT_BRANCH_NAME) {
         $branchSuffix = Get-BranchName -Description $featureDesc
     }
 
-    if ($Timestamp -and $Number -ne 0) {
+    # Warn if -Number and -Timestamp are both specified. Use ContainsKey (not
+    # `-ne 0`) so an explicit `-Number 0` is also detected, matching the bash twin's
+    # `[ -n "$BRANCH_NUMBER" ]` check.
+    if ($Timestamp -and $PSBoundParameters.ContainsKey('Number')) {
         Write-Warning "[specify] Warning: -Number is ignored when -Timestamp is used"
         $Number = 0
     }
 
     if ($Timestamp) {
         $featureNum = Get-Date -Format 'yyyyMMdd-HHmmss'
-        $branchName = "$featureNum-$branchSuffix"
+        $branchName = New-BranchName -FeatureNum $featureNum -BranchSuffix $branchSuffix
     } else {
-        if ($Number -eq 0) {
+        $branchScopePrefix = Get-BranchScopePrefix -Template $branchTemplate -BranchSuffix $branchSuffix
+        # Auto-detect the next number only when -Number was not supplied; an
+        # explicit value (including 0) is honored, matching the bash twin's
+        # `[ -z "$BRANCH_NUMBER" ]` check.
+        if (-not $PSBoundParameters.ContainsKey('Number')) {
             if ($DryRun -and $hasGit) {
-                $Number = Get-NextBranchNumber -SpecsDir $specsDir -SkipFetch
+                $Number = Get-NextBranchNumber -SpecsDir $specsDir -SkipFetch -ScopePrefix $branchScopePrefix
             } elseif ($DryRun) {
                 $Number = (Get-HighestNumberFromSpecs -SpecsDir $specsDir) + 1
             } elseif ($hasGit) {
-                $Number = Get-NextBranchNumber -SpecsDir $specsDir
+                $Number = Get-NextBranchNumber -SpecsDir $specsDir -ScopePrefix $branchScopePrefix
             } else {
                 $Number = (Get-HighestNumberFromSpecs -SpecsDir $specsDir) + 1
             }
         }
 
         $featureNum = ('{0:000}' -f $Number)
-        $branchName = "$featureNum-$branchSuffix"
+        $branchName = New-BranchName -FeatureNum $featureNum -BranchSuffix $branchSuffix
     }
 }
 
 $maxBranchLength = 244
-if ($branchName.Length -gt $maxBranchLength) {
-    $prefixLength = $featureNum.Length + 1
-    $maxSuffixLength = $maxBranchLength - $prefixLength
-
-    $truncatedSuffix = $branchSuffix.Substring(0, [Math]::Min($branchSuffix.Length, $maxSuffixLength))
-    $truncatedSuffix = $truncatedSuffix -replace '-$', ''
-
+if ((Get-Utf8ByteCount -Value $branchName) -gt $maxBranchLength) {
     $originalBranchName = $branchName
-    $branchName = "$featureNum-$truncatedSuffix"
+    $truncatedSuffix = $branchSuffix
+    while ((Get-Utf8ByteCount -Value $branchName) -gt $maxBranchLength -and $truncatedSuffix.Length -gt 0) {
+        $truncatedSuffix = $truncatedSuffix.Substring(0, $truncatedSuffix.Length - 1) -replace '-$', ''
+        $branchName = New-BranchName -FeatureNum $featureNum -BranchSuffix $truncatedSuffix
+    }
+    if ((Get-Utf8ByteCount -Value $branchName) -gt $maxBranchLength) {
+        throw "Branch template prefix exceeds GitHub's 244-byte branch name limit."
+    }
 
     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)"
+    Write-Warning "[specify] Original: $originalBranchName ($(Get-Utf8ByteCount -Value $originalBranchName) bytes)"
+    Write-Warning "[specify] Truncated to: $branchName ($(Get-Utf8ByteCount -Value $branchName) bytes)"
 }
 
 if (-not $DryRun) {

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

@@ -37,14 +37,15 @@ function Test-FeatureBranch {
 
     $raw = $Branch
     $Branch = Get-SpecKitEffectiveBranchName $raw
+    $featureSegment = ($Branch -split '/')[-1]
 
-    # Accept sequential prefix (3+ digits) but exclude malformed timestamps
-    # Malformed: 7-or-8 digit date + 6-digit time with no trailing slug (e.g. "2026031-143022" or "20260319-143022")
-    $hasMalformedTimestamp = ($Branch -match '^[0-9]{7}-[0-9]{6}-') -or ($Branch -match '^(?:\d{7}|\d{8})-\d{6}$')
-    $isSequential = ($Branch -match '^[0-9]{3,}-') -and (-not $hasMalformedTimestamp)
-    if (-not $isSequential -and $Branch -notmatch '^\d{8}-\d{6}-') {
+    # Accept sequential prefix (3+ digits), at the start or after namespace
+    # segments, but exclude malformed timestamps.
+    $hasMalformedTimestamp = ($featureSegment -match '^[0-9]{7}-[0-9]{6}-') -or ($featureSegment -match '^(?:\d{7}|\d{8})-\d{6}$')
+    $isSequential = ($featureSegment -match '^[0-9]{3,}-') -and (-not $hasMalformedTimestamp)
+    if (-not $isSequential -and $featureSegment -notmatch '^\d{8}-\d{6}-') {
         [Console]::Error.WriteLine("ERROR: Not on a feature branch. Current branch: $raw")
-        [Console]::Error.WriteLine("Feature branches should be named like: 001-feature-name, 1234-feature-name, or 20260319-143022-feature-name")
+        [Console]::Error.WriteLine("Feature branches should be named like: 001-feature-name, 1234-feature-name, 20260319-143022-feature-name, or <prefix>/001-feature-name")
         return $false
     }
     return $true

extensions/selftest/commands/selftest.md

@@ -48,7 +48,7 @@ cat .specify/extensions/.registry/$ARGUMENTS.json
 
 ### Step 4: Verification Report
 
-Analyze the standard output of the three steps. 
+Analyze the standard output of the three steps.
 Generate a terminal-style test output format detailing the results of discovery, installation, and registration. Return this directly to the user.
 
 Example output format:

newsletters/2026-March.md

@@ -76,5 +76,3 @@ Areas under discussion or in progress for future development:
 - **Continued agent expansion** -- seven new agents were added in March alone. The agent-agnostic design means support for emerging tools can be added by anyone. [\[byteiota.com\]](https://byteiota.com/spec-driven-development-kills-vibe-coding-march-2026/)
 - **Experience simplification** -- the preset system, custom workflows, and growing walkthrough library lower the learning curve, but extension discoverability will need a more robust solution as the catalog grows. [\[github.com\]](https://github.com/github/spec-kit/releases)
 - **Toward a stable release** -- nine releases in one month reflects pre-1.0 momentum. Reaching 1.0 will require stabilizing the extension and preset APIs and ensuring backward compatibility across the agent and extension surface area. [\[github.com\]](https://github.com/github/spec-kit/blob/main/newsletters/2026-February.md)
-
-

