chore: bump version to 0.12.15

Update autonomous-run-governance preset submitted by @hindermath to:
- presets/catalog.community.json (version, download_url, documentation, provides)
- docs/community/presets.md community presets table

Closes #3510

Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous)

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.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/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

.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 +2,97 @@
 
 <!-- insert new changelog below this comment -->
 
+## [0.12.15] - 2026-07-14
+
+### Changed
+
+- Update Autonomous Run Governance preset to v0.1.4 (#3511)
+- fix(workflows): raise catalog error, not raw ValueError, on a malformed catalog URL (#3484)
+- fix(workflows): evaluate 'in'/'not in' safely on a non-iterable right operand (#3447) (#3468)
+- fix: add trailing newline to init-options.json output (#3509)
+- feat(workflows): align workflow CLI with extension command surface (#3419)
+- fix(extensions): stop env-var config leaking across prefix-colliding extension IDs (#3497)
+- fix(integrations): escape control characters in goose recipe YAML renderer (#3384)
+- [extension] Update DocGuard — CDD Enforcement extension to v0.32.0 (#3489)
+- [extension] Add Multi-Repo Branch Sync extension to community catalog (#3411)
+- chore: release 0.12.14, begin 0.12.15.dev0 development (#3506)
+
+## [0.12.14] - 2026-07-13
+
+### Changed
+
+- [extension] Add Spec Kit Memory extension to community catalog (#3455)
+- Add Test-First Governance preset to community catalog (#3504)
+- Add Autonomous Run Governance preset to community catalog (#3501)
+- fix(workflows): validate command step input/options are mappings (#3262)
+- fix(presets): resolve() honors manifest-declared file: for installed presets (#3351)
+- fix(init): don't block on confirmation for 'init --here' without a TTY (#3236)
+- [extension] Add Quality Gates (Enforcement Layer) extension to community catalog (#3431)
+- fix(integrations): exit cleanly on unbalanced quote in --integration-options (#3457) (#3466)
+- fix(integrations): declare kiro-cli multi-install safe (#3471) (#3485)
+- fix(workflows): fail fan-in step on non-list wait_for instead of crashing (#3482)
+- chore: release 0.12.13, begin 0.12.14.dev0 development (#3498)
+
+## [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

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

docs/.gitignore

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

docs/community/extensions.md

@@ -51,7 +51,8 @@ The following community-contributed extensions are available in [`catalog.commun
 | Confluence Extension | Create a doc in Confluence summarizing the specifications and planning files | `integration` | Read+Write | [spec-kit-confluence](https://github.com/aaronrsun/spec-kit-confluence) |
 | Cost Tracker | Track real LLM dollar cost across SDD workflows — per-feature budgets, per-integration comparison, and finance-ready exports | `visibility` | Read+Write | [spec-kit-cost](https://github.com/Quratulain-bilal/spec-kit-cost) |
 | Data Model Diagram | Generates Mermaid ER diagrams from Spec Kit data models after planning | `docs` | Read+Write | [spec-kit-data-model-diagram](https://github.com/benizzio/spec-kit-data-model-diagram) |
-| DocGuard — CDD Enforcement | The only doc-integrity engine with an MCP server, SARIF output, and a deterministic zero-LLM core. Validates, scores, and traces documentation against code — 24 validators, stable finding codes, GitHub Action with PR annotations, spec-kit hooks. Pure Node.js, one pinned dep. | `docs` | Read+Write | [spec-kit-docguard](https://github.com/raccioly/docguard) |
+| DocGuard — CDD Enforcement | Doc-integrity engine with MCP server, SARIF output, and zero-LLM core. Validates, scores, and traces documentation against code — 24 validators, stable finding codes, spec-kit hooks. Pure Node.js. | `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) |
@@ -83,6 +84,7 @@ The following community-contributed extensions are available in [`catalog.commun
 | MemoryLint | Evidence-driven instruction drift checker: audits agent memory files for boundary, reality, conflict, and redundancy drift. | `process` | Read+Write | [memorylint](https://github.com/RbBtSn0w/spec-kit-extensions/tree/main/memorylint) |
 | Microsoft 365 Integration | Fetch Teams messages, meeting transcripts, and SharePoint/OneDrive files as local Markdown for spec generation | `integration` | Read+Write | [spec-kit-m365](https://github.com/BenBtg/spec-kit-m365) |
 | Multi-Model Review | Cross-model Spec Kit handoffs for spec authoring, implementation routing, and review. | `process` | Read+Write | [multi-model-review](https://github.com/formin/multi-model-review) |
+| Multi-Repo Branch Sync | Creates the feature branch in affected sub-repositories and git submodules via plan/tasks hooks | `process` | Read+Write | [multi-repo-sync](https://github.com/fyloss/spec-kit-multi-repo-sync) |
 | Multi-Sites Spec Kit | Multi-site aware specify command with per-site spec folders, auto-increment, and Drupal support | `process` | Read+Write | [spec-kit-multi-sites](https://github.com/teeyo/spec-kit-multi-sites) |
 | .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) |
@@ -97,6 +99,7 @@ The following community-contributed extensions are available in [`catalog.commun
 | Project Health Check | Diagnose a Spec Kit project and report health issues across structure, agents, features, scripts, extensions, and git | `visibility` | Read-only | [spec-kit-doctor](https://github.com/KhawarHabibKhan/spec-kit-doctor) |
 | Project Status | Show current SDD workflow progress — active feature, artifact status, task completion, workflow phase, and extensions summary | `visibility` | Read-only | [spec-kit-status](https://github.com/KhawarHabibKhan/spec-kit-status) |
 | QA Testing Extension | Systematic QA testing with browser-driven or CLI-based validation of acceptance criteria from spec | `code` | Read-only | [spec-kit-qa](https://github.com/arunt14/spec-kit-qa) |
+| Quality Gates (Enforcement Layer) | Deterministic quality enforcement for Spec Kit projects at three boundaries — agent hooks, git pre-commit, CI — with one policy file and provable enforcement (attestations, canaries, verified parity). | `process` | Read+Write | [spec-gates](https://github.com/schwichtgit/spec-gates) |
 | RAG Azure Builder | Spec Kit extension for onboarding and operating an Azure RAG stack with guided workflows. | `process` | Read+Write | [spec-kit-extension-rag-azure-builder](https://github.com/Sertxito/spec-kit-extension-rag-azure-builder) |
 | Ralph Loop | Autonomous implementation loop using AI agent CLI | `code` | Read+Write | [spec-kit-ralph](https://github.com/Rubiss-Projects/spec-kit-ralph) |
 | Reconcile Extension | Reconcile implementation drift by surgically updating feature artifacts. | `docs` | Read+Write | [spec-kit-reconcile](https://github.com/stn1slv/spec-kit-reconcile) |
@@ -117,6 +120,8 @@ 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 Memory | Recalls prior specs and decisions from configurable memory tools (e.g. memsearch) before SDLC stages, so planning and specification start from what the project already knows | `docs` | Read+Write | [spec-kit-memory](https://github.com/zaytsevand/spec-kit-memory) |
 | 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) |
@@ -146,6 +151,7 @@ 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/presets.md