presets/ARCHITECTURE.md

@@ -158,8 +158,7 @@ presets/
         ├── plan-template.md
         ├── tasks-template.md
         ├── checklist-template.md
-        ├── constitution-template.md
-        └── agent-file-template.md
+        └── constitution-template.md
 ```
 
 ## Module Structure

presets/self-test/preset.yml

@@ -44,12 +44,6 @@ provides:
       description: "Self-test constitution template"
       replaces: "constitution-template"
 
-    - type: "template"
-      name: "agent-file-template"
-      file: "templates/agent-file-template.md"
-      description: "Self-test agent file template"
-      replaces: "agent-file-template"
-
     - type: "command"
       name: "speckit.specify"
       file: "commands/speckit.specify.md"

presets/self-test/templates/agent-file-template.md

@@ -1,9 +0,0 @@
-# Agent File (Self-Test Preset)
-
-<!-- preset:self-test -->
-
-> This template is provided by the self-test preset.
-
-## Agent Instructions
-
-Follow these guidelines when working on this project.

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "specify-cli"
-version = "0.12.4.dev0"
+version = "0.12.13"
 description = "Specify CLI, part of GitHub Spec Kit. A tool to bootstrap your projects for Spec-Driven Development (SDD)."
 readme = "README.md"
 requires-python = ">=3.11"
@@ -83,4 +83,3 @@ extend-select = [
     "S604",  # call-with-shell-equals-true
     "S605",  # start-process-with-a-shell
 ]
-

scripts/bash/check-prerequisites.sh

@@ -57,13 +57,13 @@ OPTIONS:
 EXAMPLES:
   # Check task prerequisites (plan.md required)
   ./check-prerequisites.sh --json
-  
+
   # Check implementation prerequisites (plan.md + tasks.md required)
   ./check-prerequisites.sh --json --require-tasks --include-tasks
-  
+
   # Get feature paths only (no validation)
   ./check-prerequisites.sh --paths-only
-  
+
 EOF
             exit 0
             ;;
@@ -182,13 +182,13 @@ else
     # Text output
     echo "FEATURE_DIR:$FEATURE_DIR"
     echo "AVAILABLE_DOCS:"
-    
+
     # Show status of each potential document
     check_file "$RESEARCH" "research.md"
     check_file "$DATA_MODEL" "data-model.md"
     check_dir "$CONTRACTS_DIR" "contracts/"
     check_file "$QUICKSTART" "quickstart.md"
-    
+
     if $INCLUDE_TASKS; then
         check_file "$TASKS" "tasks.md"
     fi

scripts/bash/common.sh

@@ -97,17 +97,26 @@ read_feature_json_feature_directory() {
     local fj="$repo_root/.specify/feature.json"
     [[ -f "$fj" ]] || { printf '%s' ''; return 0; }
 
+    # Try parsers in order (jq -> python3 -> grep/sed), falling through on
+    # failure. Selection is by *parse success*, not mere availability: on
+    # Windows `python3` commonly resolves to the Microsoft Store App Execution
+    # Alias stub, which passes `command -v` but fails at runtime (exit 49), so
+    # an availability-gated `elif` would pick python3, swallow its failure, and
+    # never reach the grep/sed fallback -- leaving feature.json unreadable even
+    # though it is valid (issue #3304).
     local _fd=''
     if command -v jq >/dev/null 2>&1; then
         if ! _fd=$(jq -r '.feature_directory // empty' "$fj" 2>/dev/null); then
             _fd=''
         fi
-    elif command -v python3 >/dev/null 2>&1; then
+    fi
+    if [[ -z "$_fd" ]] && command -v python3 >/dev/null 2>&1; then
         # Use Python so pretty-printed/multi-line JSON still parses correctly.
         if ! _fd=$(python3 -c "import json,sys; d=json.load(open(sys.argv[1])); v=d.get('feature_directory'); print(v if v else '')" "$fj" 2>/dev/null); then
             _fd=''
         fi
-    else
+    fi
+    if [[ -z "$_fd" ]]; then
         # Last-resort single-line grep/sed fallback. The `|| true` guards against
         # grep returning 1 (no match) aborting under `set -e` / `pipefail`.
         _fd=$( { grep -E '"feature_directory"[[:space:]]*:' "$fj" 2>/dev/null || true; } \
@@ -235,21 +244,29 @@ get_invoke_separator() {
 
     local integration_json="$repo_root/.specify/integration.json"
     local separator="."
-    local parsed_with_jq=0
+    local parsed=0
 
     if [[ -f "$integration_json" ]]; then
+        # Try parsers in order (jq -> python3 -> awk), falling through on
+        # failure. Selection is by *parse success*, not mere availability: on
+        # Windows `python3` commonly resolves to the Microsoft Store App
+        # Execution Alias stub, which passes `command -v` but fails at runtime
+        # (exit 49). An availability-gated branch would pick python3, swallow
+        # its failure, and — because this function historically had no text
+        # fallback — silently return "." even for `-`-separator integrations
+        # (e.g. forge, cline), yielding wrong command hints (issue #3304).
         if command -v jq >/dev/null 2>&1; then
             local jq_separator
             if jq_separator=$(jq -r '(.default_integration // .integration // "") as $k | if $k == "" then "." else (.integration_settings[$k].invoke_separator // ".") end' "$integration_json" 2>/dev/null); then
-                parsed_with_jq=1
                 case "$jq_separator" in
-                    "."|"-") separator="$jq_separator" ;;
+                    "."|"-") separator="$jq_separator"; parsed=1 ;;
                 esac
             fi
         fi
 
-        if [[ "$parsed_with_jq" -eq 0 ]] && command -v python3 >/dev/null 2>&1; then
-            if separator=$(python3 - "$integration_json" <<'PY' 2>/dev/null
+        if [[ "$parsed" -eq 0 ]] && command -v python3 >/dev/null 2>&1; then
+            local py_separator
+            if py_separator=$(python3 - "$integration_json" <<'PY' 2>/dev/null
 import json
 import sys
 
@@ -265,17 +282,64 @@ try:
             separator = entry["invoke_separator"]
     print(separator)
 except Exception:
-    print(".")
+    sys.exit(1)
 PY
 ); then
-                case "$separator" in
-                    "."|"-") ;;
-                    *) separator="." ;;
+                case "$py_separator" in
+                    "."|"-") separator="$py_separator"; parsed=1 ;;
                 esac
-            else
-                separator="."
             fi
         fi
+
+        if [[ "$parsed" -eq 0 ]]; then
+            # Last-resort text fallback for environments with neither jq nor a
+            # working python3 (e.g. stock Windows + Git Bash). Reads the active
+            # integration key (default_integration, else integration) and its
+            # invoke_separator from within the integration_settings object.
+            # Handles both pretty-printed (the written form) and compact JSON.
+            # Accumulate all lines into one buffer in END rather than using
+            # gawk-only whole-file slurp (RS="^$"), so this stays portable to
+            # the BSD awk on macOS.
+            local awk_separator
+            awk_separator=$(awk '
+                function keyval(d, name,   v) {
+                    if (match(d, "\"" name "\"[ \t\r\n]*:[ \t\r\n]*\"[^\"]*\"")) {
+                        v=substr(d,RSTART,RLENGTH); sub(/^.*:[ \t\r\n]*"/,"",v); sub(/"$/,"",v); return v
+                    }
+                    return ""
+                }
+                { doc = doc $0 "\n" }
+                END {
+                    key=keyval(doc,"default_integration"); if (key=="") key=keyval(doc,"integration")
+                    sep="."
+                    if (key!="") {
+                        settings=doc
+                        if (match(doc, /"integration_settings"[ \t\r\n]*:[ \t\r\n]*[{]/)) {
+                            settings=substr(doc, RSTART+RLENGTH-1)
+                        }
+                        if (match(settings, "\"" key "\"[ \t\r\n]*:[ \t\r\n]*[{]")) {
+                            start=RSTART+RLENGTH-1
+                            depth=0
+                            obj=""
+                            for (i=start; i<=length(settings); i++) {
+                                c=substr(settings,i,1)
+                                obj=obj c
+                                if (c=="{") depth++
+                                else if (c=="}") { depth--; if (depth==0) break }
+                            }
+                            if (match(obj, /"invoke_separator"[ \t\r\n]*:[ \t\r\n]*"[-.]"/)) {
+                                tok=substr(obj,RSTART,RLENGTH); s=substr(tok,length(tok)-1,1)
+                                if (s=="." || s=="-") sep=s
+                            }
+                        }
+                    }
+                    print sep
+                }
+            ' "$integration_json" 2>/dev/null)
+            case "$awk_separator" in
+                "."|"-") separator="$awk_separator" ;;
+            esac
+        fi
     fi
 
     _SPECIFY_INVOKE_SEPARATOR_CACHE_REPO_ROOT="$repo_root"

scripts/bash/create-new-feature.sh

@@ -94,7 +94,7 @@ fi
 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
@@ -109,7 +109,7 @@ get_highest_from_specs() {
             fi
         done
     fi
-    
+
     echo "$highest"
 }
 
@@ -135,19 +135,19 @@ fi
 # 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=$(printf '%s' "$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
@@ -160,12 +160,12 @@ generate_branch_name() {
             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
@@ -221,15 +221,15 @@ if [ ${#BRANCH_NAME} -gt $MAX_BRANCH_LENGTH ]; then
     # Account for prefix length: timestamp (15) + hyphen (1) = 16, or sequential (3) + hyphen (1) = 4
     PREFIX_LENGTH=$(( ${#FEATURE_NUM} + 1 ))
     MAX_SUFFIX_LENGTH=$((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)"

scripts/bash/setup-plan.sh

@@ -8,17 +8,17 @@ ARGS=()
 
 for arg in "$@"; do
     case "$arg" in
-        --json) 
-            JSON_MODE=true 
+        --json)
+            JSON_MODE=true
             ;;
-        --help|-h) 
+        --help|-h)
             echo "Usage: $0 [--json]"
             echo "  --json    Output results in JSON format"
             echo "  --help    Show this help message"
-            exit 0 
+            exit 0
             ;;
-        *) 
-            ARGS+=("$arg") 
+        *)
+            ARGS+=("$arg")
             ;;
     esac
 done
@@ -77,8 +77,7 @@ if $JSON_MODE; then
     fi
 else
     echo "FEATURE_SPEC: $FEATURE_SPEC"
-    echo "IMPL_PLAN: $IMPL_PLAN" 
+    echo "IMPL_PLAN: $IMPL_PLAN"
     echo "SPECS_DIR: $FEATURE_DIR"
     echo "BRANCH: $CURRENT_BRANCH"
 fi
-

scripts/powershell/check-prerequisites.ps1

@@ -42,10 +42,10 @@ OPTIONS:
 EXAMPLES:
   # Check task prerequisites (plan.md required)
   .\check-prerequisites.ps1 -Json
-  
+
   # Check implementation prerequisites (plan.md + tasks.md required)
   .\check-prerequisites.ps1 -Json -RequireTasks -IncludeTasks
-  
+
   # Get feature paths only (no validation)
   .\check-prerequisites.ps1 -PathsOnly
 
@@ -118,35 +118,35 @@ if (Test-Path $paths.RESEARCH) { $docs += 'research.md' }
 if (Test-Path $paths.DATA_MODEL) { $docs += 'data-model.md' }
 
 # Check contracts directory (only if it exists and has files)
-if ((Test-Path $paths.CONTRACTS_DIR) -and (Get-ChildItem -Path $paths.CONTRACTS_DIR -ErrorAction SilentlyContinue | Select-Object -First 1)) { 
-    $docs += 'contracts/' 
+if ((Test-Path $paths.CONTRACTS_DIR) -and (Get-ChildItem -Path $paths.CONTRACTS_DIR -ErrorAction SilentlyContinue | Select-Object -First 1)) {
+    $docs += 'contracts/'
 }
 
 if (Test-Path $paths.QUICKSTART) { $docs += 'quickstart.md' }
 
 # Include tasks.md if requested and it exists
-if ($IncludeTasks -and (Test-Path $paths.TASKS)) { 
-    $docs += 'tasks.md' 
+if ($IncludeTasks -and (Test-Path $paths.TASKS)) {
+    $docs += 'tasks.md'
 }
 
 # Output results
 if ($Json) {
     # JSON output
-    [PSCustomObject]@{ 
+    [PSCustomObject]@{
         FEATURE_DIR = $paths.FEATURE_DIR
-        AVAILABLE_DOCS = $docs 
+        AVAILABLE_DOCS = $docs
     } | ConvertTo-Json -Compress
 } else {
     # Text output
     Write-Output "FEATURE_DIR:$($paths.FEATURE_DIR)"
     Write-Output "AVAILABLE_DOCS:"
-    
+
     # Show status of each potential document
     Test-FileExists -Path $paths.RESEARCH -Description 'research.md' | Out-Null
     Test-FileExists -Path $paths.DATA_MODEL -Description 'data-model.md' | Out-Null
     Test-DirHasFiles -Path $paths.CONTRACTS_DIR -Description 'contracts/' | Out-Null
     Test-FileExists -Path $paths.QUICKSTART -Description 'quickstart.md' | Out-Null
-    
+
     if ($IncludeTasks) {
         Test-FileExists -Path $paths.TASKS -Description 'tasks.md' | Out-Null
     }

scripts/powershell/common.ps1

@@ -191,7 +191,7 @@ function Get-FeaturePathsEnv {
         [Console]::Error.WriteLine("ERROR: Feature directory not found. Set SPECIFY_FEATURE_DIRECTORY or run the specify command to create .specify/feature.json.")
         exit 1
     }
-    
+
     # When no branch context exists (no SPECIFY_FEATURE, feature resolved via
     # SPECIFY_FEATURE_DIRECTORY or feature.json), fall back to the feature
     # directory basename so CURRENT_BRANCH is a usable identifier rather than

scripts/powershell/setup-plan.ps1

@@ -63,7 +63,7 @@ if (Test-Path $paths.IMPL_PLAN -PathType Leaf) {
 
 # Output results
 if ($Json) {
-    $result = [PSCustomObject]@{ 
+    $result = [PSCustomObject]@{
         FEATURE_SPEC = $paths.FEATURE_SPEC
         IMPL_PLAN = $paths.IMPL_PLAN
         SPECS_DIR = $paths.FEATURE_DIR

scripts/python/check_prerequisites.py

@@ -0,0 +1,207 @@
+#!/usr/bin/env python3
+"""Consolidated prerequisite checking script."""
+
+from __future__ import annotations
+
+import json
+import sys
+from dataclasses import dataclass
+from pathlib import Path
+
+try:
+    from common import FeaturePaths, format_speckit_command, get_feature_paths
+except ImportError:  # pragma: no cover - direct execution from unusual cwd
+    sys.path.insert(0, str(Path(__file__).resolve().parent))
+    from common import FeaturePaths, format_speckit_command, get_feature_paths
+
+
+def _json_line(payload: object) -> str:
+    return json.dumps(payload, ensure_ascii=False, separators=(",", ":")) + "\n"
+
+
+HELP_TEXT = """Usage: check_prerequisites.py [OPTIONS]
+
+Consolidated prerequisite checking for Spec-Driven Development workflow.
+
+OPTIONS:
+  --json              Output in JSON format
+  --require-tasks     Require tasks.md to exist (for implementation phase)
+  --include-tasks     Include tasks.md in AVAILABLE_DOCS list
+  --paths-only        Only output path variables (no prerequisite validation)
+  --help, -h          Show this help message
+
+EXAMPLES:
+  # Check task prerequisites (plan.md required)
+  ./check_prerequisites.py --json
+
+  # Check implementation prerequisites (plan.md + tasks.md required)
+  ./check_prerequisites.py --json --require-tasks --include-tasks
+
+  # Get feature paths only (no validation)
+  ./check_prerequisites.py --paths-only
+
+"""
+
+
+@dataclass(frozen=True)
+class Args:
+    json_mode: bool = False
+    require_tasks: bool = False
+    include_tasks: bool = False
+    paths_only: bool = False
+
+
+def _parse_args(argv: list[str]) -> Args:
+    json_mode = False
+    require_tasks = False
+    include_tasks = False
+    paths_only = False
+
+    for arg in argv:
+        if arg == "--json":
+            json_mode = True
+        elif arg == "--require-tasks":
+            require_tasks = True
+        elif arg == "--include-tasks":
+            include_tasks = True
+        elif arg == "--paths-only":
+            paths_only = True
+        elif arg in {"--help", "-h"}:
+            sys.stdout.write(HELP_TEXT)
+            raise SystemExit(0)
+        else:
+            print(
+                f"ERROR: Unknown option '{arg}'. Use --help for usage information.",
+                file=sys.stderr,
+            )
+            raise SystemExit(1)
+
+    return Args(
+        json_mode=json_mode,
+        require_tasks=require_tasks,
+        include_tasks=include_tasks,
+        paths_only=paths_only,
+    )
+
+
+def _dir_has_entries(path: Path) -> bool:
+    try:
+        return path.is_dir() and any(path.iterdir())
+    except OSError:
+        return False
+
+
+def _available_docs(paths: FeaturePaths, include_tasks: bool) -> list[str]:
+    docs: list[str] = []
+    if paths.research.is_file():
+        docs.append("research.md")
+    if paths.data_model.is_file():
+        docs.append("data-model.md")
+    if _dir_has_entries(paths.contracts_dir):
+        docs.append("contracts/")
+    if paths.quickstart.is_file():
+        docs.append("quickstart.md")
+    if include_tasks and paths.tasks.is_file():
+        docs.append("tasks.md")
+    return docs
+
+
+def _print_paths_only(paths: FeaturePaths, json_mode: bool) -> None:
+    if json_mode:
+        sys.stdout.write(
+            _json_line(
+                {
+                    "REPO_ROOT": str(paths.repo_root),
+                    "BRANCH": paths.current_branch,
+                    "FEATURE_DIR": str(paths.feature_dir),
+                    "FEATURE_SPEC": str(paths.feature_spec),
+                    "IMPL_PLAN": str(paths.impl_plan),
+                    "TASKS": str(paths.tasks),
+                }
+            )
+        )
+        return
+
+    print(f"REPO_ROOT: {paths.repo_root}")
+    print(f"BRANCH: {paths.current_branch}")
+    print(f"FEATURE_DIR: {paths.feature_dir}")
+    print(f"FEATURE_SPEC: {paths.feature_spec}")
+    print(f"IMPL_PLAN: {paths.impl_plan}")
+    print(f"TASKS: {paths.tasks}")
+
+
+def _check_file(path: Path, description: str) -> None:
+    marker = "✓" if path.is_file() else "✗"
+    print(f"  {marker} {description}")
+
+
+def _check_dir(path: Path, description: str) -> None:
+    marker = "✓" if _dir_has_entries(path) else "✗"
+    print(f"  {marker} {description}")
+
+
+def _print_text_results(paths: FeaturePaths, include_tasks: bool) -> None:
+    print(f"FEATURE_DIR:{paths.feature_dir}")
+    print("AVAILABLE_DOCS:")
+    _check_file(paths.research, "research.md")
+    _check_file(paths.data_model, "data-model.md")
+    _check_dir(paths.contracts_dir, "contracts/")
+    _check_file(paths.quickstart, "quickstart.md")
+    if include_tasks:
+        _check_file(paths.tasks, "tasks.md")
+
+
+def main(argv: list[str] | None = None) -> int:
+    args = _parse_args(list(argv if argv is not None else sys.argv[1:]))
+
+    try:
+        paths = get_feature_paths(
+            no_persist=args.paths_only,
+            script_file=Path(__file__),
+        )
+    except SystemExit as exc:
+        if exc.code == 0:
+            return 0
+        print("ERROR: Failed to resolve feature paths", file=sys.stderr)
+        return int(exc.code) if isinstance(exc.code, int) else 1
+
+    if args.paths_only:
+        _print_paths_only(paths, args.json_mode)
+        return 0
+
+    if not paths.feature_dir.is_dir():
+        print(f"ERROR: Feature directory not found: {paths.feature_dir}", file=sys.stderr)
+        print(
+            f"Run {format_speckit_command('specify', paths.repo_root)} first to create the feature structure.",
+            file=sys.stderr,
+        )
+        return 1
+
+    if not paths.impl_plan.is_file():
+        print(f"ERROR: plan.md not found in {paths.feature_dir}", file=sys.stderr)
+        print(
+            f"Run {format_speckit_command('plan', paths.repo_root)} first to create the implementation plan.",
+            file=sys.stderr,
+        )
+        return 1
+
+    if args.require_tasks and not paths.tasks.is_file():
+        print(f"ERROR: tasks.md not found in {paths.feature_dir}", file=sys.stderr)
+        print(
+            f"Run {format_speckit_command('tasks', paths.repo_root)} first to create the task list.",
+            file=sys.stderr,
+        )
+        return 1
+
+    docs = _available_docs(paths, args.include_tasks)
+    if args.json_mode:
+        sys.stdout.write(
+            _json_line({"FEATURE_DIR": str(paths.feature_dir), "AVAILABLE_DOCS": docs})