@@ -11,6 +11,7 @@ The following community-contributed presets customize how Spec Kit behaves — o
 | Agent Parity Governance | Adds shared-guidance parity, audit-ready Spec-Kit run evidence, and agent-neutral model-routing guidance across a project's declared AI-agent instruction surfaces so agent guidance does not drift. | 6 templates, 3 commands | — | [spec-kit-preset-agent-parity-governance](https://github.com/hindermath/spec-kit-preset-agent-parity-governance) |
 | AIDE In-Place Migration | Adapts the AIDE extension workflow for in-place technology migrations (X → Y pattern) — adds migration objectives, verification gates, knowledge documents, and behavioral equivalence criteria | 2 templates, 8 commands | AIDE extension | [spec-kit-presets](https://github.com/mnriem/spec-kit-presets) |
 | Architecture Governance | Adds secure software architecture, STRIDE+CAPEC threat modeling, arc42 security cross-cutting concepts, S-ADRs, Zero Trust applicability, OWASP SAMM governance, BSI C3A cloud autonomy, BSI C5 cloud compliance assurance, and audit-ready Spec Kit run evidence | 13 templates, 3 commands | — | [spec-kit-preset-architecture-governance](https://github.com/hindermath/spec-kit-preset-architecture-governance) |
+| Autonomous Run Governance | Adds permission-bounded, evidence-first governance for autonomous Spec Kit delivery, convergence, resume, closeout, and retrospective learning. | 12 templates, 2 commands, 2 scripts | — | [spec-kit-preset-autonomous-run-governance](https://github.com/hindermath/spec-kit-preset-autonomous-run-governance) |
 | Canon Core | Adapts original Spec Kit workflow to work together with Canon extension | 2 templates, 8 commands | — | [spec-kit-canon](https://github.com/maximiliamus/spec-kit-canon) |
 | Claude AskUserQuestion | Upgrades `/speckit.clarify` and `/speckit.checklist` on Claude Code from Markdown-table prompts to the native AskUserQuestion picker, with a recommended option and reasoning on every question | 2 commands | — | [spec-kit-preset-claude-ask-questions](https://github.com/0xrafasec/spec-kit-preset-claude-ask-questions) |
 | Command Density | Compacts the nine core Spec Kit command prompts while preserving scripts, handoffs, placeholders, hook output blocks, and rule structure | 9 commands | — | [spec-kit-preset-command-density](https://github.com/Xopoko/spec-kit-preset-command-density) |
@@ -28,6 +29,7 @@ The following community-contributed presets customize how Spec Kit behaves — o
 | SicarioSpec Core | Baseline secure-by-default Spec Kit governance profile. | 5 templates | — | [sicario-spec](https://github.com/dfirs1car1o/sicario-spec) |
 | Spec2Cloud | Spec-driven workflow tuned for shipping to Azure: spec → plan → tasks → implement → deploy | 5 templates, 8 commands | — | [spec2cloud](https://github.com/Azure-Samples/Spec2Cloud) |
 | Table of Contents Navigation | Adds a navigable Table of Contents to generated spec.md, plan.md, and tasks.md documents | 3 templates, 3 commands | — | [spec-kit-preset-toc-navigation](https://github.com/Quratulain-bilal/spec-kit-preset-toc-navigation) |
+| Test-First Governance | Governs TDD with coverage-complete BDD/ATDD Gherkin scenarios, explicit suite ownership, professional test reports, traceability, and risk-based quality gates. | 10 templates, 8 commands | — | [spec-kit-preset-test-first-governance](https://github.com/ka-zo/spec-kit-preset-test-first-governance) |
 | VS Code Ask Questions | Enhances the clarify command to use `vscode/askQuestions` for batched interactive questioning. | 1 command | — | [spec-kit-presets](https://github.com/fdcastel/spec-kit-presets) |
 | Workflow Preset | Behavior-first specification, design artifacts, and agent-native handoff orchestration — adds requirement-phase behavior drafts, formal BDD/UIF/behavior contracts, optional design artifacts, and scoped implementation handoffs with Core Agent, Vertical Planner Agent, and Worker Agent modes | 22 templates, 8 commands | — | [spec-kit-workflow-preset](https://github.com/bigsmartben/spec-kit-workflow-preset) |
 

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/integrations.md

@@ -18,7 +18,7 @@ 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                                                                                                                           |
@@ -219,6 +219,7 @@ Some integrations accept additional options via `--integration-options`:
 | ----------- | ------------------- | -------------------------------------------------------------- |
 | `generic`   | `--commands-dir`    | Required. Directory for command files                          |
 | `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:
 

docs/reference/workflows.md

@@ -86,8 +86,30 @@ Lists workflows installed in the current project.
 specify workflow add <source>
 ```
 
+| Option          | Description                                            |
+| --------------- | ------------------------------------------------------ |
+| `--dev`         | Install from a local workflow YAML file or directory   |
+| `--from <url>`  | Install from a custom URL (`<source>` names the expected workflow ID) |
+
 Installs a workflow from the catalog, a URL (HTTPS required), or a local file path.
 
+## Update Workflows
+
+```bash
+specify workflow update [workflow_id]
+```
+
+Updates one installed catalog workflow — or all of them when no ID is given — to the latest catalog version. Prompts for confirmation and keeps the installed copy if a download or validation fails.
+
+## Enable or Disable a Workflow
+
+```bash
+specify workflow enable <workflow_id>
+specify workflow disable <workflow_id>
+```
+
+Disabled workflows stay installed and listed (marked `[disabled]`) but refuse to run until re-enabled.
+
 ## Remove a Workflow
 