+        )
+    else:
+        _print_text_results(paths, args.include_tasks)
+    return 0
+
+
+if __name__ == "__main__":
+    raise SystemExit(main())

scripts/python/common.py

@@ -0,0 +1,210 @@
+"""Shared helpers for Spec Kit Python scripts."""
+
+from __future__ import annotations
+
+import json
+import os
+import sys
+from dataclasses import dataclass
+from pathlib import Path
+
+
+def _trim_trailing_separators(value: Path) -> str:
+    text = str(value)
+    while len(text) > 1 and text.endswith((os.sep, "/")):
+        text = text[:-1]
+    return text
+
+
+def find_specify_root(start_dir: Path | None = None) -> Path | None:
+    current = (start_dir or Path.cwd()).resolve()
+    while True:
+        if (current / ".specify").is_dir():
+            return current
+        parent = current.parent
+        if parent == current:
+            return None
+        current = parent
+
+
+def resolve_specify_init_dir() -> Path:
+    raw = os.environ.get("SPECIFY_INIT_DIR", "")
+    candidate = Path(raw)
+    if not candidate.is_absolute():
+        candidate = Path.cwd() / candidate
+    try:
+        init_root = candidate.resolve(strict=True)
+    except OSError:
+        print(
+            f"ERROR: SPECIFY_INIT_DIR does not point to an existing directory: {raw}",
+            file=sys.stderr,
+        )
+        raise SystemExit(1)
+    if not init_root.is_dir():
+        print(
+            f"ERROR: SPECIFY_INIT_DIR does not point to an existing directory: {raw}",
+            file=sys.stderr,
+        )
+        raise SystemExit(1)
+    if not (init_root / ".specify").is_dir():
+        print(
+            "ERROR: SPECIFY_INIT_DIR is not a Spec Kit project "
+            f"(no .specify/ directory): {init_root}",
+            file=sys.stderr,
+        )
+        raise SystemExit(1)
+    return init_root
+
+
+def get_repo_root(script_file: Path | None = None) -> Path:
+    if os.environ.get("SPECIFY_INIT_DIR"):
+        return resolve_specify_init_dir()
+
+    specify_root = find_specify_root()
+    if specify_root is not None:
+        return specify_root
+
+    if script_file is not None:
+        script_root = find_specify_root(script_file.resolve().parent)
+        if script_root is not None:
+            return script_root
+
+        # Installed scripts live at .specify/scripts/python/<script>.py.
+        return script_file.resolve().parents[3]
+    return Path.cwd().resolve()
+
+
+def get_current_branch() -> str:
+    return os.environ.get("SPECIFY_FEATURE", "")
+
+
+def read_feature_json_feature_directory(repo_root: Path) -> str:
+    feature_json = repo_root / ".specify" / "feature.json"
+    if not feature_json.is_file():
+        return ""
+    try:
+        data = json.loads(feature_json.read_text(encoding="utf-8"))
+    except (OSError, json.JSONDecodeError):
+        return ""
+    value = data.get("feature_directory") if isinstance(data, dict) else None
+    return value if isinstance(value, str) else ""
+
+
+def _json_dump(data: dict[str, str]) -> str:
+    return json.dumps(data, ensure_ascii=False, separators=(",", ":")) + "\n"
+
+
+def persist_feature_json(repo_root: Path, feature_dir_value: str) -> None:
+    value = feature_dir_value
+    try:
+        relative = Path(value)
+        if relative.is_absolute():
+            try:
+                value = relative.resolve().relative_to(repo_root.resolve()).as_posix()
+            except ValueError:
+                value = str(relative)
+    except OSError:
+        pass
+
+    current = read_feature_json_feature_directory(repo_root)
+    if current == value:
+        return
+
+    specify_dir = repo_root / ".specify"
+    specify_dir.mkdir(parents=True, exist_ok=True)
+    (specify_dir / "feature.json").write_text(
+        _json_dump({"feature_directory": value}),
+        encoding="utf-8",
+    )
+
+
+@dataclass(frozen=True)
+class FeaturePaths:
+    repo_root: Path
+    current_branch: str
+    feature_dir: Path
+    feature_spec: Path
+    impl_plan: Path
+    tasks: Path
+    research: Path
+    data_model: Path
+    quickstart: Path
+    contracts_dir: Path
+
+
+def get_feature_paths(
+    *, no_persist: bool = False, script_file: Path | None = None
+) -> FeaturePaths:
+    repo_root = get_repo_root(script_file)
+    current_branch = get_current_branch()
+
+    feature_dir_raw = os.environ.get("SPECIFY_FEATURE_DIRECTORY", "")
+    if feature_dir_raw:
+        feature_dir = Path(feature_dir_raw)
+        if not feature_dir.is_absolute():
+            feature_dir = repo_root / feature_dir
+        if not no_persist:
+            persist_feature_json(repo_root, feature_dir_raw)
+    elif (repo_root / ".specify" / "feature.json").is_file():
+        stored = read_feature_json_feature_directory(repo_root)
+        if not stored:
+            print(
+                "ERROR: Feature directory not found. Set SPECIFY_FEATURE_DIRECTORY "
+                "or ensure .specify/feature.json contains feature_directory.",
+                file=sys.stderr,
+            )
+            raise SystemExit(1)
+        feature_dir = Path(stored)
+        if not feature_dir.is_absolute():
+            feature_dir = repo_root / feature_dir
+    else:
+        print(
+            "ERROR: Feature directory not found. Set SPECIFY_FEATURE_DIRECTORY "
+            "or run the specify command to create .specify/feature.json.",
+            file=sys.stderr,
+        )
+        raise SystemExit(1)
+
+    if not current_branch:
+        current_branch = Path(_trim_trailing_separators(feature_dir)).name
+
+    return FeaturePaths(
+        repo_root=repo_root,
+        current_branch=current_branch,
+        feature_dir=feature_dir,
+        feature_spec=feature_dir / "spec.md",
+        impl_plan=feature_dir / "plan.md",
+        tasks=feature_dir / "tasks.md",
+        research=feature_dir / "research.md",
+        data_model=feature_dir / "data-model.md",
+        quickstart=feature_dir / "quickstart.md",
+        contracts_dir=feature_dir / "contracts",
+    )
+
+
+def get_invoke_separator(repo_root: Path) -> str:
+    integration_json = repo_root / ".specify" / "integration.json"
+    if not integration_json.is_file():
+        return "."
+    try:
+        state = json.loads(integration_json.read_text(encoding="utf-8"))
+        key = state.get("default_integration") or state.get("integration") or ""
+        settings = state.get("integration_settings")
+        if isinstance(key, str) and isinstance(settings, dict):
+            entry = settings.get(key)
+            if isinstance(entry, dict) and entry.get("invoke_separator") in {".", "-"}:
+                return entry["invoke_separator"]
+    except (OSError, json.JSONDecodeError):
+        pass
+    return "."
+
+
+def format_speckit_command(command_name: str, repo_root: Path) -> str:
+    separator = get_invoke_separator(repo_root)
+    name = command_name.lstrip("/")
+    if name.startswith("speckit."):
+        name = name[len("speckit.") :]
+    elif name.startswith("speckit-"):
+        name = name[len("speckit-") :]
+    name = name.replace(".", separator)
+    return f"/speckit{separator}{name}"

spec-kit.code-workspace

@@ -5,4 +5,4 @@
 		}
 	],
 	"settings": {}
-}
+}

src/specify_cli/__init__.py

@@ -141,8 +141,9 @@ def _install_shared_infra(
 
     Copies ``.specify/scripts/<variant>/`` and ``.specify/templates/`` from
     the bundled core_pack or source checkout, where ``<variant>`` is
-    ``bash`` when *script_type* is ``"sh"`` and ``powershell`` when it is
-    ``"ps"``.  Tracks all installed files in ``speckit.manifest.json``.
+    ``bash`` when *script_type* is ``"sh"``, ``python`` when it is ``"py"``,
+    and ``powershell`` when it is ``"ps"``.  Tracks all installed files in
+    ``speckit.manifest.json``.
 
     Shared scripts and page templates are processed to resolve
     ``__SPECKIT_COMMAND_<NAME>__`` placeholders using *invoke_separator*

src/specify_cli/_github_http.py

@@ -127,7 +127,14 @@ def resolve_github_release_asset_api_url(
     if hostname == "github.com":
         api_base = "https://api.github.com"
     elif is_ghes:
-        authority = hostname if parsed.port is None else f"{hostname}:{parsed.port}"
+        # ``parsed.port`` raises ValueError on a malformed port (e.g.
+        # ``host:notaport``); the function's contract is to return None for
+        # anything it can't resolve, not to raise.
+        try:
+            port = parsed.port
+        except ValueError:
+            return None
+        authority = hostname if port is None else f"{hostname}:{port}"
         api_base = f"{parsed.scheme}://{authority}/api/v3"
     else:
         return None

src/specify_cli/_toml_string.py

@@ -0,0 +1,60 @@
+"""Shared TOML string-escaping helpers.
+
+Both TOML command renderers — ``TomlIntegration`` (gemini, tabnine) in
+``specify_cli.integrations.base`` and ``CommandRegistrar.render_toml_command``
+(extension/preset commands) in ``specify_cli.agents`` — need the same rules for
+detecting characters TOML forbids literally and for emitting a fully-escaped
+basic string. Keeping one implementation here avoids the two drifting apart if
+the escaping rules change again.
+"""
+from __future__ import annotations
+
+
+def has_illegal_toml_control(value: str) -> bool:
+    """True when *value* contains a character TOML forbids literally.
+
+    TOML basic/literal strings (single- or multi-line) allow tab and, in the
+    multiline forms, newlines — but every other control character
+    (``U+0000``–``U+001F`` and ``U+007F``) must be ``\\u``-escaped, which only a
+    basic string can do. A bare carriage return counts too: a multiline basic
+    string treats ``\\r`` as a newline only when paired into ``\\r\\n``; a lone
+    ``\\r`` is an illegal control character.
+    """
+    length = len(value)
+    for i, ch in enumerate(value):
+        code = ord(ch)
+        if ch == "\r":
+            # Only a CR that is part of a CRLF newline is allowed literally.
+            if i + 1 < length and value[i + 1] == "\n":
+                continue
+            return True
+        if (code < 0x20 and ch not in ("\t", "\n")) or code == 0x7F:
+            return True
+    return False
+
+
+def escape_toml_basic(value: str) -> str:
+    """Render *value* as a single-line basic string, escaping everything.
+
+    Always valid TOML: backslash/quote are escaped, the common control chars
+    use their short escapes, and any remaining control character is emitted as
+    a ``\\uXXXX`` sequence.
+    """
+    out: list[str] = []
+    for ch in value:
+        code = ord(ch)
+        if ch == "\\":
+            out.append("\\\\")
+        elif ch == '"':
+            out.append('\\"')
+        elif ch == "\n":
+            out.append("\\n")
+        elif ch == "\r":
+            out.append("\\r")
+        elif ch == "\t":
+            out.append("\\t")
+        elif code < 0x20 or code == 0x7F:
+            out.append(f"\\u{code:04x}")
+        else:
+            out.append(ch)
+    return '"' + "".join(out) + '"'

src/specify_cli/agents.py

@@ -16,6 +16,8 @@ from typing import Any, Dict, List, Optional
 import yaml
 
 from ._init_options import is_ai_skills_enabled, load_init_options
+from ._toml_string import escape_toml_basic as _escape_toml_basic
+from ._toml_string import has_illegal_toml_control as _has_illegal_toml_control
 from ._utils import relative_extension_path_violation
 
 
@@ -148,7 +150,9 @@ class CommandRegistrar:
         )
         return f"---\n{yaml_str}---\n"
 
-    def _adjust_script_paths(self, frontmatter: dict) -> dict:
+    def _adjust_script_paths(
+        self, frontmatter: dict, extension_id: Optional[str] = None
+    ) -> dict:
         """Normalize script paths in frontmatter to generated project locations.
 
         Rewrites known repo-relative and top-level script paths under the
@@ -158,6 +162,7 @@ class CommandRegistrar:
 
         Args:
             frontmatter: Frontmatter dictionary
+            extension_id: Extension id when rendering extension-owned commands.
 
         Returns:
             Modified frontmatter with normalized project paths
@@ -168,11 +173,15 @@ class CommandRegistrar:
         if isinstance(scripts, dict):
             for key, script_path in scripts.items():
                 if isinstance(script_path, str):
-                    scripts[key] = self.rewrite_project_relative_paths(script_path)
+                    scripts[key] = self.rewrite_project_relative_paths(
+                        script_path, extension_id=extension_id
+                    )
         return frontmatter
 
     @staticmethod
-    def rewrite_project_relative_paths(text: str) -> str:
+    def rewrite_project_relative_paths(
+        text: str, extension_id: Optional[str] = None
+    ) -> str:
         """Rewrite repo-relative paths to their generated project locations."""
         if not isinstance(text, str) or not text:
             return text
@@ -184,10 +193,18 @@ class CommandRegistrar:
         ):
             text = text.replace(old, new)
 
-        # Only rewrite top-level style references so extension-local paths like
-        # ".specify/extensions/<ext>/scripts/..." remain intact.
+        # Only rewrite top-level style references so existing generated paths
+        # like ".specify/extensions/<ext>/scripts/..." remain intact. When
+        # rendering extension commands, top-level "scripts/" is extension-local.
+        scripts_replacement = (
+            f".specify/extensions/{extension_id}/scripts/"
+            if extension_id
+            else ".specify/scripts/"
+        )
         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`"\'(])(?:\.?/)?scripts/', rf"\1{scripts_replacement}", text
+        )
         text = re.sub(
             r'(^|[\s`"\'(])(?:\.?/)?templates/', r"\1.specify/templates/", text
         )
@@ -196,6 +213,52 @@ class CommandRegistrar:
             ".specify.specify/", ".specify/"
         )
 
+    @staticmethod
+    def rewrite_extension_paths(
+        text: str, extension_id: str, extension_dir: Path
+    ) -> str:
+        """Rewrite extension-relative paths to their installed locations.
+
+        Extension command bodies reference bundled files relative to the
+        extension root (e.g. ``agents/control/commander.md``). After install
+        those files live under ``.specify/extensions/<id>/``, so bare
+        references would resolve against the workspace root and never be
+        found (#2101).
+
+        Only directories that actually exist inside *extension_dir* are
+        rewritten, keeping the behaviour conservative and avoiding false
+        positives on prose. ``commands`` (slash-command sources), ``specs``
+        (user project artifacts) and dot-directories are never rewritten.
+        """
+        if not isinstance(text, str) or not text:
+            return text
+
+        skip = {"commands", ".git", "specs"}
+        try:
+            subdirs = [
+                entry.name
+                for entry in extension_dir.iterdir()
+                if entry.is_dir()
+                and entry.name not in skip
+                and not entry.name.startswith(".")
+            ]
+        except OSError:
+            return text
+
+        for subdir in subdirs:
+            # Only rewrite relative references (subdir/... or ./subdir/...);
+            # absolute paths like /subdir/... keep their meaning. Use a
+            # callable replacement: subdir/extension_id come from the
+            # filesystem and could contain backslashes or "\1"-like
+            # sequences, which would corrupt a string replacement template.
+            replacement = f".specify/extensions/{extension_id}/{subdir}/"
+            text = re.sub(
+                r'(^|[\s`"\'(])(?:\./)?' + re.escape(subdir) + "/",
+                lambda m: m.group(1) + replacement,
+                text,
+            )
+        return text
+
     def render_markdown_command(
         self, frontmatter: dict, body: str, source_id: str, context_note: str = None
     ) -> str:
@@ -243,7 +306,12 @@ class CommandRegistrar:
         # ``C:\\Users\\...`` whose ``\\U`` reads as an invalid unicode escape) would
         # produce unparseable TOML — route those to the *literal* form ('''...'''),
         # which does not process escapes, or to the escaped basic string.
-        if '"""' not in body and "\\" not in body:
+        # Control characters (U+0000–U+001F except tab/newline, U+007F) and a bare
+        # CR are illegal in every TOML string form, so a body containing them must
+        # go to the escaped basic string regardless of which delimiters it uses.
+        if self._has_illegal_toml_control(body):
+            toml_lines.append(f"prompt = {self._render_basic_toml_string(body)}")
+        elif '"""' not in body and "\\" not in body:
             toml_lines.append('prompt = """')
             toml_lines.append(body)
             toml_lines.append('"""')
@@ -256,17 +324,11 @@ class CommandRegistrar:
 
         return "\n".join(toml_lines)
 
-    @staticmethod
-    def _render_basic_toml_string(value: str) -> str:
-        """Render *value* as a TOML basic string literal."""
-        escaped = (
-            value.replace("\\", "\\\\")
-            .replace('"', '\\"')
-            .replace("\n", "\\n")
-            .replace("\r", "\\r")
-            .replace("\t", "\\t")
-        )
-        return f'"{escaped}"'
+    # Control-char detection and basic-string escaping are shared with the
+    # gemini/tabnine renderer in ``specify_cli.integrations.base`` via
+    # ``specify_cli._toml_string`` so the two never drift apart.
+    _has_illegal_toml_control = staticmethod(_has_illegal_toml_control)
+    _render_basic_toml_string = staticmethod(_escape_toml_basic)
 
     def render_yaml_command(
         self,
@@ -312,6 +374,7 @@ class CommandRegistrar:
         source_id: str,
         source_file: str,
         project_root: Path,
+        extension_id: Optional[str] = None,
     ) -> str:
         """Render a command override as a SKILL.md file.
 
@@ -331,7 +394,7 @@ class CommandRegistrar:
         agent_config = self.AGENT_CONFIGS.get(agent_name, {})
         if agent_config.get("extension") == "/SKILL.md":
             body = self.resolve_skill_placeholders(
-                agent_name, frontmatter, body, project_root
+                agent_name, frontmatter, body, project_root, extension_id=extension_id
             )
 
         description = frontmatter.get(
@@ -393,7 +456,11 @@ class CommandRegistrar:
 
     @staticmethod
     def resolve_skill_placeholders(
-        agent_name: str, frontmatter: dict, body: str, project_root: Path
+        agent_name: str,
+        frontmatter: dict,
+        body: str,
+        project_root: Path,
+        extension_id: Optional[str] = None,
     ) -> str:
         """Resolve script placeholders for skills-backed agents."""
         if not isinstance(frontmatter, dict):
@@ -433,7 +500,9 @@ class CommandRegistrar:
 
         body = body.replace("{ARGS}", "$ARGUMENTS").replace("__AGENT__", agent_name)
 
-        return CommandRegistrar.rewrite_project_relative_paths(body)
+        return CommandRegistrar.rewrite_project_relative_paths(
+            body, extension_id=extension_id
+        )
 
     def _convert_argument_placeholder(
         self, content: str, from_placeholder: str, to_placeholder: str
@@ -528,6 +597,7 @@ class CommandRegistrar:
         context_note: str = None,
         _resolved_dir: Path = None,
         link_outputs: bool = False,
+        extension_id: Optional[str] = None,
     ) -> List[str]:
         """Register commands for a specific agent.
 
@@ -545,6 +615,7 @@ class CommandRegistrar:
             link_outputs: If True, write rendered output to a source-local
                 dev cache and symlink the agent command file to it. Falls back
                 to a normal file write when symlinks are unavailable.
+            extension_id: Extension id when rendering extension-owned commands.
 
         Returns:
             List of registered command names
@@ -614,7 +685,12 @@ class CommandRegistrar:
                         frontmatter[key] = core_frontmatter[key]
                 frontmatter.pop("strategy", None)
 
-            frontmatter = self._adjust_script_paths(frontmatter)
+            if extension_id:
+                body = self.rewrite_extension_paths(body, extension_id, source_root)
+
+            frontmatter = self._adjust_script_paths(
+                frontmatter, extension_id=extension_id
+            )
 
             for key in agent_config.get("strip_frontmatter_keys", []):
                 frontmatter.pop(key, None)
@@ -653,10 +729,11 @@ class CommandRegistrar:
                     source_id,
                     cmd_file,
                     project_root,
+                    extension_id=extension_id,
                 )
             elif agent_config["format"] == "markdown":
                 body = self.resolve_skill_placeholders(
-                    agent_name, frontmatter, body, project_root
+                    agent_name, frontmatter, body, project_root, extension_id=extension_id
                 )
                 body = self._convert_argument_placeholder(
                     body, "$ARGUMENTS", agent_config["args"]
@@ -666,19 +743,36 @@ class CommandRegistrar:
                 )
             elif agent_config["format"] == "toml":
                 body = self.resolve_skill_placeholders(
-                    agent_name, frontmatter, body, project_root
+                    agent_name, frontmatter, body, project_root, extension_id=extension_id
                 )
                 body = self._convert_argument_placeholder(
                     body, "$ARGUMENTS", agent_config["args"]
                 )
                 output = self.render_toml_command(frontmatter, body, source_id)
             elif agent_config["format"] == "yaml":
+                body = self.resolve_skill_placeholders(
+                    agent_name, frontmatter, body, project_root
+                )
+                body = self._convert_argument_placeholder(
+                    body, "$ARGUMENTS", agent_config["args"]
+                )
                 output = self.render_yaml_command(
                     frontmatter, body, source_id, cmd_name
                 )
             else:
                 raise ValueError(f"Unsupported format: {agent_config['format']}")
 
+            # -- Post-process for non-skills agents -----------------------
+            _integration = None
+            if agent_config["extension"] != "/SKILL.md":
+                from specify_cli.integrations import (  # noqa: PLC0415
+                    get_integration,
+                )
+
+                _integration = get_integration(agent_name)
+                if _integration is not None:
+                    output = _integration.post_process_command_content(output)
+
             dest_file = commands_dir / f"{output_name}{agent_config['extension']}"
             self._ensure_inside(dest_file, commands_dir)
             dest_file.parent.mkdir(parents=True, exist_ok=True)
@@ -721,6 +815,7 @@ class CommandRegistrar:
                             source_id,
                             cmd_file,
                             project_root,
+                            extension_id=extension_id,
                         )
                     elif agent_config["format"] == "markdown":
                         alias_output = self.render_markdown_command(
@@ -738,6 +833,9 @@ class CommandRegistrar:
                         raise ValueError(
                             f"Unsupported format: {agent_config['format']}"
                         )
+
+                    if agent_config["extension"] != "/SKILL.md" and _integration is not None:
+                        alias_output = _integration.post_process_command_content(alias_output)
                 else:
                     # For other agents, reuse the primary output
                     alias_output = output
@@ -750,6 +848,7 @@ class CommandRegistrar:
                             source_id,
                             cmd_file,
                             project_root,
+                            extension_id=extension_id,
                         )
 
                 alias_file = (
@@ -881,6 +980,7 @@ class CommandRegistrar:
         context_note: str = None,
         link_outputs: bool = False,
         create_missing_active_skills_dir: bool = False,
+        extension_id: Optional[str] = None,
     ) -> Dict[str, List[str]]:
         """Register commands for all detected agents in the project.
 
@@ -897,6 +997,7 @@ class CommandRegistrar:
                 Recovery requires active skills mode (or Kimi's existing native
                 skills directory) and is skipped when safe resolution or
                 creation fails.
+            extension_id: Extension id when rendering extension-owned commands.
 
         Returns:
             Dictionary mapping agent names to list of registered commands
@@ -999,6 +1100,7 @@ class CommandRegistrar:
                         context_note=context_note,
                         _resolved_dir=agent_dir,
                         link_outputs=link_outputs,
+                        extension_id=extension_id,
                     )
                     if registered:
                         results[agent_name] = registered
@@ -1023,6 +1125,7 @@ class CommandRegistrar:
         project_root: Path,
         context_note: Optional[str] = None,
         link_outputs: bool = False,
+        extension_id: Optional[str] = None,
     ) -> Dict[str, List[str]]:
         """Register commands for all non-skill agents in the project.
 
@@ -1038,6 +1141,7 @@ class CommandRegistrar:
             context_note: Custom context comment for markdown output
             link_outputs: If True, create dev-mode symlinks for rendered
                 command files when supported by the OS.
+            extension_id: Extension id when rendering extension-owned commands.
 
         Returns:
             Dictionary mapping agent names to list of registered commands
@@ -1066,6 +1170,7 @@ class CommandRegistrar:
                         context_note=context_note,
                         _resolved_dir=agent_dir,
                         link_outputs=link_outputs,
+                        extension_id=extension_id,
                     )
                     if registered:
                         results[agent_name] = registered

src/specify_cli/authentication/config.py

@@ -196,7 +196,15 @@ def find_entries_for_url(
     url: str, entries: list[AuthConfigEntry]
 ) -> list[AuthConfigEntry]:
     """Return entries whose ``hosts`` match the hostname of *url*."""
-    hostname = (urlparse(url).hostname or "").lower()
+    # A malformed authority (e.g. an unterminated IPv6 bracket "https://[::1")
+    # makes urlparse/hostname raise ValueError. Treat that the same as a
+    # host-less URL: no entry can match, so return no matches rather than
+    # leaking a raw ValueError out of the shared HTTP client (build_request /
+    # open_url call this before any URL validation).
+    try:
+        hostname = (urlparse(url).hostname or "").lower()
+    except ValueError:
+        return []
     if not hostname:
         return []
     return [

src/specify_cli/authentication/http.py

@@ -73,6 +73,13 @@ class _StripAuthOnRedirect(urllib.request.HTTPRedirectHandler):
         self._redirect_validator = redirect_validator
 
     def redirect_request(self, req, fp, code, msg, headers, newurl):
+        try:
+            new_parsed = urlparse(newurl)
+        except ValueError as exc:
+            # Malformed redirect target (e.g. unterminated IPv6 bracket).
+            # Surface as URLError so callers' download error handling applies.
+            raise urllib.error.URLError(f"malformed redirect URL: {exc}") from exc
+
         if self._redirect_validator is not None:
             self._redirect_validator(req.full_url, newurl)
 
@@ -83,7 +90,6 @@ class _StripAuthOnRedirect(urllib.request.HTTPRedirectHandler):
         new_req = super().redirect_request(req, fp, code, msg, headers, newurl)
         if new_req is not None:
             old_scheme = urlparse(req.full_url).scheme
-            new_parsed = urlparse(newurl)
             hostname = (new_parsed.hostname or "").lower()
             is_https_downgrade = old_scheme == "https" and new_parsed.scheme != "https"
             if _hostname_in_hosts(hostname, self._hosts) and not is_https_downgrade:

src/specify_cli/bundler/commands_impl/catalog_config.py

@@ -95,7 +95,11 @@ def _is_local_path(url: str) -> bool:
     """True when *url* denotes a local filesystem path rather than a URL."""
     if _WINDOWS_DRIVE_RE.match(url):
         return True
-    scheme = urlparse(url).scheme.lower()
+    try:
+        scheme = urlparse(url).scheme.lower()
+    except ValueError:
+        # Malformed URLs (e.g. an unclosed IPv6 bracket) are not local paths.
+        return False
     return scheme not in _REMOTE_SCHEMES
 
 
@@ -137,7 +141,10 @@ def add_source(
     url = url.strip()
     if not url:
         raise BundlerError("A catalog url is required.")
-    parsed = urlparse(url)
+    try:
+        parsed = urlparse(url)
+    except ValueError as exc:
+        raise BundlerError(f"Invalid catalog url: '{url}'.") from exc
     if not (parsed.scheme or parsed.path):
         raise BundlerError(f"Invalid catalog url: '{url}'.")
     # Reject unsupported URL schemes (e.g. ssh://, ftp://) up front so they are
@@ -148,6 +155,20 @@ def add_source(
             f"Unsupported catalog url scheme '{parsed.scheme}://' in '{url}'. "
             "Use http(s)://, file://, builtin://, or a local path."
         )
+    if parsed.scheme.lower() in {"http", "https"}:
+        # Mirror specify_cli.catalogs._validate_catalog_url (#3209/#3210):
+        # HTTPS only (HTTP just for localhost), and check hostname, not
+        # netloc — netloc is truthy for host-less URLs like "https://:8080"
+        # or "https://user@". Validating here keeps junk out of
+        # bundle-catalogs.yml instead of failing later at fetch time.
+        is_localhost = parsed.hostname in ("localhost", "127.0.0.1", "::1")
+        if parsed.scheme.lower() != "https" and not is_localhost:
+            raise BundlerError(
+                f"Catalog url must use HTTPS (got {parsed.scheme}://). "
+                "HTTP is only allowed for localhost."
+            )
+        if not parsed.hostname:
+            raise BundlerError(f"Catalog url must be a valid URL with a host: {url}")
 
     url = _canonicalize_url(url)
     install_policy = InstallPolicy.parse(policy)

src/specify_cli/bundler/services/adapters.py

@@ -68,14 +68,28 @@ def _validate_remote_url(source_id: str, url: str) -> None:
     Mirrors ``specify_cli.catalogs`` URL validation to avoid MITM/downgrade
     issues before any network call.
     """
-    parsed = urlparse(url)
-    is_localhost = parsed.hostname in ("localhost", "127.0.0.1", "::1")
+    # A malformed authority (e.g. an unclosed IPv6 bracket ``https://[::1``)
+    # makes urlparse / hostname access raise ValueError. This function's
+    # contract is to raise BundlerError for a bad URL, so surface that as a
+    # clean error rather than leaking a raw ValueError to the caller.
+    try:
+        parsed = urlparse(url)
+        hostname = parsed.hostname
+    except ValueError:
+        raise BundlerError(
+            f"Catalog '{source_id}' URL is malformed: {url}"
+        ) from None
+    is_localhost = hostname in ("localhost", "127.0.0.1", "::1")
     if parsed.scheme != "https" and not (parsed.scheme == "http" and is_localhost):
         raise BundlerError(
             f"Catalog '{source_id}' URL must use HTTPS (got {parsed.scheme}://). "
             "HTTP is only allowed for localhost."
         )
-    if not parsed.netloc:
+    # Check hostname, not netloc: netloc is truthy for host-less URLs like
+    # "https://:8080" or "https://user@...", so requiring netloc would let
+    # those through even though they carry no host. hostname is None in those
+    # cases. Mirrors the fix in ``specify_cli.catalogs`` (#3210).
+    if not hostname:
         raise BundlerError(
             f"Catalog '{source_id}' URL must be a valid URL with a host: {url}"
         )

src/specify_cli/bundler/services/catalog_stack.py

@@ -88,17 +88,25 @@ class CatalogStack:
         Results are sorted by bundle id for deterministic output.
         """
         needle = query.strip().lower()
-        seen: dict[str, ResolvedBundle] = {}
+        # Resolve each id to its highest-precedence entry FIRST, then filter by
+        # the query. Claiming an id only when it matches would let a lower-
+        # precedence entry with the same id surface when the highest-precedence
+        # one doesn't match the query — but that shadowed entry is not what
+        # `resolve()`/install would use, so search would advertise a bundle
+        # (name, version, author) the user can never actually get.
+        resolved: dict[str, ResolvedBundle] = {}
         for source in self._sources:
             for bundle_id, entry in self._entries_for(source).items():
-                if bundle_id in seen:
+                if bundle_id in resolved:
                     continue
-                if needle and not _matches(entry, needle):
-                    continue
-                seen[bundle_id] = ResolvedBundle(
+                resolved[bundle_id] = ResolvedBundle(
                     entry=entry.with_provenance(source), source=source
                 )
-        return [seen[k] for k in sorted(seen)]
+        return [
+            resolved[k]
+            for k in sorted(resolved)
+            if not needle or _matches(resolved[k].entry, needle)
+        ]
 
 
 def _matches(entry: CatalogEntry, needle: str) -> bool:

src/specify_cli/bundler/services/installer.py

@@ -130,6 +130,28 @@ def install_bundle(
             done.append(component)
             result.installed.append(component)
             contributed.append(component)
+
+        # On update (refresh), uninstall components this bundle used to own
+        # that the new version no longer ships. Otherwise they are dropped
+        # from the record below (contributed only holds plan.components) yet
+        # left on disk — permanently orphaned, since no bundle record can
+        # ever remove them. A stale component still owned by another bundle
+        # is kept installed and simply de-attributed here (it stays in that
+        # bundle's record). Mirrors remove_bundle's refcount logic.
+        if refresh and existing is not None:
+            planned = {(c.kind, c.id) for c in plan.components}
+            still_needed = components_still_needed(
+                records, exclude_bundle_id=plan.bundle_id
+            )
+            for component in existing.contributed_components:
+                key = (component.kind, component.id)
+                if key in planned:
+                    continue
+                if key in still_needed:
+                    continue
+                if installer.is_installed(project_root, component):
+                    installer.remove(project_root, component)
+                    result.uninstalled.append(component)
     except BundlerError:
         _rollback(project_root, installer, done)
         raise

src/specify_cli/bundler/services/primitives.py

@@ -33,12 +33,13 @@ DEFAULT_PRIORITY = 10
 def _assert_pinned_version(
     kind: str, component_id: str, pinned: str | None, advertised: object
 ) -> None:
-    """Refuse to install when the catalog version differs from the manifest pin.
+    """Refuse to install when the resolved version differs from the manifest pin.
 
     Bundle manifests pin component versions for reproducibility; installing
-    whatever the active catalog currently serves would silently violate the
-    pin. When the catalog advertises no version we cannot enforce the pin, so
-    installation proceeds (the catalog, not the bundler, owns that gap).
+    whatever the resolved source (catalog *or* bundled asset) provides would
+    silently violate the pin. When the source advertises no version we cannot
+    enforce the pin, so installation proceeds (the source, not the bundler,
+    owns that gap).
     """
     if not pinned or advertised is None:
         return
@@ -54,11 +55,35 @@ def _assert_pinned_version(
     if not matches:
         raise BundlerError(
             f"{kind} '{component_id}' is pinned to version {pinned} in the bundle "
-            f"manifest, but the active catalog serves {actual}. Update the bundle's "
-            "pinned version or the catalog before installing."
+            f"manifest, but the resolved version is {actual}. Update the bundle's "
+            "pinned version or the source before installing."
         )
 
 
+def _bundled_manifest_version(manifest_path: Path, root_key: str) -> str | None:
+    """Best-effort read of a bundled asset's declared version from its manifest.
+
+    Returns ``None`` when the manifest is missing/unreadable/invalid, which
+    ``_assert_pinned_version`` treats as "cannot enforce" (proceed) — matching
+    the catalog "advertises no version" escape hatch.
+    """
+    try:
+        import yaml
+
+        data = yaml.safe_load(manifest_path.read_text(encoding="utf-8"))
+        if isinstance(data, dict):
+            section = data.get(root_key)
+            if isinstance(section, dict):
+                version = section.get("version")
+                # Only a non-empty string is a usable version; anything else
+                # (missing / non-string / whitespace) means "cannot enforce".
+                if isinstance(version, str) and version.strip():
+                    return version
+    except Exception:  # noqa: BLE001 - unreadable/invalid manifest: skip pin
+        return None
+    return None
+
+
 class _KindManager(Protocol):
     def is_installed(self, component: ComponentRef) -> bool: ...
 
@@ -134,6 +159,15 @@ class _PresetKindManager:
 
         bundled = _locate_bundled_preset(component.id)
         if bundled is not None:
+            # Enforce the manifest pin against the bundled asset's own version,
+            # mirroring the catalog path below (the bundled path previously
+            # skipped the pin entirely).
+            _assert_pinned_version(
+                "Preset",
+                component.id,
+                component.version,
+                _bundled_manifest_version(bundled / "preset.yml", "preset"),
+            )
             self._manager.install_from_directory(bundled, speckit_version, priority)
             return
 
@@ -198,6 +232,15 @@ class _ExtensionKindManager:
 
         bundled = _locate_bundled_extension(component.id)
         if bundled is not None:
+            # Enforce the manifest pin against the bundled asset's own version,
+            # mirroring the catalog path below (the bundled path previously
+            # skipped the pin entirely).
+            _assert_pinned_version(
+                "Extension",
+                component.id,
+                component.version,
+                _bundled_manifest_version(bundled / "extension.yml", "extension"),
+            )
             self._manager.install_from_directory(
                 bundled, speckit_version, priority=priority
             )

src/specify_cli/catalogs.py

@@ -71,8 +71,12 @@ class CatalogStackBase:
         """Validate that a catalog URL uses HTTPS, except localhost HTTP."""
         from urllib.parse import urlparse
 
-        parsed = urlparse(url)
-        is_localhost = parsed.hostname in ("localhost", "127.0.0.1", "::1")