 ```bash
@@ -102,9 +124,10 @@ Removes an installed workflow from the project.
 specify workflow search [query]
 ```
 
-| Option  | Description     |
-| ------- | --------------- |
-| `--tag` | Filter by tag   |
+| Option     | Description       |
+| ---------- | ----------------- |
+| `--tag`    | Filter by tag     |
+| `--author` | Filter by author  |
 
 Searches all active catalogs for workflows matching the query.
 

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/**/plan.md`, any depth).
+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` (any depth, so scoped layouts like `specs/<scope>/<feature>/plan.md` are found).
+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

@@ -307,16 +307,28 @@ import sys
 from pathlib import Path
 root = Path(sys.argv[1]).resolve()
 specs = root / "specs"
-plan = max(
-    specs.glob("**/plan.md"),
-    key=lambda p: p.stat().st_mtime,
-    default=None,
-)
-if plan:
+
+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(plan.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

@@ -426,7 +426,11 @@ if (-not $PlanPath) {
     if (-not $PlanPath) {
         try {
             $specsDir = Join-Path $ProjectRoot 'specs'
-            $candidate = Get-ChildItem -Path $specsDir -Recurse -File -Filter 'plan.md' -ErrorAction SilentlyContinue |
+            # 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/catalog.community.json

@@ -1,6 +1,6 @@
 {
   "schema_version": "1.0",
-  "updated_at": "2026-07-07T00:00:00Z",
+  "updated_at": "2026-07-13T00:00:00Z",
   "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/extensions/catalog.community.json",
   "extensions": {
     "aide": {
@@ -1106,10 +1106,10 @@
     "docguard": {
       "name": "DocGuard — CDD Enforcement",
       "id": "docguard",
-      "description": "The only doc-integrity engine with an MCP server, SARIF output, and a deterministic zero-LLM core. Validates, scores, and traces documentation against code — 24 validators, stable finding codes, GitHub Action with PR annotations, spec-kit hooks. Pure Node.js, one pinned dep.",
+      "description": "Doc-integrity engine with MCP server, SARIF output, and zero-LLM core. Validates, scores, and traces documentation against code — 24 validators, stable finding codes, spec-kit hooks. Pure Node.js.",
       "author": "raccioly",
-      "version": "0.30.0",
-      "download_url": "https://github.com/raccioly/docguard/releases/download/v0.30.0/spec-kit-docguard-v0.30.0.zip",
+      "version": "0.32.0",
+      "download_url": "https://github.com/raccioly/docguard/releases/download/v0.32.0/spec-kit-docguard-v0.32.0.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",
@@ -1124,6 +1124,14 @@
             "name": "node",
             "version": ">=18.0.0",
             "required": true
+          },
+          {
+            "name": "npx",
+            "required": true
+          },
+          {
+            "name": "specify",
+            "required": false
           }
         ]
       },
@@ -1145,7 +1153,7 @@
       "downloads": 0,
       "stars": 0,
       "created_at": "2026-03-13T00:00:00Z",
-      "updated_at": "2026-07-06T00:00:00Z"
+      "updated_at": "2026-07-13T00:00:00Z"
     },
     "doctor": {
       "name": "Project Health Check",
@@ -1180,6 +1188,39 @@
       "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",
@@ -1213,6 +1254,47 @@
       "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",
@@ -1353,6 +1435,57 @@
       "created_at": "2026-05-06T00:00:00Z",
       "updated_at": "2026-05-06T00:00:00Z"
     },
+    "gates": {
+      "name": "Quality Gates (Enforcement Layer)",
+      "id": "gates",
+      "description": "Deterministic quality enforcement for Spec Kit projects at three boundaries — agent hooks, git pre-commit, CI — with one policy file and provable enforcement (attestations, canaries, verified parity).",
+      "author": "schwichtgit",
+      "version": "0.1.0",
+      "download_url": "https://github.com/schwichtgit/spec-gates/releases/download/v0.1.0/gates-0.1.0.zip",
+      "repository": "https://github.com/schwichtgit/spec-gates",
+      "homepage": "https://github.com/schwichtgit/spec-gates",
+      "documentation": "https://github.com/schwichtgit/spec-gates/blob/main/docs/how-it-works.md",
+      "license": "MIT",
+      "category": "process",
+      "effect": "read-write",
+      "requires": {
+        "speckit_version": ">=0.12.0",
+        "tools": [
+          {
+            "name": "jq",
+            "required": true
+          },
+          {
+            "name": "git",
+            "required": true
+          },
+          {
+            "name": "node",
+            "required": false
+          },
+          {
+            "name": "shellcheck",
+            "required": false
+          }
+        ]
+      },
+      "provides": {
+        "commands": 5,
+        "hooks": 1
+      },
+      "tags": [
+        "quality",
+        "enforcement",
+        "hooks",
+        "ci",
+        "governance"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-07-09T00:00:00Z",
+      "updated_at": "2026-07-13T00:00:00Z"
+    },
     "github-issues": {
       "name": "GitHub Issues Integration 1",
       "id": "github-issues",
@@ -2143,6 +2276,42 @@
       "created_at": "2026-05-08T00:00:00Z",
       "updated_at": "2026-05-08T00:00:00Z"
     },
+    "memory": {
+      "name": "Spec Kit Memory",
+      "id": "memory",
+      "description": "Recalls prior specs and decisions from configurable memory tools (e.g. memsearch) before SDLC stages, so planning and specification start from what the project already knows.",
+      "author": "Andrey Zaytsev",
+      "version": "0.3.0",
+      "download_url": "https://github.com/zaytsevand/spec-kit-memory/archive/refs/tags/v0.3.0.zip",
+      "repository": "https://github.com/zaytsevand/spec-kit-memory",
+      "homepage": "https://github.com/zaytsevand/spec-kit-memory",
+      "documentation": "https://github.com/zaytsevand/spec-kit-memory/blob/main/README.md",
+      "changelog": "",
+      "license": "MIT",
+      "category": "docs",
+      "effect": "read-write",
+      "requires": {
+        "speckit_version": ">=0.2.0",
+        "tools": [
+          { "name": "memsearch", "required": false }
+        ]
+      },
+      "provides": {
+        "commands": 2,
+        "hooks": 3
+      },
+      "tags": [
+        "memory",
+        "recall",
+        "research",
+        "memsearch"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-07-10T00:00:00Z",
+      "updated_at": "2026-07-10T00:00:00Z"
+    },
     "memory-loader": {
       "name": "Memory Loader",
       "id": "memory-loader",
@@ -2297,6 +2466,48 @@
       "created_at": "2026-05-04T02:51:52Z",
       "updated_at": "2026-06-18T00:00:00Z"
     },
+    "multi-repo-sync": {
+      "name": "Multi-Repo Branch Sync",
+      "id": "multi-repo-sync",
+      "description": "Creates the feature branch in affected sub-repositories and git submodules via plan/tasks hooks",
+      "author": "Fyloss",
+      "version": "1.0.0",
+      "download_url": "https://github.com/fyloss/spec-kit-multi-repo-sync/releases/download/v1.0.0/spec-kit-multi-repo-sync.zip",
+      "sha256": "12a5c7392145b4424b20715aaa3d8b6a8218c143dea596873e344146c1a76ba0",
+      "repository": "https://github.com/fyloss/spec-kit-multi-repo-sync",
+      "homepage": "https://github.com/fyloss/spec-kit-multi-repo-sync",
+      "documentation": "https://github.com/fyloss/spec-kit-multi-repo-sync/blob/main/README.md",
+      "changelog": "https://github.com/fyloss/spec-kit-multi-repo-sync/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "category": "process",
+      "effect": "read-write",
+      "requires": {
+        "speckit_version": ">=0.2.0",
+        "tools": [
+          {
+            "name": "git",
+            "version": ">=2.31",
+            "required": true
+          }
+        ]
+      },
+      "provides": {
+        "commands": 3,
+        "hooks": 2
+      },
+      "tags": [
+        "git",
+        "branching",
+        "multi-repo",
+        "submodules",
+        "workflow"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-07-13T00:00:00Z",
+      "updated_at": "2026-07-13T00:00:00Z"
+    },
     "multi-sites": {
       "name": "Multi-Sites Spec Kit",
       "id": "multi-sites",
@@ -4282,6 +4493,40 @@
       "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",

extensions/catalog.json

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

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/catalog.community.json

@@ -1,6 +1,6 @@
 {
   "schema_version": "1.0",
-  "updated_at": "2026-06-30T00:00:00Z",
+  "updated_at": "2026-07-14T00:00:00Z",
   "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/presets/catalog.community.json",
   "presets": {
     "a11y-governance": {
@@ -131,6 +131,35 @@
       "created_at": "2026-04-27T00:00:00Z",
       "updated_at": "2026-06-14T00:00:00Z"
     },
+    "autonomous-run-governance": {
+      "name": "Autonomous Run Governance",
+      "id": "autonomous-run-governance",
+      "version": "0.1.4",
+      "description": "Adds permission-bounded, evidence-first governance for autonomous Spec Kit delivery, convergence, resume, closeout, and retrospective learning.",
+      "author": "Thorsten Hindermann",
+      "repository": "https://github.com/hindermath/spec-kit-preset-autonomous-run-governance",
+      "download_url": "https://github.com/hindermath/spec-kit-preset-autonomous-run-governance/archive/refs/tags/v0.1.4.zip",
+      "homepage": "https://github.com/hindermath/spec-kit-preset-autonomous-run-governance",
+      "documentation": "https://github.com/hindermath/spec-kit-preset-autonomous-run-governance/blob/v0.1.4/README.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.8.3"
+      },
+      "provides": {
+        "templates": 12,
+        "commands": 2,
+        "scripts": 2
+      },
+      "tags": [
+        "autonomous",
+        "governance",
+        "evidence",
+        "permissions",
+        "retrospective"
+      ],
+      "created_at": "2026-07-13T00:00:00Z",
+      "updated_at": "2026-07-14T00:00:00Z"
+    },
     "canon-core": {
       "name": "Canon Core",
       "id": "canon-core",
@@ -618,6 +647,34 @@
       "created_at": "2026-04-30T00:00:00Z",
       "updated_at": "2026-04-30T00:00:00Z"
     },
+    "test-first-governance": {
+      "name": "Test-First Governance",
+      "id": "test-first-governance",
+      "version": "1.3.0",
+      "description": "Governs TDD with coverage-complete BDD/ATDD Gherkin scenarios, explicit suite ownership, professional test reports, traceability, and risk-based quality gates.",
+      "author": "Zoltán Katona, PhD",
+      "repository": "https://github.com/ka-zo/spec-kit-preset-test-first-governance",
+      "download_url": "https://github.com/ka-zo/spec-kit-preset-test-first-governance/archive/refs/tags/1.3.0.zip",
+      "homepage": "https://github.com/ka-zo/spec-kit-preset-test-first-governance",
+      "documentation": "https://github.com/ka-zo/spec-kit-preset-test-first-governance/blob/main/README.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.12.11"
+      },
+      "provides": {
+        "templates": 10,
+        "commands": 8
+      },
+      "tags": [
+        "tdd",
+        "bdd",
+        "atdd",
+        "quality-gates",
+        "traceability"
+      ],
+      "created_at": "2026-07-13T00:00:00Z",
+      "updated_at": "2026-07-13T00:00:00Z"
+    },
     "toc-navigation": {
       "name": "Table of Contents Navigation",
       "id": "toc-navigation",

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 = "0.12.10.dev0"
+version = "0.12.15"
 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/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

spec-kit.code-workspace

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

src/specify_cli/_github_http.py

@@ -24,6 +24,7 @@ GITHUB_HOSTS = frozenset({
     "api.github.com",
     "codeload.github.com",
 })
+_MAX_RELEASE_METADATA_BYTES = 5 * 1024 * 1024
 
 
 def build_github_request(url: str) -> urllib.request.Request:
@@ -68,6 +69,8 @@ def resolve_github_release_asset_api_url(
     open_url_fn: Callable,
     timeout: int = 60,
     github_hosts: tuple[str, ...] = (),
+    redirect_validator: Callable[[str, str], None] | None = None,
+    max_metadata_bytes: int = _MAX_RELEASE_METADATA_BYTES,
 ) -> Optional[str]:
     """Resolve a GitHub release browser-download URL to its REST API asset URL.
 
@@ -91,6 +94,8 @@ def resolve_github_release_asset_api_url(
             authenticated release-metadata lookup.
         timeout: Per-request timeout in seconds.
         github_hosts: Host patterns to treat as GitHub Enterprise Server.
+        redirect_validator: Optional policy applied to metadata redirects.
+        max_metadata_bytes: Maximum release-metadata response size.
     """
     import json
     import urllib.error
@@ -149,13 +154,33 @@ def resolve_github_release_asset_api_url(
     release_url = f"{api_base}/repos/{owner}/{repo}/releases/tags/{encoded_tag}"
 
     try:
-        with open_url_fn(release_url, timeout=timeout) as response:
-            release_data = json.loads(response.read())
-    except (urllib.error.URLError, json.JSONDecodeError):
+        open_kwargs = {"timeout": timeout}
+        if redirect_validator is not None:
+            open_kwargs["redirect_validator"] = redirect_validator
+        with open_url_fn(release_url, **open_kwargs) as response:
+            raw_release_data = response.read(max_metadata_bytes + 1)
+            if len(raw_release_data) > max_metadata_bytes:
+                raise ValueError("GitHub release metadata exceeds size limit")
+            release_data = json.loads(raw_release_data)
+    except (
+        urllib.error.URLError,
+        json.JSONDecodeError,
+        TypeError,
+        ValueError,
+    ):
         return None
 
-    for asset in release_data.get("assets", []):
-        if asset.get("name") == asset_name and asset.get("url"):
+    if not isinstance(release_data, dict):
+        return None
+    assets = release_data.get("assets", [])
+    if not isinstance(assets, list):
+        return None