+        try:
+            parsed = urlparse(url)
+            hostname = parsed.hostname
+        except ValueError:
+            raise cls._error(f"Catalog URL is malformed: {url}") from None
+        is_localhost = hostname in ("localhost", "127.0.0.1", "::1")
         if parsed.scheme != "https" and not (parsed.scheme == "http" and is_localhost):
             raise cls._error(
                 f"Catalog URL must use HTTPS (got {parsed.scheme}://). "
@@ -81,7 +85,7 @@ class CatalogStackBase:
         # Check hostname, not netloc: netloc is truthy for host-less URLs like
         # "https://:8080" or "https://user@", so the host guarantee this error
         # promises would not actually hold. hostname is None in those cases (#3209).
-        if not parsed.hostname:
+        if not hostname:
             raise cls._error("Catalog URL must be a valid URL with a host.")
 
     def _load_catalog_config(self, config_path: Path) -> list[CatalogEntry] | None:

src/specify_cli/commands/bundle/__init__.py

@@ -746,11 +746,16 @@ def _resolve_manifest_path(path: Path | None) -> Path:
 def _download_manifest(resolved, *, offline: bool):
     """Resolve a bundle's manifest from its catalog ``download_url``.
 
-    Local/``file://`` URLs always work offline and may point at a ``.zip``
-    artifact, a bundle directory, or a ``bundle.yml`` (handled by
-    :func:`_local_manifest_source`). Remote ``https://`` URLs are fetched with
-    the shared authenticated, redirect-validated HTTP client, and only when not
-    ``--offline``.
+    Catalog ``download_url``s are HTTPS-only (``http`` allowed for localhost),
+    matching the extensions/presets/workflows catalog systems. Remote URLs are
+    fetched with the shared authenticated, redirect-validated HTTP client, and
+    only when not ``--offline``.
+
+    Local and ``file://`` sources are intentionally not resolved here: to
+    install a bundle from disk, pass the path positionally
+    (``specify bundle install ./path/to/bundle.yml`` — a bundle directory or a
+    ``.zip`` artifact also works), which :func:`_local_manifest_source` handles
+    before catalog resolution and which never touches ``download_url``.
     """
     from urllib.parse import urlparse
 
@@ -763,26 +768,35 @@ def _download_manifest(resolved, *, offline: bool):
     parsed = urlparse(url)
     scheme = parsed.scheme.lower()
 
-    # On Windows an absolute path like ``C:\bundle.yml`` parses with a
-    # single-letter ``scheme``; treat it as a local file, not a URL scheme.
+    # ``file://`` URLs and bare filesystem paths (including Windows drive paths
+    # like ``C:\bundle.yml``, which urlparse reads as a single-letter scheme)
+    # are not valid catalog download URLs. Catalog URLs are HTTPS-only across
+    # every catalog system; installing from disk is done by passing the path
+    # positionally, which never reaches URL resolution. Give an actionable
+    # error rather than accepting a scheme the rest of the codebase rejects.
     if scheme in ("", "file") or re.match(r"^[A-Za-z]:[\\/]", url):
-        local = Path(parsed.path if scheme == "file" else url)
-        manifest = _local_manifest_source(str(local))
-        if manifest is None:
-            raise BundlerError(f"Bundle manifest not found: {local}")
-        return manifest
+        raise BundlerError(
+            f"Catalog entry '{resolved.entry.id}' has a non-HTTP(S) download_url "
+            f"({url}); catalog download URLs must be HTTPS (http for localhost) — "
+            "a file:// URL, a local filesystem path, or a scheme-less value "
+            "(e.g. 'example.com/bundle.zip') is not accepted. "
+            "To install a bundle from disk, pass the path directly: "
+            "'specify bundle install <path-to-bundle.yml | bundle-dir | .zip>'."
+        )
 
-    if scheme in ("http", "https"):
-        if offline:
-            raise BundlerError(
-                f"Network access disabled; cannot download bundle '{resolved.entry.id}' "
-                f"from {url}."
-            )
-        return _download_remote_manifest(resolved.entry.id, url)
+    # Validate the scheme/host *before* the offline gate so an invalid or
+    # non-HTTPS download_url reports the real problem in every mode, rather
+    # than a misleading "Network access disabled" under --offline.
+    # (_download_remote_manifest re-checks this, but only once network access
+    # is permitted.) HTTPS-only, http allowed for localhost.
+    _require_https(f"bundle '{resolved.entry.id}'", url)
 
-    raise BundlerError(
-        f"Unsupported download_url scheme for bundle '{resolved.entry.id}': {url}"
-    )
+    if offline:
+        raise BundlerError(
+            f"Network access disabled; cannot download bundle '{resolved.entry.id}' "
+            f"from {url}."
+        )
+    return _download_remote_manifest(resolved.entry.id, url)
 
 
 def _require_https(label: str, url: str) -> None:

src/specify_cli/extensions/__init__.py

@@ -1075,9 +1075,16 @@ class ExtensionManager:
                         pass  # best-effort cleanup
                 continue
             frontmatter, body = registrar.parse_frontmatter(content)
-            frontmatter = registrar._adjust_script_paths(frontmatter)
+            frontmatter = registrar._adjust_script_paths(
+                frontmatter, extension_id=manifest.id
+            )
+            # Mirror the register_commands() rewrite (#2101): resolve
+            # extension-relative subdir references (agents/, knowledge-base/,
+            # etc.) to their installed .specify/extensions/<id>/ location
+            # before the generic placeholder/path resolution below.
+            body = registrar.rewrite_extension_paths(body, manifest.id, extension_dir)
             body = registrar.resolve_skill_placeholders(
-                selected_ai, frontmatter, body, self.project_root
+                selected_ai, frontmatter, body, self.project_root, extension_id=manifest.id
             )
 
             original_desc = frontmatter.get("description", "")
@@ -1958,6 +1965,7 @@ class CommandRegistrar:
             project_root,
             context_note=context_note,
             link_outputs=link_outputs,
+            extension_id=manifest.id,
         )
 
     def register_commands_for_all_agents(
@@ -1978,6 +1986,7 @@ class CommandRegistrar:
             context_note=context_note,
             link_outputs=link_outputs,
             create_missing_active_skills_dir=create_missing_active_skills_dir,
+            extension_id=manifest.id,
         )
 
     def unregister_commands(
@@ -2688,7 +2697,12 @@ class ConfigManager:
             return {}
 
         try:
-            return yaml.safe_load(file_path.read_text(encoding="utf-8")) or {}
+            data = yaml.safe_load(file_path.read_text(encoding="utf-8"))
+            # Coerce a non-mapping root (list/scalar, or None for an empty
+            # file) to {} so callers that iterate/merge the result — e.g.
+            # _merge_configs' .items() — never crash. Mirrors the same
+            # non-dict-root guard in get_project_config().
+            return data if isinstance(data, dict) else {}
         except (yaml.YAMLError, OSError, UnicodeError):
             return {}
 
@@ -2746,18 +2760,32 @@ class ConfigManager:
             if not key.startswith(prefix):
                 continue
 
-            # Remove prefix and split into parts
-            config_path = key[len(prefix) :].lower().split("_")
+            # Remove prefix and split into parts. Drop empty components from a
+            # malformed name (e.g. ``SPECKIT_<EXT>_`` with no key, or
+            # consecutive underscores ``SPECKIT_X__Y``) so we never create an
+            # entry under an empty key.
+            config_path = [p for p in key[len(prefix) :].lower().split("_") if p]
+            if not config_path:
+                continue
 
-            # Build nested dict
+            # Build nested dict. Two env vars can collide on a prefix, e.g.
+            # SPECKIT_X_CONNECTION=a and SPECKIT_X_CONNECTION_URL=b. Guard the
+            # walk so a colliding scalar is replaced by a dict (deeper/more
+            # specific vars win) instead of being indexed into — which raised
+            # TypeError ('str' object does not support item assignment) — and
+            # guard the leaf so a scalar processed after the nested var does
+            # not clobber the nested dict. Order-independent: both insertion
+            # orders yield {'connection': {'url': ...}}. Nested-wins mirrors
+            # _merge_configs' dict-preserving semantics.
             current = env_config
             for part in config_path[:-1]:
-                if part not in current:
+                if not isinstance(current.get(part), dict):
                     current[part] = {}
                 current = current[part]
 
-            # Set the final value
-            current[config_path[-1]] = value
+            # Set the final value, unless a nested dict already occupies it.
+            if not isinstance(current.get(config_path[-1]), dict):
+                current[config_path[-1]] = value
 
         return env_config
 

src/specify_cli/extensions/_commands.py

@@ -426,7 +426,11 @@ def extension_add(
     if from_url and not dev:
         from urllib.parse import urlparse
 
-        parsed = urlparse(from_url)
+        try:
+            parsed = urlparse(from_url)
+        except ValueError:
+            console.print(f"[red]Error:[/red] Invalid URL: {_escape_markup(from_url)}")
+            raise typer.Exit(1)
         is_localhost = parsed.hostname in ("localhost", "127.0.0.1", "::1")
 
         if parsed.scheme != "https" and not (parsed.scheme == "http" and is_localhost):
@@ -1562,7 +1566,14 @@ def extension_set_priority(
     raw_priority = metadata.get("priority")
     # Only skip if the stored value is already a valid int equal to requested priority
     # This ensures corrupted values (e.g., "high") get repaired even when setting to default (10)
-    if isinstance(raw_priority, int) and raw_priority == priority:
+    # A bool is an int in Python (isinstance(True, int) is True), so exclude it explicitly —
+    # mirroring normalize_priority's bool guard — otherwise a corrupted True/False priority
+    # equals 1/0 here and is never repaired.
+    if (
+        isinstance(raw_priority, int)
+        and not isinstance(raw_priority, bool)
+        and raw_priority == priority
+    ):
         console.print(f"[yellow]Extension '{_escape_markup(str(display_name))}' already has priority {priority}[/yellow]")
         raise typer.Exit(0)
 

src/specify_cli/integrations/agy/__init__.py

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

src/specify_cli/integrations/base.py

@@ -17,6 +17,7 @@ import os
 import re
 import shlex
 import shutil
+import subprocess
 import sys
 from abc import ABC
 from dataclasses import dataclass
@@ -25,6 +26,9 @@ from typing import TYPE_CHECKING, Any
 
 import yaml
 
+from .._toml_string import escape_toml_basic as _escape_toml_basic
+from .._toml_string import has_illegal_toml_control as _has_illegal_toml_control
+
 if TYPE_CHECKING:
     from .manifest import IntegrationManifest
 
@@ -51,6 +55,18 @@ _CORE_COMMAND_TEMPLATE_RANK = {
 }
 
 
+def yaml_quote(value: str) -> str:
+    """Emit *value* as a double-quoted YAML scalar on a single line.
+
+    A hand-rolled quote cannot carry raw newlines (YAML folds them to
+    spaces) or control characters (the reader rejects them), so let the
+    YAML emitter produce the escapes.
+    """
+    return yaml.safe_dump(
+        str(value), default_style='"', allow_unicode=True, width=sys.maxsize
+    ).strip()
+
+
 # ---------------------------------------------------------------------------
 # IntegrationOption
 # ---------------------------------------------------------------------------
@@ -123,6 +139,19 @@ class IntegrationBase(ABC):
     integration that sets this flag.
     """
 
+    def post_process_command_content(self, content: str) -> str:
+        """Transform command content after format rendering.
+
+        Called by ``register_commands()`` for non-skills format types
+        (Markdown, TOML, YAML) after the command has been rendered into
+        its target format and before writing to disk.  Skills-format
+        agents use ``post_process_skill_content()`` instead.
+
+        Subclasses may override to inject agent-specific content.
+        The default implementation returns *content* unchanged.
+        """
+        return content
+
     # -- Public API -------------------------------------------------------
 
     @classmethod
@@ -576,10 +605,42 @@ class IntegrationBase(ABC):
                 if candidate.exists():
                     return relative
         for name in ("python3", "python"):
-            if shutil.which(name):
-                return name
+            found = shutil.which(name)
+            if not found:
+                continue
+            # On Windows, python3/python on PATH may be the Microsoft
+            # Store App Execution Alias stub: it exists but only prints
+            # an installer hint and exits non-zero, so existence is not
+            # enough (see #3304 for the same defect in the sh scripts).
+            if sys.platform == "win32" and not IntegrationBase._interpreter_runs(
+                found
+            ):
+                continue
+            return name
         return sys.executable or "python3"
 
+    @staticmethod
+    def _interpreter_runs(path: str) -> bool:
+        """Return True when *path* executes as a Python interpreter.
+
+        Runs isolated (``-I``) without ``site`` (``-S``) and discards
+        I/O so the probe is a fast liveness check that cannot trigger
+        ``sitecustomize``/user startup hooks.
+        """
+        try:
+            return (
+                subprocess.run(
+                    [path, "-I", "-S", "-c", ""],
+                    stdin=subprocess.DEVNULL,
+                    stdout=subprocess.DEVNULL,
+                    stderr=subprocess.DEVNULL,
+                    timeout=15,
+                ).returncode
+                == 0
+            )
+        except (OSError, subprocess.SubprocessError):
+            return False
+
     @staticmethod
     def process_template(
         content: str,
@@ -940,6 +1001,12 @@ class TomlIntegration(IntegrationBase):
         body = "".join(lines[frontmatter_end + 1 :])
         return frontmatter, body
 
+    # Control-char detection and basic-string escaping are shared with the
+    # extension/preset renderer in ``specify_cli.agents`` via
+    # ``specify_cli._toml_string`` so the two never drift apart.
+    _has_illegal_toml_control = staticmethod(_has_illegal_toml_control)
+    _escape_toml_basic = staticmethod(_escape_toml_basic)
+
     @staticmethod
     def _render_toml_string(value: str) -> str:
         """Render *value* as a TOML string literal.
@@ -949,6 +1016,12 @@ class TomlIntegration(IntegrationBase):
         literal string or escaped basic string when delimiters appear in
         the content.
         """
+        # Control characters other than tab/newline (and a bare CR) cannot
+        # appear literally in any TOML string; route them to a fully-escaped
+        # basic string so the generated file stays parseable.
+        if TomlIntegration._has_illegal_toml_control(value):
+            return TomlIntegration._escape_toml_basic(value)
+
         if "\n" not in value and "\r" not in value:
             escaped = value.replace("\\", "\\\\").replace('"', '\\"')
             return f'"{escaped}"'
@@ -961,17 +1034,7 @@ class TomlIntegration(IntegrationBase):
         if "'''" not in value and not value.endswith("'"):
             return "'''\n" + value + "'''"
 
-        return (
-            '"'
-            + (
-                value.replace("\\", "\\\\")
-                .replace('"', '\\"')
-                .replace("\n", "\\n")
-                .replace("\r", "\\r")
-                .replace("\t", "\\t")
-            )
-            + '"'
-        )
+        return TomlIntegration._escape_toml_basic(value)
 
     @staticmethod
     def _render_toml(description: str, body: str) -> str:
@@ -1059,7 +1122,6 @@ class TomlIntegration(IntegrationBase):
 # YamlIntegration — YAML-format agents (Goose)
 # ---------------------------------------------------------------------------
 
-
 class YamlIntegration(IntegrationBase):
     """Concrete base for integrations that use YAML recipe format.
 
@@ -1178,12 +1240,18 @@ class YamlIntegration(IntegrationBase):
             default_flow_style=False,
         ).strip()
 
-        # Indent the body for YAML block scalar
+        # Indent the body for YAML block scalar. Use an explicit indentation
+        # indicator ("|2") rather than a bare "|": YAML infers a plain block
+        # scalar's indentation from its first non-empty line, so a body whose
+        # first line is itself indented (e.g. a markdown code block or a nested
+        # list item) would make the parser expect that deeper indent for the
+        # whole block and reject the later, less-indented lines. Pinning the
+        # indent to 2 keeps the recipe parseable whatever the body looks like.
         indented = "\n".join(f"  {line}" for line in body.split("\n"))
 
         lines = [
             header_yaml,
-            "prompt: |",
+            "prompt: |2",
             indented,
             "",
             f"# Source: {source_id}",
@@ -1456,21 +1524,17 @@ class SkillsIntegration(IntegrationBase):
             if not description:
                 description = f"Spec Kit: {command_name} workflow"
 
-            # Build SKILL.md with manually formatted frontmatter to match
-            # the release packaging script output exactly (double-quoted
-            # values, no yaml.safe_dump quoting differences).
-            def _quote(v: str) -> str:
-                escaped = v.replace("\\", "\\\\").replace('"', '\\"')
-                return f'"{escaped}"'
-
+            # Build SKILL.md with manually formatted frontmatter (stable
+            # double-quoted values). yaml_quote escapes newlines and control
+            # characters that a plain quoted f-string cannot carry.
             skill_content = (
                 f"---\n"
-                f"name: {_quote(skill_name)}\n"
-                f"description: {_quote(description)}\n"
-                f"compatibility: {_quote('Requires spec-kit project structure with .specify/ directory')}\n"
+                f"name: {yaml_quote(skill_name)}\n"
+                f"description: {yaml_quote(description)}\n"
+                f"compatibility: {yaml_quote('Requires spec-kit project structure with .specify/ directory')}\n"
                 f"metadata:\n"
-                f"  author: {_quote('github-spec-kit')}\n"
-                f"  source: {_quote('templates/commands/' + src_file.name)}\n"
+                f"  author: {yaml_quote('github-spec-kit')}\n"
+                f"  source: {yaml_quote('templates/commands/' + src_file.name)}\n"
                 f"---\n"
                 f"{processed_body}"
             )

src/specify_cli/integrations/cursor_agent/__init__.py

@@ -75,7 +75,15 @@ class CursorAgentIntegration(SkillsIntegration):
         either drops tool calls or exits non-zero on the first approval
         prompt.
         """
-        args = [self.key, "-p", "--trust", "--approve-mcps", "--force", prompt]
+        args = [
+            self._resolve_executable(),
+            "-p",
+            "--trust",
+            "--approve-mcps",
+            "--force",
+            prompt,
+        ]
+        self._apply_extra_args_env_var(args)
         if model:
             args.extend(["--model", model])
         if output_json:

src/specify_cli/integrations/devin/__init__.py

@@ -62,4 +62,4 @@ class DevinIntegration(SkillsIntegration):
                 default=True,
                 help="Install as agent skills (default for Devin)",
             ),
-        ]
+        ]

src/specify_cli/integrations/forge/__init__.py

@@ -18,13 +18,13 @@ from ..manifest import IntegrationManifest
 
 def format_forge_command_name(cmd_name: str) -> str:
     """Convert command name to Forge-compatible hyphenated format.
-    
+
     Forge requires command names to use hyphens instead of dots for
     compatibility with ZSH and other shells. This function converts
     dot-notation command names to hyphenated format.
-    
+
     The function is idempotent: already-formatted names are returned unchanged.
-    
+
     Examples:
         >>> format_forge_command_name("plan")
         'speckit-plan'
@@ -38,26 +38,26 @@ def format_forge_command_name(cmd_name: str) -> str:
         'speckit-my-extension-example'
         >>> format_forge_command_name("speckit.jira.sync-status")
         'speckit-jira-sync-status'
-    
+
     Args:
-        cmd_name: Command name in dot notation (speckit.foo.bar), 
+        cmd_name: Command name in dot notation (speckit.foo.bar),
                   hyphenated format (speckit-foo-bar), or plain name (foo)
-    
+
     Returns:
         Hyphenated command name with 'speckit-' prefix
     """
     # Already in hyphenated format - return as-is (idempotent)
     if cmd_name.startswith("speckit-"):
         return cmd_name
-    
+
     # Strip 'speckit.' prefix if present
     short_name = cmd_name
     if short_name.startswith("speckit."):
         short_name = short_name[len("speckit."):]
-    
+
     # Replace all dots with hyphens
     short_name = short_name.replace(".", "-")
-    
+
     # Return with 'speckit-' prefix
     return f"speckit-{short_name}"
 

src/specify_cli/integrations/hermes/__init__.py

@@ -18,7 +18,7 @@ from typing import Any
 
 import yaml
 
-from ..base import IntegrationOption, SkillsIntegration
+from ..base import IntegrationOption, SkillsIntegration, yaml_quote
 from ..manifest import IntegrationManifest
 
 
@@ -153,20 +153,18 @@ class HermesIntegration(SkillsIntegration):
             if not description:
                 description = f"Spec Kit: {command_name} workflow"
 
-            # Build SKILL.md with manually formatted frontmatter
-            def _quote(v: str) -> str:
-                escaped = v.replace("\\", "\\\\").replace('"', '\\"')
-                return f'"{escaped}"'
-
+            # Build SKILL.md with manually formatted frontmatter. yaml_quote
+            # escapes newlines and control characters that a plain quoted
+            # f-string cannot carry.
             skill_content = (
                 f"---\n"
-                f"name: {_quote(skill_name)}\n"
-                f"description: {_quote(description)}\n"
+                f"name: {yaml_quote(skill_name)}\n"
+                f"description: {yaml_quote(description)}\n"
                 f"compatibility: "
-                f"{_quote('Requires spec-kit project structure with .specify/ directory')}\n"
+                f"{yaml_quote('Requires spec-kit project structure with .specify/ directory')}\n"
                 f"metadata:\n"
-                f"  author: {_quote('github-spec-kit')}\n"
-                f"  source: {_quote('templates/commands/' + src_file.name)}\n"
+                f"  author: {yaml_quote('github-spec-kit')}\n"
+                f"  source: {yaml_quote('templates/commands/' + src_file.name)}\n"
                 f"---\n"
                 f"{processed_body}"
             )
@@ -253,6 +251,11 @@ class HermesIntegration(SkillsIntegration):
         """
         args = [self._resolve_executable(), "chat", "-Q"]
 
+        # Operator-supplied SPECKIT_INTEGRATION_HERMES_EXTRA_ARGS go here —
+        # after the base command but before Spec Kit's canonical -m/--json/-s/-q
+        # flags — so they can't displace or clobber them (mirrors opencode).
+        self._apply_extra_args_env_var(args)
+
         if model:
             args.extend(["-m", model])
         if output_json:

src/specify_cli/integrations/kiro_cli/__init__.py

@@ -13,6 +13,7 @@ _KIRO_ARG_FALLBACK = "(the user will provide the argument in this conversation)"
 
 class KiroCliIntegration(MarkdownIntegration):
     key = "kiro-cli"
+    multi_install_safe = True
     config = {
         "name": "Kiro CLI",
         "folder": ".kiro/",

src/specify_cli/integrations/manifest.py

@@ -309,7 +309,14 @@ class IntegrationManifest:
             if abs_path.is_symlink() or not abs_path.is_file():
                 modified.append(rel)
                 continue
-            if _sha256(abs_path) != expected_hash:
+            try:
+                changed = _sha256(abs_path) != expected_hash
+            except OSError:
+                # Unreadable regular file (e.g. permission denied): treat as
+                # modified, consistent with the symlink / non-regular-file
+                # handling above, rather than letting the OSError escape.
+                changed = True
+            if changed:
                 modified.append(rel)
         return modified
 
@@ -358,9 +365,17 @@ class IntegrationManifest:
                     skipped.append(path)
                     continue
             else:
-                if not force and _sha256(path) != expected_hash:
-                    skipped.append(path)
-                    continue
+                if not force:
+                    try:
+                        matches = _sha256(path) == expected_hash
+                    except OSError:
+                        # Unreadable: can't verify it's ours, so preserve it
+                        # (mirrors the path.unlink() OSError guard below).
+                        skipped.append(path)
+                        continue
+                    if not matches:
+                        skipped.append(path)
+                        continue
             try:
                 path.unlink()
             except OSError:

src/specify_cli/presets/__init__.py

@@ -778,6 +778,7 @@ class PresetManager:
                                         matching_cmds, ext_id, ext_dir,
                                         self.project_root,
                                         context_note=f"\n<!-- Extension: {ext_id} -->\n<!-- Config: .specify/extensions/{ext_id}/ -->\n",
+                                        extension_id=ext_id,
                                     )
                                     registered = True
                             except Exception:
@@ -1199,6 +1200,8 @@ class PresetManager:
                     "command_name": cmd_name,
                     "source_file": source_file,
                     "source": f"extension:{manifest.id}",
+                    "extension_id": manifest.id,
+                    "extension_dir": ext_root,
                 }
                 modern_skill_name, legacy_skill_name = self._skill_names_for_command(cmd_name)
                 restore_index.setdefault(modern_skill_name, restore_info)
@@ -1463,6 +1466,17 @@ class PresetManager:
             if extension_restore:
                 content = extension_restore["source_file"].read_text(encoding="utf-8")
                 frontmatter, body = registrar.parse_frontmatter(content)
+                # Mirror the register-time rewrite (#2101): resolve
+                # extension-relative subdir references (agents/,
+                # knowledge-base/, etc.) to their installed location before
+                # the generic placeholder resolution below, otherwise
+                # restoring after a preset override removal would leave
+                # bare, unresolvable paths in the skill body.
+                body = registrar.rewrite_extension_paths(
+                    body,
+                    extension_restore["extension_id"],
+                    extension_restore["extension_dir"],
+                )
                 if isinstance(selected_ai, str):
                     body = registrar.resolve_skill_placeholders(
                         selected_ai, frontmatter, body, self.project_root
@@ -3038,6 +3052,8 @@ class PresetResolver:
                     "path": candidate,
                     "source": source,
                     "strategy": "replace",
+                    "extension_id": ext_id,
+                    "extension_dir": ext_dir,
                 })
 
         # Priority 4: Core templates (always "replace")
@@ -3157,10 +3173,32 @@ class PresetResolver:
         if not layers:
             return None
 
+        def _read_layer_content(layer: Dict[str, Any]) -> str:
+            """Read a layer's raw text, rewriting extension-relative subdir
+            references (agents/, knowledge-base/, etc.) to their installed
+            location when the layer is extension-provided (#2101).
+
+            Extension layers are always inserted with strategy "replace"
+            (see collect_all_layers), so a layer only ever needs this
+            rewrite when it wins outright above or serves as the
+            composition base below — never as a mid-stack composing
+            (append/prepend/wrap) layer.
+            """
+            text = layer["path"].read_text(encoding="utf-8")
+            extension_id = layer.get("extension_id")
+            extension_dir = layer.get("extension_dir")
+            if extension_id and extension_dir:
+                from ..agents import CommandRegistrar
+
+                text = CommandRegistrar.rewrite_extension_paths(
+                    text, extension_id, extension_dir
+                )
+            return text
+
         # If the top (highest-priority) layer is replace, it wins entirely —
         # lower layers are irrelevant regardless of their strategies.
         if layers[0]["strategy"] == "replace":
-            return layers[0]["path"].read_text(encoding="utf-8")
+            return _read_layer_content(layers[0])
 
         # Composition: build content bottom-up from the effective base.
         # The base is the nearest replace layer scanning from highest priority
@@ -3183,7 +3221,7 @@ class PresetResolver:
 
         # Convert to reversed_layers index
         base_reversed_idx = len(layers) - 1 - base_layer_idx
-        content = layers[base_layer_idx]["path"].read_text(encoding="utf-8")
+        content = _read_layer_content(layers[base_layer_idx])
         # Compose only the layers above the base (higher priority = lower index in layers,
         # higher index in reversed_layers). Process bottom-up from base+1.
         start_idx = base_reversed_idx + 1

src/specify_cli/presets/_commands.py

@@ -104,7 +104,13 @@ def preset_add(
             from ipaddress import ip_address
             from urllib.parse import urlparse as _urlparse
 
-            _parsed = _urlparse(from_url)
+            try:
+                _parsed = _urlparse(from_url)
+            except ValueError:
+                from rich.markup import escape as _escape_markup
+
+                console.print(f"[red]Error:[/red] Invalid URL: {_escape_markup(from_url)}")
+                raise typer.Exit(1)
 
             def _is_allowed_download_url(parsed_url):
                 host = parsed_url.hostname
@@ -135,7 +141,9 @@ def preset_add(
                 )
                 raise typer.Exit(1)
 
-            console.print(f"Installing preset from [cyan]{from_url}[/cyan]...")
+            from rich.markup import escape as _esc
+
+            console.print(f"Installing preset from [cyan]{_esc(from_url)}[/cyan]...")
             import urllib.error
             import tempfile
             import shutil
@@ -461,7 +469,14 @@ def preset_set_priority(
     raw_priority = metadata.get("priority")
     # Only skip if the stored value is already a valid int equal to requested priority
     # This ensures corrupted values (e.g., "high") get repaired even when setting to default (10)
-    if isinstance(raw_priority, int) and raw_priority == priority:
+    # A bool is an int in Python (isinstance(True, int) is True), so exclude it explicitly —
+    # mirroring normalize_priority's bool guard — otherwise a corrupted True/False priority
+    # equals 1/0 here and is never repaired.
+    if (
+        isinstance(raw_priority, int)
+        and not isinstance(raw_priority, bool)
+        and raw_priority == priority
+    ):
         console.print(f"[yellow]Preset '{preset_id}' already has priority {priority}[/yellow]")
         raise typer.Exit(0)
 

src/specify_cli/shared_infra.py

@@ -328,7 +328,10 @@ def refresh_shared_templates(
         _ensure_safe_shared_destination(project_path, dst)
         rel = dst.relative_to(project_path).as_posix()
         if dst.exists() and not force:
-            if rel not in tracked_files or rel in modified:
+            if rel not in tracked_files or rel in modified or manifest.is_recovered(rel):
+                # Never overwrite a recovered (pre-existing user) file without
+                # --force, matching install_shared_infra's is_recovered gate
+                # (#2918). Without this, refresh clobbers user content.
                 skipped_files.append(rel)
                 continue
 
@@ -344,7 +347,7 @@ def refresh_shared_templates(
 
     if skipped_files:
         console.print(
-            f"[yellow]⚠[/yellow]  {len(skipped_files)} modified or untracked shared template file(s) were not updated:"
+            f"[yellow]⚠[/yellow]  {len(skipped_files)} modified, untracked, or preserved (recovered) shared template file(s) were not updated:"
         )
         for rel in skipped_files:
             console.print(f"    {rel}")
@@ -400,7 +403,7 @@ def install_shared_infra(
     # manifest entries the core no longer ships (stale-script cleanup, #3076).
     seen_rels: set[str] = set()
     scripts_scanned = False
-    variant_dir = "bash" if script_type == "sh" else "powershell"
+    variant_dir = {"sh": "bash", "py": "python"}.get(script_type, "powershell")
 
     def _decide_overwrite(rel: str, dst: Path) -> tuple[bool, str | None]:
         """Return (write, bucket) where bucket is 'skip', 'preserved', or None."""
@@ -462,6 +465,10 @@ def install_shared_infra(
                     for src_path in variant_src.rglob("*"):
                         if not src_path.is_file():
                             continue
+                        # Python bytecode caches are local artifacts, not
+                        # workflow scripts — never install them.
+                        if "__pycache__" in src_path.parts:
+                            continue
                         # Mark scanned only once a real source file is seen. An
                         # empty (or symlink-skipped) variant keeps this False, so
                         # stale-cleanup is skipped — otherwise it would treat every

src/specify_cli/workflows/_commands.py

@@ -50,7 +50,17 @@ workflow_step_catalog_app = typer.Typer(
 workflow_step_app.add_typer(workflow_step_catalog_app, name="catalog")
 
 
-def _parse_input_values(input_values: list[str] | None) -> dict[str, Any]:
+def _error_console(json_output: bool):
+    """Console for error text: stderr under ``--json`` so the JSON stdout
+    stream stays parseable, the normal console otherwise. Mirrors the
+    stderr-only error routing already used by ``specify bundle``.
+    """
+    return err_console if json_output else console
+
+
+def _parse_input_values(
+    input_values: list[str] | None, *, json_output: bool = False
+) -> dict[str, Any]:
     """Parse repeated ``key=value`` CLI inputs into a dict.
 
     Shared by ``workflow run`` and ``workflow resume``. Exits with an error
@@ -59,7 +69,9 @@ def _parse_input_values(input_values: list[str] | None) -> dict[str, Any]:
     inputs: dict[str, Any] = {}
     for kv in input_values or []:
         if "=" not in kv:
-            console.print(f"[red]Error:[/red] Invalid input format: {kv!r} (expected key=value)")
+            _error_console(json_output).print(
+                f"[red]Error:[/red] Invalid input format: {kv!r} (expected key=value)"
+            )
             raise typer.Exit(1)
         key, _, value = kv.partition("=")
         inputs[key.strip()] = value.strip()
@@ -335,25 +347,26 @@ def workflow_run(
     if not json_output:
         engine.on_step_start = lambda sid, label: console.print(f"  \u25b8 [{sid}] {label} \u2026")
 
+    err = _error_console(json_output)
     try:
         definition = engine.load_workflow(source_path if is_file_source else source)
     except FileNotFoundError:
-        console.print(f"[red]Error:[/red] Workflow not found: {source}")
+        err.print(f"[red]Error:[/red] Workflow not found: {source}")
         raise typer.Exit(1)
     except ValueError as exc:
-        console.print(f"[red]Error:[/red] Invalid workflow: {exc}")
+        err.print(f"[red]Error:[/red] Invalid workflow: {exc}")
         raise typer.Exit(1)
 
     # Validate
     errors = engine.validate(definition)
     if errors:
-        console.print("[red]Workflow validation failed:[/red]")
-        for err in errors:
-            console.print(f"  • {err}")
+        err.print("[red]Workflow validation failed:[/red]")
+        for verr in errors:
+            err.print(f"  • {verr}")
         raise typer.Exit(1)
 
     # Parse inputs
-    inputs = _parse_input_values(input_values)
+    inputs = _parse_input_values(input_values, json_output=json_output)
 
     if not json_output:
         console.print(f"\n[bold cyan]Running workflow:[/bold cyan] {definition.name} ({definition.id})")
@@ -363,10 +376,10 @@ def workflow_run(
         with _stdout_to_stderr_when(json_output):
             state = engine.execute(definition, inputs)
     except ValueError as exc:
-        console.print(f"[red]Error:[/red] {exc}")
+        err.print(f"[red]Error:[/red] {exc}")
         raise typer.Exit(1)
     except Exception as exc:
-        console.print(f"[red]Workflow failed:[/red] {exc}")
+        err.print(f"[red]Workflow failed:[/red] {exc}")
         raise typer.Exit(1)
 
     if json_output:
@@ -411,19 +424,20 @@ def workflow_resume(
     if not json_output:
         engine.on_step_start = lambda sid, label: console.print(f"  \u25b8 [{sid}] {label} \u2026")
 
-    inputs = _parse_input_values(input_values)
+    inputs = _parse_input_values(input_values, json_output=json_output)
+    err = _error_console(json_output)
 
     try:
         with _stdout_to_stderr_when(json_output):
             state = engine.resume(run_id, inputs or None)
     except FileNotFoundError:
-        console.print(f"[red]Error:[/red] Run not found: {run_id}")
+        err.print(f"[red]Error:[/red] Run not found: {run_id}")
         raise typer.Exit(1)
     except ValueError as exc:
-        console.print(f"[red]Error:[/red] {exc}")
+        err.print(f"[red]Error:[/red] {exc}")
         raise typer.Exit(1)
     except Exception as exc:
-        console.print(f"[red]Resume failed:[/red] {exc}")
+        err.print(f"[red]Resume failed:[/red] {exc}")
         raise typer.Exit(1)
 
     if json_output:
@@ -587,7 +601,15 @@ def workflow_add(
         except (ValueError, yaml.YAMLError) as exc:
             console.print(f"[red]Error:[/red] Invalid workflow YAML: {exc}")
             raise typer.Exit(1)
-        if not definition.id or not definition.id.strip():
+        # Non-string ids (e.g. unquoted ``id: 123`` or ``id: 0``) fall through
+        # to validate_workflow below, which reports a typed error instead of
+        # crashing on ``.strip()`` here. Only None/empty/whitespace-only ids
+        # are rejected as missing.
+        if (
+            definition.id is None
+            or definition.id == ""
+            or (isinstance(definition.id, str) and not definition.id.strip())
+        ):
             console.print("[red]Error:[/red] Workflow definition has an empty or missing 'id'")