+    for asset in assets:
+        if (
+            isinstance(asset, dict)
+            and asset.get("name") == asset_name
+            and asset.get("url")
+        ):
             return str(asset["url"])
 
     return None

src/specify_cli/_init_options.py

@@ -14,7 +14,7 @@ def save_init_options(project_path: Path, options: dict[str, Any]) -> None:
     dest = project_path / INIT_OPTIONS_FILE
     dest.parent.mkdir(parents=True, exist_ok=True)
     dest.write_text(
-        json.dumps(options, indent=2, sort_keys=True, ensure_ascii=False),
+        json.dumps(options, indent=2, sort_keys=True, ensure_ascii=False) + "\n",
         encoding="utf-8",
     )
 

src/specify_cli/agents.py

@@ -213,6 +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:
@@ -639,6 +685,9 @@ class CommandRegistrar:
                         frontmatter[key] = core_frontmatter[key]
                 frontmatter.pop("strategy", None)
 
+            if extension_id:
+                body = self.rewrite_extension_paths(body, extension_id, source_root)
+
             frontmatter = self._adjust_script_paths(
                 frontmatter, extension_id=extension_id
             )

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/bundler/lib/yamlio.py

@@ -10,6 +10,8 @@ from __future__ import annotations
 import json
 import os
 import re
+import stat
+import tempfile
 from pathlib import Path, PurePosixPath
 from typing import Any
 
@@ -87,17 +89,63 @@ def loads_json(text: str, *, origin: str = "<string>") -> Any:
 
 
 def dump_json(path: Path, data: Any, *, within: Path | None = None) -> Path:
-    """Write *data* as pretty JSON to *path* (optionally confined to *within*)."""
+    """Atomically write pretty JSON to *path* (optionally confined to *within*)."""
     path = Path(path)
     if within is not None:
         path = ensure_within(within, path)
+    fd = -1
+    temp_path: Path | None = None
     try:
         path.parent.mkdir(parents=True, exist_ok=True)
-        with path.open("w", encoding="utf-8") as handle:
+        fd, temp_name = tempfile.mkstemp(
+            dir=path.parent,
+            prefix=f".{path.name}.",
+            suffix=".tmp",
+        )
+        temp_path = Path(temp_name)
+        with os.fdopen(os.dup(fd), "w", encoding="utf-8") as handle:
             json.dump(data, handle, indent=2, sort_keys=False)
             handle.write("\n")
+
+        try:
+            if path.exists():
+                existing = path.stat(follow_symlinks=False)
+                if stat.S_ISREG(existing.st_mode) and hasattr(os, "fchmod"):
+                    os.fchmod(fd, stat.S_IMODE(existing.st_mode))
+                if stat.S_ISREG(existing.st_mode) and hasattr(os, "fchown"):
+                    try:
+                        os.fchown(fd, existing.st_uid, existing.st_gid)
+                    except PermissionError:
+                        pass
+        except OSError:
+            pass
+
+        staged = os.stat(temp_path, follow_symlinks=False)
+        opened = os.fstat(fd)
+        if (
+            not stat.S_ISREG(staged.st_mode)
+            or staged.st_dev != opened.st_dev
+            or staged.st_ino != opened.st_ino
+        ):
+            raise OSError("staged JSON file changed before commit")
+
+        os.close(fd)
+        fd = -1
+        os.replace(temp_path, path)
+        temp_path = None
     except OSError as exc:
         raise BundlerError(f"Could not write {path}: {exc}") from exc
+    finally:
+        if fd >= 0:
+            try:
+                os.close(fd)
+            except OSError:
+                pass
+        if temp_path is not None:
+            try:
+                temp_path.unlink(missing_ok=True)
+            except OSError:
+                pass
     return path
 
 

src/specify_cli/bundler/services/adapters.py

@@ -68,8 +68,18 @@ 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}://). "
@@ -79,7 +89,7 @@ def _validate_remote_url(source_id: str, url: str) -> None:
     # "https://:8080" or "https://user@...", so requiring netloc would let
     # those through even though they carry no host. hostname is None in those
     # cases. Mirrors the fix in ``specify_cli.catalogs`` (#3210).
-    if not parsed.hostname:
+    if not hostname:
         raise BundlerError(
             f"Catalog '{source_id}' URL must be a valid URL with a host: {url}"
         )

src/specify_cli/bundler/services/installer.py

@@ -187,19 +187,41 @@ def remove_bundle(
 
     still_needed = components_still_needed(records, exclude_bundle_id=bundle_id)
     result = InstallResult(bundle_id=bundle_id)
+    remove_attempted = False
 
-    for component in target.contributed_components:
-        key = (component.kind, component.id)
-        if key in still_needed:
-            result.skipped.append(component)
-            continue
-        if installer.is_installed(project_root, component):
-            installer.remove(project_root, component)
-            result.uninstalled.append(component)
+    try:
+        for component in target.contributed_components:
+            key = (component.kind, component.id)
+            if key in still_needed:
+                result.skipped.append(component)
+                continue
+            if installer.is_installed(project_root, component):
+                remove_attempted = True
+                installer.remove(project_root, component)
+                result.uninstalled.append(component)
+        save_records(project_root, remove_record(records, bundle_id))
+    except Exception as exc:  # noqa: BLE001
+        if result.uninstalled:
+            detail = (
+                f"{len(result.uninstalled)} component(s) were already removed "
+                "before this failure; the bundle record was left unchanged, "
+                "so the project may be partially uninstalled."
+            )
+        elif remove_attempted:
+            detail = (
+                "No components were removed, but the failing component may "
+                "have made partial changes before raising, so the project "
+                "may be partially uninstalled."
+            )
         else:
-            result.skipped.append(component)
+            detail = (
+                "No components were removed and no removal was attempted; "
+                "the bundle record was left unchanged."
+            )
+        raise BundlerError(
+            f"Failed to remove bundle '{bundle_id}': {exc}. {detail}"
+        ) from exc
 
-    save_records(project_root, remove_record(records, bundle_id))
     return result
 
 

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/commands/init.py

@@ -220,16 +220,45 @@ def register(app: typer.Typer) -> None:
                 console.print(
                     f"[yellow]Warning:[/yellow] Current directory is not empty ({len(existing_items)} items)"
                 )
-                console.print(
-                    "[yellow]Template files will be merged with existing content and may overwrite existing files[/yellow]"
-                )
                 if force:
+                    # Proceeding: the merge/overwrite warning is accurate here.
+                    console.print(
+                        "[yellow]Template files will be merged with existing content and may overwrite existing files[/yellow]"
+                    )
                     console.print(
                         "[cyan]--force supplied: skipping confirmation and proceeding with merge[/cyan]"
                     )
                 else:
-                    response = typer.confirm("Do you want to continue?")
-                    if not response:
+                    # Fold the merge risk into the confirmation prompt rather than
+                    # printing it unconditionally first: on the EOF/no-input path
+                    # below the command exits without changing anything, so a
+                    # standalone "will be merged" line would mislead. Interactive
+                    # users still see the risk as part of the question.
+                    #
+                    # Call typer.confirm normally so piped y/n is honored — e.g.
+                    # `echo y | specify init --here` keeps reaching the
+                    # non-destructive preserve-merge path.
+                    try:
+                        proceed = typer.confirm(
+                            "Template files will be merged with existing content "
+                            "and may overwrite existing files. Do you want to continue?"
+                        )
+                    except (typer.Abort, EOFError):
+                        # typer.confirm raises Abort for BOTH an interactive Ctrl+C
+                        # and an EOF on closed/empty stdin. Distinguish them: a real
+                        # TTY cancellation is a normal exit (0, "cancelled"), while a
+                        # missing-input EOF (non-interactive) becomes an actionable
+                        # error pointing at --force.
+                        if _stdin_is_interactive():
+                            console.print("[yellow]Operation cancelled[/yellow]")
+                            raise typer.Exit(0) from None
+                        console.print(
+                            "[red]Error:[/red] Current directory is not empty and no "
+                            "confirmation input is available. Re-run with "
+                            "[bold]--force[/bold] to merge into it."
+                        )
+                        raise typer.Exit(1) from None
+                    if not proceed:
                         console.print("[yellow]Operation cancelled[/yellow]")
                         raise typer.Exit(0)
         else:

src/specify_cli/extensions/__init__.py

@@ -1078,6 +1078,11 @@ class ExtensionManager:
             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, extension_id=manifest.id
             )
@@ -2732,6 +2737,36 @@ class ConfigManager:
         config_file = self.extension_dir / "local-config.yml"
         return self._load_yaml_config(config_file)
 
+    def _sibling_extension_ids(self) -> list[str]:
+        """Return IDs of other extensions installed alongside this one.
+
+        Sourced from ``ExtensionRegistry`` (``.specify/extensions/.registry``)
+        rather than a directory scan: ``ExtensionManager.remove(...,
+        keep_config=True)`` deliberately preserves the extension directory
+        while dropping the registry entry, so a directory scan would treat
+        that config-only leftover as an installed sibling and keep silently
+        absorbing its ``SPECKIT_<sibling>_*`` env vars into no one. The
+        registry is the source of truth for "installed".
+
+        Returns an empty list if the registry is missing or corrupted
+        (fresh project, ad-hoc test harness) so ``_get_env_config`` degrades
+        to its pre-fix behaviour rather than crashing. ``UnicodeError`` is
+        caught alongside ``OSError`` because ``ExtensionRegistry._load()``
+        opens the file in text mode and only handles ``JSONDecodeError`` /
+        ``FileNotFoundError``, so a registry file with non-UTF-8 bytes would
+        otherwise surface a ``UnicodeDecodeError`` here and break *every*
+        config read instead of degrading gracefully.
+
+        Used by ``_get_env_config`` to detect env vars whose remainder claims
+        a longer, sibling-owned prefix (e.g. ``SPECKIT_GIT_HOOKS_URL`` is
+        owned by ``git-hooks`` when it is co-installed with ``git``).
+        """
+        extensions_dir = self.project_root / ".specify" / "extensions"
+        try:
+            return list(ExtensionRegistry(extensions_dir).keys())
+        except (OSError, UnicodeError):
+            return []
+
     def _get_env_config(self) -> Dict[str, Any]:
         """Get configuration from environment variables.
 
@@ -2751,22 +2786,70 @@ class ConfigManager:
         ext_id_upper = self.extension_id.replace("-", "_").upper()
         prefix = f"SPECKIT_{ext_id_upper}_"
 
+        # Cross-extension prefix collision: because ``_`` doubles as both the
+        # separator between the extension ID and the config path *and* the
+        # substitute for ``-`` inside an extension ID, an env var like
+        # ``SPECKIT_GIT_HOOKS_URL`` begins with *both* the ``SPECKIT_GIT_``
+        # prefix of the ``git`` extension and the ``SPECKIT_GIT_HOOKS_`` prefix
+        # of a co-installed ``git-hooks`` extension. It logically belongs to
+        # the extension whose normalized ID is the longer, more specific match
+        # — otherwise config intended for one extension silently surfaces
+        # inside another and can drive hooks that only inspect
+        # ``config.<field> is set``. Build the list of sibling-owned
+        # remainder-prefixes here so a later env var can be skipped if it
+        # matches one.
+        sibling_prefixes: list[str] = []
+        for sibling_id in self._sibling_extension_ids():
+            if sibling_id == self.extension_id:
+                continue
+            sib_upper = sibling_id.replace("-", "_").upper()
+            # A sibling collides only when its normalized ID *extends* our own
+            # (i.e. starts with ``<US>_``). ``git`` vs ``not-git`` is not a
+            # collision; ``git`` vs ``git-hooks`` is.
+            if sib_upper.startswith(ext_id_upper + "_"):
+                # The portion of the env-var *remainder* the sibling claims,
+                # including the trailing ``_`` so a shorter ID that shares a
+                # non-boundary prefix cannot false-positive (e.g. sibling
+                # ``hook`` would not eat env vars under key ``hooks``).
+                sibling_prefixes.append(sib_upper[len(ext_id_upper) + 1 :] + "_")
+
         for key, value in os.environ.items():
             if not key.startswith(prefix):
                 continue
 
-            # Remove prefix and split into parts
-            config_path = key[len(prefix) :].lower().split("_")
+            remainder = key[len(prefix) :]
+            # Skip when a longer sibling ID claims this var — see the block