             raise typer.Exit(1)
 
@@ -617,7 +639,11 @@ def workflow_add(
         from urllib.parse import urlparse
         from specify_cli.authentication.http import open_url as _open_url
 
-        parsed_src = urlparse(source)
+        try:
+            parsed_src = urlparse(source)
+        except ValueError:
+            console.print(f"[red]Error:[/red] Invalid URL: {_escape_markup(source)}")
+            raise typer.Exit(1)
         src_host = parsed_src.hostname or ""
         src_loopback = src_host == "localhost"
         if not src_loopback:

src/specify_cli/workflows/catalog.py

@@ -76,8 +76,16 @@ class WorkflowRegistry:
         if self.registry_path.exists():
             try:
                 with open(self.registry_path, encoding="utf-8") as f:
-                    return json.load(f)
-            except (json.JSONDecodeError, ValueError):
+                    data = json.load(f)
+                # Validate shape: must be a dict with a dict "workflows" field,
+                # otherwise every method that indexes data["workflows"] crashes.
+                # Mirrors StepRegistry._load.
+                if not isinstance(data, dict):
+                    return {"schema_version": self.SCHEMA_VERSION, "workflows": {}}
+                if not isinstance(data.get("workflows"), dict):
+                    data["workflows"] = {}
+                return data
+            except (json.JSONDecodeError, ValueError, OSError, UnicodeError):
                 # Corrupted registry file — reset to default
                 return {"schema_version": self.SCHEMA_VERSION, "workflows": {}}
         return {"schema_version": self.SCHEMA_VERSION, "workflows": {}}
@@ -438,9 +446,9 @@ class WorkflowCatalog:
                 q = query.lower()
                 searchable = " ".join(
                     [
-                        wf_data.get("name", ""),
-                        wf_data.get("description", ""),
-                        wf_data.get("id", ""),
+                        str(wf_data.get("name") or ""),
+                        str(wf_data.get("description") or ""),
+                        str(wf_data.get("id") or ""),
                     ]
                 ).lower()
                 if q not in searchable:

src/specify_cli/workflows/engine.py

@@ -129,26 +129,49 @@ def validate_workflow(definition: WorkflowDefinition) -> list[str]:
     errors: list[str] = []
 
     # -- Schema version ---------------------------------------------------
-    if definition.schema_version not in ("1.0", "1"):
+    # str() so an unquoted ``schema_version: 1.0`` (YAML float) is accepted —
+    # rejecting it would print "Unsupported schema_version 1.0. Expected '1.0'."
+    if str(definition.schema_version) != "1.0":
         errors.append(
             f"Unsupported schema_version {definition.schema_version!r}. "
             f"Expected '1.0'."
         )
 
     # -- Top-level fields -------------------------------------------------
-    if not definition.id:
+    # YAML parses unquoted scalars like ``id: 123`` or ``version: 1.0`` as
+    # int/float; check types before regex/string operations so authoring
+    # mistakes surface as validation errors instead of tracebacks. Only
+    # ``None``/empty-string count as missing so falsey non-strings
+    # (``id: 0``, ``name: false``) still get the typed error.
+    if definition.id is None or definition.id == "":
         errors.append("Workflow is missing 'workflow.id'.")
+    elif not isinstance(definition.id, str):
+        errors.append(
+            f"'workflow.id' must be a string, got "
+            f"{type(definition.id).__name__} ({definition.id!r})."
+        )
     elif not _ID_PATTERN.match(definition.id):
         errors.append(
             f"Workflow ID {definition.id!r} must be lowercase alphanumeric "
             f"with hyphens."
         )
 
-    if not definition.name:
+    if definition.name is None or definition.name == "":
         errors.append("Workflow is missing 'workflow.name'.")
+    elif not isinstance(definition.name, str):
+        errors.append(
+            f"'workflow.name' must be a string, got "
+            f"{type(definition.name).__name__} ({definition.name!r})."
+        )
 
-    if not definition.version:
+    if definition.version is None or definition.version == "":
         errors.append("Workflow is missing 'workflow.version'.")
+    elif not isinstance(definition.version, str):
+        errors.append(
+            f"'workflow.version' must be a string, got "
+            f"{type(definition.version).__name__} ({definition.version!r}) — "
+            f'quote it in YAML (version: "1.0.0").'
+        )
     elif not re.match(r"^\d+\.\d+\.\d+$", definition.version):
         errors.append(
             f"Workflow version {definition.version!r} is not valid "
@@ -256,9 +279,15 @@ def _validate_steps(
             continue
 
         step_id = step_config.get("id")
-        if not step_id:
+        if step_id is None or step_id == "":
             errors.append("Step is missing 'id' field.")
             continue
+        if not isinstance(step_id, str):
+            errors.append(
+                f"Step ID must be a string, got "
+                f"{type(step_id).__name__} ({step_id!r})."
+            )
+            continue
 
         if ":" in step_id:
             errors.append(
@@ -953,7 +982,16 @@ class WorkflowEngine:
                     from .expressions import evaluate_condition
 
                     max_iters = step_config.get("max_iterations")
-                    if not isinstance(max_iters, int) or max_iters < 1:
+                    # A bool is an int in Python (isinstance(True, int) is True
+                    # and True == 1), so a bool max_iterations would slip past
+                    # the int check and cap the loop at range(0)==1 iteration
+                    # instead of the default. Exclude bools, mirroring the
+                    # while/do-while validators and the continue_on_error guard.
+                    if (
+                        isinstance(max_iters, bool)
+                        or not isinstance(max_iters, int)
+                        or max_iters < 1
+                    ):
                         max_iters = 10
                     condition = step_config.get("condition", False)
                     for _loop_iter in range(max_iters - 1):

src/specify_cli/workflows/expressions.py

@@ -183,6 +183,85 @@ def _is_single_expression(stripped: str) -> bool:
     return True
 
 
+def _interpolate_expressions(template: str, namespace: dict[str, Any]) -> str:
+    """Substitute every top-level ``{{ ... }}`` block in *template*, quote-aware.
+
+    Walks the template and, for each block, finds the closing ``}}`` that lies
+    outside string literals -- the same quote-scanning used by
+    ``_is_single_expression``. This keeps a literal ``}}`` inside a string
+    argument (e.g. ``| default('}}')``) from prematurely closing a block.
+
+    ``_EXPR_PATTERN.sub`` cannot do this: its non-greedy body stops at the first
+    ``}}`` regardless of quoting, so in a multi-expression template any block
+    whose argument contains a literal ``}}`` is captured truncated and mis-parsed
+    (raising ``ValueError`` from the filter parser). #3208/#3228 fixed exactly
+    this for the single-expression fast path but left the interpolation path on
+    the old regex.
+    """
+    out: list[str] = []
+    i = 0
+    n = len(template)
+    while i < n:
+        start = template.find("{{", i)
+        if start == -1:
+            out.append(template[i:])
+            break
+        out.append(template[i:start])
+        # Scan for the block-closing ``}}`` that is outside any string literal.
+        j = start + 2
+        quote: str | None = None
+        close = -1
+        while j < n:
+            ch = template[j]
+            if quote is not None:
+                if ch == quote:
+                    quote = None
+            elif ch in ("'", '"'):
+                quote = ch
+            elif ch == "}" and j + 1 < n and template[j + 1] == "}":
+                close = j
+                break
+            j += 1
+        if close == -1:
+            # No quote-aware close. Two sub-cases, both kept identical to the old
+            # regex so a malformed template is never silently hidden:
+            #   * a raw ``}}`` still exists in the tail (e.g. an unbalanced quote
+            #     in a filter arg swallowed the real delimiter) -- fall back to
+            #     that first raw ``}}`` and evaluate, letting the parser surface
+            #     a ValueError just as ``_EXPR_PATTERN.sub`` would have.
+            #   * no ``}}`` at all -- a genuinely unterminated ``{{``; leave the
+            #     tail verbatim, again matching the regex (which cannot match).
+            raw_close = template.find("}}", start + 2)
+            if raw_close == -1:
+                out.append(template[start:])
+                break
+            close = raw_close
+        val = _evaluate_simple_expression(template[start + 2:close].strip(), namespace)
+        out.append(str(val) if val is not None else "")
+        i = close + 2
+    return "".join(out)
+
+
+def _split_top_level(text: str, sep: str) -> list[str]:
+    """Split *text* on each occurrence of *sep* that lies outside any quoted
+    string or nested brackets.
+
+    Used to break a filter chain (``a | map('x') | join(',')``) into its
+    individual filter segments without splitting on a ``|`` that appears inside
+    a quoted argument. Each returned segment is a slice at a top-level
+    boundary, so the quote/bracket scan restarts cleanly on the remainder.
+    """
+    parts: list[str] = []
+    start = 0
+    while True:
+        idx = _find_top_level(text[start:], sep)
+        if idx == -1:
+            parts.append(text[start:])
+            return parts
+        parts.append(text[start:start + idx])
+        start += idx + len(sep)
+
+
 def _split_top_level_commas(text: str) -> list[str]:
     """Split *text* on commas that are not inside quotes or nested brackets.
 
@@ -246,6 +325,68 @@ def _find_top_level(text: str, token: str) -> int:
     return -1
 
 
+def _apply_filter(value: Any, filter_expr: str, namespace: dict[str, Any]) -> Any:
+    """Apply a single pipe filter segment to *value*.
+
+    *filter_expr* is one link of a filter chain — the text between two
+    top-level ``|`` separators, already stripped (e.g. ``map('name')``,
+    ``default('x')``, ``from_json``). Returns the filtered value so the caller
+    can feed it into the next link.
+
+    Raises ``ValueError`` on any mis-wired or unknown filter rather than
+    silently returning *value* unchanged: a passthrough would turn a mistyped
+    or unsupported filter into a wrong result with no signal.
+    """
+    # `from_json` is strict: it takes no arguments and tolerates no trailing
+    # tokens. Match on the leading filter name and require the whole filter to
+    # be exactly `from_json`, so every mis-wired form (`from_json()`,
+    # `from_json('x')`, `from_json)`, `from_json extra`) fails loudly instead of
+    # silently falling through to the unknown-filter path.
+    leading = re.match(r"\w+", filter_expr)
+    if leading and leading.group(0) == "from_json":
+        if filter_expr != "from_json":
+            raise ValueError(
+                "from_json: expected '| from_json' with no arguments or "
+                f"trailing tokens, got '| {filter_expr}'"
+            )
+        return _filter_from_json(value)
+
+    # Parse filter name and argument
+    filter_match = re.match(r"(\w+)\((.+)\)", filter_expr)
+    if filter_match:
+        fname = filter_match.group(1)
+        farg = _evaluate_simple_expression(filter_match.group(2).strip(), namespace)
+        if fname == "default":
+            return _filter_default(value, farg)
+        if fname == "join":
+            return _filter_join(value, farg)
+        if fname == "map":
+            return _filter_map(value, farg)
+        if fname == "contains":
+            return _filter_contains(value, farg)
+    # Filter without args
+    if filter_expr == "default":
+        return _filter_default(value)
+    # No recognized filter matched. Fail loudly rather than silently returning
+    # the unfiltered value. Distinguish a *registered* filter used in an
+    # unsupported form (e.g. `| join` or `| map` with no argument) from a
+    # genuinely unknown filter name, so the message names the real problem
+    # instead of calling a known filter "unknown".
+    name = leading.group(0) if leading else filter_expr
+    expected = (
+        "expected one of default or default('x'), join('sep'), "
+        "map('attr'), contains('s'), or from_json"
+    )
+    if name in _REGISTERED_FILTERS:
+        raise ValueError(
+            f"filter '{name}' used in an unsupported form (got "
+            f"'| {filter_expr}'): {expected}"
+        )
+    raise ValueError(
+        f"unknown filter '{name}': {expected} (got '| {filter_expr}')"
+    )
+
+
 def _evaluate_simple_expression(expr: str, namespace: dict[str, Any]) -> Any:
     """Evaluate a simple expression against the namespace.
 
@@ -270,65 +411,17 @@ def _evaluate_simple_expression(expr: str, namespace: dict[str, Any]) -> Any:
     # Handle pipe filters. Detect the pipe at the top level only, so a literal
     # '|' inside a quoted operand (e.g. `inputs.x == 'a|b'`) or nested brackets is
     # not mistaken for a filter separator — mirroring the operator parsing below.
+    # Filters chain left-to-right: `list | map('name') | join(', ')` feeds each
+    # filter's result into the next, so `map` (which yields a list) can be
+    # rendered by `join`. Splitting only at the first pipe would hand the whole
+    # tail to one filter and mangle any later `|`.
     pipe_idx = _find_top_level(expr, "|")
     if pipe_idx != -1:
-        value = _evaluate_simple_expression(expr[:pipe_idx].strip(), namespace)
-        filter_expr = expr[pipe_idx + 1:].strip()
-
-        # `from_json` is strict: it takes no arguments and tolerates no
-        # trailing tokens. Match on the leading filter name and require the
-        # whole filter to be exactly `from_json`, so every mis-wired form
-        # (`from_json()`, `from_json('x')`, `from_json)`, `from_json extra`)
-        # fails loudly instead of silently falling through to the
-        # unknown-filter path and returning the unparsed value. (filter_expr
-        # is already stripped above.)
-        leading = re.match(r"\w+", filter_expr)
-        if leading and leading.group(0) == "from_json":
-            if filter_expr != "from_json":
-                raise ValueError(
-                    "from_json: expected '| from_json' with no arguments or "
-                    f"trailing tokens, got '| {filter_expr}'"
-                )
-            return _filter_from_json(value)
-
-        # Parse filter name and argument
-        filter_match = re.match(r"(\w+)\((.+)\)", filter_expr)
-        if filter_match:
-            fname = filter_match.group(1)
-            farg = _evaluate_simple_expression(filter_match.group(2).strip(), namespace)
-            if fname == "default":
-                return _filter_default(value, farg)
-            if fname == "join":
-                return _filter_join(value, farg)
-            if fname == "map":
-                return _filter_map(value, farg)
-            if fname == "contains":
-                return _filter_contains(value, farg)
-        # Filter without args
-        filter_name = filter_expr.strip()
-        if filter_name == "default":
-            return _filter_default(value)
-        # No recognized filter matched. Fail loudly rather than silently
-        # returning the unfiltered value: a passthrough turns a mis-typed or
-        # unsupported filter into a wrong result with no signal. Mirrors the
-        # strict `from_json` handling above. Distinguish a *registered* filter
-        # used in an unsupported form (e.g. `| join` or `| map` with no
-        # argument) from a genuinely unknown filter name, so the message names
-        # the real problem instead of calling a known filter "unknown".
-        leading_name = re.match(r"\w+", filter_expr)
-        name = leading_name.group(0) if leading_name else filter_expr
-        expected = (
-            "expected one of default or default('x'), join('sep'), "
-            "map('attr'), contains('s'), or from_json"
-        )
-        if name in _REGISTERED_FILTERS:
-            raise ValueError(
-                f"filter '{name}' used in an unsupported form (got "
-                f"'| {filter_expr}'): {expected}"
-            )
-        raise ValueError(
-            f"unknown filter '{name}': {expected} (got '| {filter_expr}')"
-        )
+        segments = _split_top_level(expr, "|")
+        value = _evaluate_simple_expression(segments[0].strip(), namespace)
+        for segment in segments[1:]:
+            value = _apply_filter(value, segment.strip(), namespace)
+        return value
 
     # Boolean operators — parse 'or' first (lower precedence) so that
     # 'a or b and c' is evaluated as 'a or (b and c)'. Splits are quote/bracket
@@ -371,9 +464,9 @@ def _evaluate_simple_expression(expr: str, namespace: dict[str, Any]) -> Any:
             if op == "<=":
                 return _safe_compare(left, right, "<=")
             if op == " in ":
-                return left in right if right is not None else False
+                return _safe_membership(left, right, negate=False)
             if op == " not in ":
-                return left not in right if right is not None else True
+                return _safe_membership(left, right, negate=True)
 
     # Numeric literal
     try:
@@ -408,15 +501,54 @@ def _evaluate_simple_expression(expr: str, namespace: dict[str, Any]) -> Any:
     return _resolve_dot_path(namespace, expr)
 
 
-def _safe_compare(left: Any, right: Any, op: str) -> bool:
-    """Safely compare two values, coercing types when possible."""
+def _coerce_number(value: Any) -> Any:
+    """Return *value* as int/float if it is a numeric string, else unchanged."""
+    if isinstance(value, str):
+        try:
+            return float(value) if "." in value else int(value)
+        except ValueError:
+            return value
+    return value
+
+
+def _safe_membership(left: Any, right: Any, *, negate: bool) -> bool:
+    """Safely evaluate ``left in right`` (or ``not in``) without crashing.
+
+    ``left in right`` raises ``TypeError`` whenever the operands don't support
+    membership testing — most commonly a non-iterable right operand (``None``,
+    an int, a bool), but also cases like an unhashable ``left`` against a set.
+    In every such case the membership relation is undefined, so treat it as
+    ``False`` (``not in`` as ``True``) rather than leaking the error out of the
+    evaluator and crashing the whole workflow. Mirrors the graceful
+    ``TypeError`` handling in ``_safe_compare`` for the ordering operators, and
+    generalizes the previous ``right is not None`` guard to any operand pair
+    that can't be membership-tested.
+    """
     try:
-        if isinstance(left, str):
-            left = float(left) if "." in left else int(left)
-        if isinstance(right, str):
-            right = float(right) if "." in right else int(right)
-    except (ValueError, TypeError):
-        return False
+        contained = left in right
+    except TypeError:
+        contained = False
+    return not contained if negate else contained
+
+
+def _safe_compare(left: Any, right: Any, op: str) -> bool:
+    """Compare two values for ordering, coercing numeric strings when possible.
+
+    Numeric coercion is applied only when *both* operands look numeric, so a
+    pair like ``"10"`` and ``"9"`` compares as numbers (10 > 9). When either
+    side is a non-numeric string, both fall back to their original values and
+    are compared directly -- so ordinary strings (dates, semver-ish tags,
+    names) compare lexicographically the way Python does, instead of every
+    such comparison silently returning ``False`` after a failed int()/float()
+    coercion. A genuinely incomparable pair (e.g. number vs non-numeric string)
+    raises ``TypeError`` and yields ``False``.
+    """
+    cl, cr = _coerce_number(left), _coerce_number(right)
+    # Only use the coerced numbers when both converted; otherwise a numeric
+    # string paired with a plain string would become an int-vs-str mismatch
+    # (always False) rather than a lexicographic string comparison.
+    if isinstance(cl, (int, float)) and isinstance(cr, (int, float)):
+        left, right = cl, cr
     try:
         if op == ">":
             return left > right  # type: ignore[operator]
@@ -472,12 +604,11 @@ def evaluate_expression(template: str, context: Any) -> Any:
     if _is_single_expression(stripped):
         return _evaluate_simple_expression(stripped[2:-2].strip(), namespace)
 
-    # Multi-expression: string interpolation
-    def _replacer(m: re.Match[str]) -> str:
-        val = _evaluate_simple_expression(m.group(1).strip(), namespace)
-        return str(val) if val is not None else ""
-
-    return _EXPR_PATTERN.sub(_replacer, template)
+    # Multi-expression: interpolate each block inline. Uses a quote-aware scan
+    # (not ``_EXPR_PATTERN.sub``) so a literal ``}}`` inside a string argument
+    # in any block does not close that block early -- matching the handling the
+    # single-expression path above already got in #3208/#3228.
+    return _interpolate_expressions(template, namespace)
 
 
 def evaluate_condition(condition: str, context: Any) -> bool:

src/specify_cli/workflows/steps/fan_in/__init__.py

@@ -58,4 +58,13 @@ class FanInStep(StepBase):
                 f"Fan-in step {config.get('id', '?')!r}: "
                 f"'wait_for' must be a non-empty list of step IDs."
             )
+        output = config.get("output")
+        if output is not None and not isinstance(output, dict):
+            # execute() silently coerces a non-mapping output to {}, so the
+            # author's declared aggregation keys would vanish with no error.
+            # Reject at validation, mirroring the command-step (#3262) fix.
+            errors.append(
+                f"Fan-in step {config.get('id', '?')!r}: 'output' must be a "
+                f"mapping of key -> expression, got {type(output).__name__}."
+            )
         return errors

src/specify_cli/workflows/steps/gate/__init__.py

@@ -73,7 +73,14 @@ class GateStep(StepBase):
         choice = self._prompt(self._compose_prompt(message, show_file), options)
         output["choice"] = choice
 
-        if choice in ("reject", "abort"):
+        # Match rejection case-insensitively. ``_prompt`` echoes the option's
+        # original casing, and ``validate`` accepts a reject option
+        # case-insensitively (``o.lower() in {"reject", "abort"}``), so a gate
+        # authored as ``options: [Approve, Reject]`` passes validation. Comparing
+        # ``choice`` case-sensitively here would then treat a ``Reject`` pick as
+        # approval and silently skip the abort — the reject path must agree with
+        # the check that let the option through.
+        if choice.lower() in ("reject", "abort"):
             if on_reject == "abort":
                 output["aborted"] = True
                 return StepResult(

src/specify_cli/workflows/steps/if_then/__init__.py

@@ -47,8 +47,8 @@ class IfThenStep(StepBase):
             errors.append(
                 f"If step {config.get('id', '?')!r}: 'then' must be a list of steps."
             )
-        else_branch = config.get("else", [])
-        if else_branch and not isinstance(else_branch, list):
+        else_branch = config.get("else")
+        if else_branch is not None and not isinstance(else_branch, list):
             errors.append(
                 f"If step {config.get('id', '?')!r}: 'else' must be a list of steps."
             )

src/specify_cli/workflows/steps/shell/__init__.py

@@ -3,6 +3,7 @@
 from __future__ import annotations
 
 import json
+import math
 import subprocess
 from typing import Any
 
@@ -25,7 +26,20 @@ class ShellStep(StepBase):
         run_cmd = str(run_cmd)
 
         cwd = context.project_root or "."
-
+        # Per-step execution timeout in seconds; defaults to 300 for backward
+        # compatibility. The engine does not auto-validate step config, so
+        # validate here as well — a caller that skips WorkflowEngine.validate()
+        # must fail the step cleanly rather than crash subprocess.run() with a
+        # TypeError (or silently coerce ``timeout: true`` to a 1s duration,
+        # since bool is an int subclass).
+        timeout = config.get("timeout", 300)
+        timeout_error = self._timeout_error(config)
+        if timeout_error is not None:
+            return StepResult(
+                status=StepStatus.FAILED,
+                error=timeout_error,
+                output={"exit_code": -1, "stdout": "", "stderr": "invalid timeout"},
+            )
         # NOTE: shell=True is required to support pipes, redirects, and
         # multi-command expressions in workflow YAML.  Workflow authors
         # control commands; catalog-installed workflows should be reviewed
@@ -37,7 +51,7 @@ class ShellStep(StepBase):
                 capture_output=True,
                 text=True,
                 cwd=cwd,
-                timeout=300,
+                timeout=timeout,
             )
             output = {
                 "exit_code": proc.returncode,
@@ -74,7 +88,7 @@ class ShellStep(StepBase):
         except subprocess.TimeoutExpired:
             return StepResult(
                 status=StepStatus.FAILED,
-                error="Shell command timed out after 300 seconds.",
+                error=f"Shell command timed out after {timeout} seconds.",
                 output={"exit_code": -1, "stdout": "", "stderr": "timeout"},
             )
         except OSError as exc:
@@ -84,16 +98,55 @@ class ShellStep(StepBase):
                 output={"exit_code": -1, "stdout": "", "stderr": str(exc)},
             )
 
+    @staticmethod
+    def _timeout_error(config: dict[str, Any]) -> str | None:
+        """Return an error message if ``config['timeout']`` is invalid, else None.
+
+        Shared by execute() and validate() so both paths reject the same
+        values with the same message. An absent ``timeout`` is valid (the
+        default is used). bool is a subclass of int, but ``timeout: true`` is a
+        config error rather than a duration, so it is rejected explicitly.
+        Non-finite floats (YAML ``.inf``/``.nan``) pass a plain ``> 0`` check
+        but would raise in subprocess.run(), so they are rejected too.
+        """
+        if "timeout" not in config:
+            return None
+        timeout = config["timeout"]
+        if (
+            isinstance(timeout, bool)
+            or not isinstance(timeout, (int, float))
+            or not math.isfinite(timeout)
+            or timeout <= 0
+        ):
+            return (
+                f"Shell step {config.get('id', '?')!r}: 'timeout' must be a "
+                f"positive number of seconds, got {timeout!r}."
+            )
+        return None
+
     def validate(self, config: dict[str, Any]) -> list[str]:
         errors = super().validate(config)
         if "run" not in config:
             errors.append(
                 f"Shell step {config.get('id', '?')!r} is missing 'run' field."
             )
+        elif not isinstance(config["run"], str):
+            # execute() str()-coerces run and invokes it under shell=True, so a
+            # null or list 'run' would run the Python repr ('None', "['echo']")
+            # as a command. Reject non-strings at validation, mirroring the
+            # command-step input/options and gate options type checks. An
+            # expression like "{{ ... }}" is still a str, so it stays valid.
+            errors.append(
+                f"Shell step {config.get('id', '?')!r}: 'run' must be a string, "
+                f"got {type(config['run']).__name__}."
+            )
         output_format = config.get("output_format")
         if output_format is not None and output_format != "json":
             errors.append(
                 f"Shell step {config.get('id', '?')!r}: 'output_format' must "
                 f"be 'json' when present, got {output_format!r}."
             )
+        timeout_error = self._timeout_error(config)
+        if timeout_error is not None:
+            errors.append(timeout_error)
         return errors

src/specify_cli/workflows/steps/switch/__init__.py

@@ -26,6 +26,20 @@ class SwitchStep(StepBase):
         str_value = str(value) if value is not None else ""
 
         cases = config.get("cases", {})
+        if not isinstance(cases, dict):
+            # The engine does not auto-validate step config, so an unvalidated
+            # run with a non-mapping ``cases`` (a list/scalar authoring mistake)
+            # would otherwise raise AttributeError from ``.items()`` below and
+            # crash the whole run. Fail this step loudly instead, mirroring the
+            # fan-out step's non-list ``items`` handling.
+            return StepResult(
+                status=StepStatus.FAILED,
+                error=(
+                    f"Switch step {config.get('id', '?')!r}: 'cases' must be a "
+                    f"mapping, got {type(cases).__name__}."
+                ),
+                output={"matched_case": None, "expression_value": value},
+            )
         for case_key, case_steps in cases.items():
             if str(case_key) == str_value:
                 return StepResult(

templates/checklist-template.md

@@ -6,16 +6,16 @@
 
 **Note**: This checklist is generated by the `__SPECKIT_COMMAND_CHECKLIST__` command based on feature context and requirements.
 
-<!-- 
+<!--
   ============================================================================
   IMPORTANT: The checklist items below are SAMPLE ITEMS for illustration only.
-  
+
   The __SPECKIT_COMMAND_CHECKLIST__ command MUST replace these with actual items based on:
   - User's specific checklist request
   - Feature requirements from spec.md
   - Technical context from plan.md
   - Implementation details from tasks.md
-  
+
   DO NOT keep these sample items in the generated checklist file.
   ============================================================================
 -->

templates/commands/analyze.md

@@ -3,6 +3,7 @@ description: Perform a non-destructive cross-artifact consistency and quality an
 scripts:
   sh: scripts/bash/check-prerequisites.sh --json --require-tasks --include-tasks
   ps: scripts/powershell/check-prerequisites.ps1 -Json -RequireTasks -IncludeTasks
+  py: scripts/python/check_prerequisites.py --json --require-tasks --include-tasks
 ---
 
 ## User Input

templates/commands/checklist.md

@@ -3,6 +3,7 @@ description: Generate a custom checklist for the current feature based on user r
 scripts:
   sh: scripts/bash/check-prerequisites.sh --json
   ps: scripts/powershell/check-prerequisites.ps1 -Json
+  py: scripts/python/check_prerequisites.py --json
 ---
 
 ## Checklist Purpose: "Unit Tests for English"

templates/commands/clarify.md

@@ -1,12 +1,13 @@
 ---
 description: Identify underspecified areas in the current feature spec by asking up to 5 highly targeted clarification questions and encoding answers back into the spec.
-handoffs: 
+handoffs:
   - label: Build Technical Plan
     agent: speckit.plan
     prompt: Create a plan for the spec. I am building with...
 scripts:
    sh: scripts/bash/check-prerequisites.sh --json --paths-only
    ps: scripts/powershell/check-prerequisites.ps1 -Json -PathsOnly
+   py: scripts/python/check_prerequisites.py --json --paths-only
 ---
 
 ## User Input

templates/commands/constitution.md

@@ -1,6 +1,6 @@
 ---
 description: Create or update the project constitution from interactive or provided principle inputs, ensuring all dependent templates stay in sync.
-handoffs: 
+handoffs:
   - label: Build Specification
     agent: speckit.specify
     prompt: Implement the feature specification based on the updated constitution. I want to build...
@@ -81,7 +81,7 @@ Follow this execution flow:
    - Read `.specify/templates/plan-template.md` and ensure any "Constitution Check" or rules align with updated principles.
    - Read `.specify/templates/spec-template.md` for scope/requirements alignment—update if constitution adds/removes mandatory sections or constraints.
    - Read `.specify/templates/tasks-template.md` and ensure task categorization reflects new or removed principle-driven task types (e.g., observability, versioning, testing discipline).
-   - Read each command file in `.specify/templates/commands/*.md` (including this one) to verify no outdated references (agent-specific names like CLAUDE only) remain when generic guidance is required.
+   - Read each installed Spec Kit command file for your agent (including this one) — named `speckit.*` or `speckit-*` (dot or hyphen depending on the agent), or laid out as `speckit-<name>/SKILL.md` for skills-based integrations, e.g. in `.github/agents/`, `.github/skills/`, `.claude/skills/`, or your agent's equivalent commands directory — to verify no outdated references (CLAUDE-only or other agent-specific names) remain when generic guidance is required.
    - Read any runtime guidance docs (e.g., `README.md`, `docs/quickstart.md`, or agent-specific guidance files if present). Update references to principles changed.
 
 5. Produce a Sync Impact Report (prepend as an HTML comment at top of the constitution file after update):

templates/commands/converge.md

@@ -3,6 +3,7 @@ description: Assess the current codebase against the feature's spec, plan, and t
 scripts:
   sh: scripts/bash/check-prerequisites.sh --json --require-tasks --include-tasks
   ps: scripts/powershell/check-prerequisites.ps1 -Json -RequireTasks -IncludeTasks
+  py: scripts/python/check_prerequisites.py --json --require-tasks --include-tasks
 ---
 
 ## User Input

templates/commands/implement.md

@@ -3,6 +3,7 @@ description: Execute the implementation plan by processing and executing all tas
 scripts:
   sh: scripts/bash/check-prerequisites.sh --json --require-tasks --include-tasks
   ps: scripts/powershell/check-prerequisites.ps1 -Json -RequireTasks -IncludeTasks
+  py: scripts/python/check_prerequisites.py --json --require-tasks --include-tasks
 ---
 
 ## User Input
@@ -42,7 +43,7 @@ You **MUST** consider the user input before proceeding (if not empty).
     **Automatic Pre-Hook**: {extension}
     Executing: `/{command}`
     EXECUTE_COMMAND: {command}
-    
+
     Wait for the result of the hook command before proceeding to the Outline.
     ```
     After emitting the block above you MUST actually invoke the hook and wait for it to finish before continuing. Run it the same way you would run the command yourself in this agent/session (the invocation may differ from the literal `{command}` id shown above, e.g. a skills-mode agent runs it as `/skill:speckit-...` or `$speckit-...`). Emitting the block alone does not run the hook.
@@ -144,7 +145,7 @@ You **MUST** consider the user input before proceeding (if not empty).
 
 6. Execute implementation following the task plan:
    - **Phase-by-phase execution**: Complete each phase before moving to the next
-   - **Respect dependencies**: Run sequential tasks in order, parallel tasks [P] can run together  
+   - **Respect dependencies**: Run sequential tasks in order, parallel tasks [P] can run together
    - **Follow TDD approach**: Execute test tasks before their corresponding implementation tasks
    - **File-based coordination**: Tasks affecting the same files must run sequentially
    - **Validation checkpoints**: Verify each phase completion before proceeding

templates/commands/plan.md

@@ -1,6 +1,6 @@
 ---
 description: Execute the implementation planning workflow using the plan template to generate design artifacts.
-handoffs: 
+handoffs:
   - label: Create Tasks
     agent: speckit.tasks
     prompt: Break the plan into tasks
@@ -68,7 +68,6 @@ You **MUST** consider the user input before proceeding (if not empty).
    - Evaluate gates (ERROR if violations unjustified)
    - Phase 0: Generate research.md (resolve all NEEDS CLARIFICATION)
    - Phase 1: Generate data-model.md, contracts/, quickstart.md
-   - Phase 1: Update agent context by running the agent script
    - Re-evaluate Constitution Check post-design
 
 ## Mandatory Post-Execution Hooks
@@ -107,7 +106,7 @@ Check if `.specify/extensions.yml` exists in the project root.
 
 ## Completion Report
 
-Command ends after Phase 2 planning. Report branch, IMPL_PLAN path, and generated artifacts.
+Command ends after Phase 1 design. Report branch, IMPL_PLAN path, and generated artifacts.
 
 ## Phases
 

templates/commands/specify.md

@@ -1,6 +1,6 @@
 ---
 description: Create or update the feature specification from a natural language feature description.
-handoffs: 
+handoffs:
   - label: Build Technical Plan
     agent: speckit.plan
     prompt: Create a plan for the spec. I am building with...
@@ -147,20 +147,20 @@ Given that feature description, do this:
 
       ```markdown
       # Specification Quality Checklist: [FEATURE NAME]
-      
+
       **Purpose**: Validate specification completeness and quality before proceeding to planning
       **Created**: [DATE]
       **Feature**: [Link to spec.md]
-      
+
       ## Content Quality
-      
+
       - [ ] No implementation details (languages, frameworks, APIs)
       - [ ] Focused on user value and business needs
       - [ ] Written for non-technical stakeholders
       - [ ] All mandatory sections completed
-      
+
       ## Requirement Completeness
-      
+
       - [ ] No [NEEDS CLARIFICATION] markers remain
       - [ ] Requirements are testable and unambiguous
       - [ ] Success criteria are measurable
@@ -169,16 +169,16 @@ Given that feature description, do this:
       - [ ] Edge cases are identified
       - [ ] Scope is clearly bounded
       - [ ] Dependencies and assumptions identified
-      
+
       ## Feature Readiness
-      
+
       - [ ] All functional requirements have clear acceptance criteria
       - [ ] User scenarios cover primary flows
       - [ ] Feature meets measurable outcomes defined in Success Criteria
       - [ ] No implementation details leak into specification
-      
+
       ## Notes
-      
+
       - Items marked incomplete require spec updates before `__SPECKIT_COMMAND_CLARIFY__` or `__SPECKIT_COMMAND_PLAN__`
       ```
 
@@ -203,20 +203,20 @@ Given that feature description, do this:
 
            ```markdown
            ## Question [N]: [Topic]
-           
+
            **Context**: [Quote relevant spec section]
-           
+
            **What we need to know**: [Specific question from NEEDS CLARIFICATION marker]
-           
+
            **Suggested Answers**:
-           
+
            | Option | Answer | Implications |
            |--------|--------|--------------|
            | A      | [First suggested answer] | [What this means for the feature] |
            | B      | [Second suggested answer] | [What this means for the feature] |
            | C      | [Third suggested answer] | [What this means for the feature] |
            | Custom | Provide your own answer | [Explain how to provide custom input] |
-           
+
            **Your choice**: _[Wait for user response]_
            ```