+            # above. Keeps ``SPECKIT_GIT_HOOKS_URL`` out of the ``git``
+            # extension's config when ``git-hooks`` is co-installed.
+            if any(remainder.startswith(sp) for sp in sibling_prefixes):
+                continue
 
-            # Build nested dict
+            # 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 remainder.lower().split("_") if p]
+            if not config_path:
+                continue
+
+            # 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

@@ -1566,7 +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/_helpers.py

@@ -190,7 +190,15 @@ def _parse_integration_options(integration: Any, raw_options: str) -> dict[str,
     """
     import shlex
     parsed: dict[str, Any] = {}
-    tokens = shlex.split(raw_options)
+    try:
+        tokens = shlex.split(raw_options)
+    except ValueError as exc:
+        # An unbalanced quote (e.g. --integration-options='--commands-dir "foo')
+        # makes shlex raise "No closing quotation". Translate it into the same
+        # clean exit-1 UX as every other bad-input path below rather than
+        # letting a raw traceback escape.
+        console.print(f"[red]Error:[/red] Could not parse integration options: {exc}.")
+        raise typer.Exit(1)
     declared_options = list(integration.options())
     declared = {opt.name.lstrip("-"): opt for opt in declared_options}
     allowed = ", ".join(sorted(opt.name for opt in declared_options))

src/specify_cli/integrations/base.py

@@ -1122,6 +1122,17 @@ class TomlIntegration(IntegrationBase):
 # YamlIntegration — YAML-format agents (Goose)
 # ---------------------------------------------------------------------------
 
+# Characters a YAML literal block scalar cannot carry: C0 controls other
+# than tab/LF (a bare CR acts as a line break inside the scalar), DEL, the
+# C1 range, lone UTF-16 surrogates, and the non-characters U+FFFE/U+FFFF.
+# NEL (U+0085) is YAML-printable but, like LS/PS (U+2028/U+2029), YAML 1.1
+# treats it as a line break, which corrupts the block scalar's structure
+# just the same, so all three are included.
+_YAML_BLOCK_SCALAR_UNSAFE = re.compile(
+    r"[\x00-\x08\x0b-\x1f\x7f-\x9f\u2028\u2029\ud800-\udfff\ufffe\uffff]"
+)
+
+
 class YamlIntegration(IntegrationBase):
     """Concrete base for integrations that use YAML recipe format.
 
@@ -1227,9 +1238,9 @@ class YamlIntegration(IntegrationBase):
     def _render_yaml(cls, title: str, description: str, body: str, source_id: str) -> str:
         """Render a YAML recipe file from title, description, and body.
 
-        Produces a Goose-compatible recipe with a literal block scalar
-        for the prompt content.  Uses ``yaml.safe_dump()`` for the
-        header fields to ensure proper escaping.
+        Produces a Goose-compatible recipe with a literal block scalar for
+        normal prompt content, or an escaped quoted scalar when control
+        characters require it. Uses ``yaml.safe_dump()`` for the header fields.
         """
         header = cls._build_yaml_header(title, description)
 
@@ -1240,6 +1251,23 @@ class YamlIntegration(IntegrationBase):
             default_flow_style=False,
         ).strip()
 
+        # YAML forbids C0 control characters (except tab and newline) and
+        # DEL in every scalar form, and a bare CR acts as a line break
+        # inside a block scalar. A literal block scalar emits such bytes
+        # verbatim, producing a recipe the YAML parser rejects, so fall
+        # back to an escaped double-quoted scalar for those bodies.
+        if _YAML_BLOCK_SCALAR_UNSAFE.search(body):
+            prompt_yaml = yaml.safe_dump(
+                {"prompt": body}, allow_unicode=True, default_style='"', width=sys.maxsize
+            ).strip()
+            lines = [
+                header_yaml,
+                prompt_yaml,
+                "",
+                f"# Source: {source_id}",
+            ]
+            return "\n".join(lines) + "\n"
+
         # 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

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/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/",
@@ -26,3 +27,10 @@ class KiroCliIntegration(MarkdownIntegration):
         "args": _KIRO_ARG_FALLBACK,
         "extension": ".md",
     }
+
+    # Kiro CLI keeps everything under a static, isolated agent root
+    # (``.kiro/`` with commands in ``.kiro/prompts``) that no other
+    # integration writes to, so it is safe to install alongside others
+    # (issue #3471). The registry's multi-install-safe contract tests
+    # enforce that isolation for every integration setting this flag.
+    multi_install_safe = True

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
@@ -2574,6 +2588,39 @@ class PresetResolver:
                 self._manifest_cache[key] = None
         return self._manifest_cache[key]
 
+    def _manifest_declared_template(
+        self, pack_dir: Path, template_name: str, template_type: str
+    ) -> tuple[dict | None, Path | None]:
+        """Resolve a preset's manifest-declared template entry and usable file.
+
+        Returns ``(entry, candidate)``:
+        - ``entry`` is the matching ``provides.templates`` mapping, or ``None`` if
+          the manifest is absent or does not list this ``(name, type)``.
+        - ``candidate`` is the declared ``file:`` resolved under ``pack_dir`` IFF
+          it is a regular file (``is_file()``); ``None`` otherwise — a missing,
+          empty, or non-file (e.g. directory) declaration yields ``(entry, None)``.
+
+        The manifest is authoritative: when it declares a template (``entry`` is
+        not ``None``) but the file is unusable (``candidate`` is ``None``),
+        callers must NOT fall back to the convention lookup — that would mask a
+        typo or pick up an undeclared file. Shared by ``resolve()`` and
+        ``collect_all_layers()`` so their manifest-first resolution cannot
+        silently diverge again (the divergence this fix addressed).
+        """
+        manifest = self._get_manifest(pack_dir)
+        if not manifest:
+            return None, None
+        for tmpl in manifest.templates:
+            if tmpl.get("name") == template_name and tmpl.get("type") == template_type:
+                file_path = tmpl.get("file")
+                if file_path:
+                    manifest_candidate = pack_dir / file_path
+                    return tmpl, (
+                        manifest_candidate if manifest_candidate.is_file() else None
+                    )
+                return tmpl, None
+        return None, None
+
     def _get_all_extensions_by_priority(self) -> list[tuple[int, str, dict | None]]:
         """Build unified list of registered and unregistered extensions sorted by priority.
 
@@ -2676,6 +2723,27 @@ class PresetResolver:
             registry = PresetRegistry(self.presets_dir)
             for pack_id, _metadata in registry.list_by_priority():
                 pack_dir = self.presets_dir / pack_id
+                # The preset manifest is authoritative: if it declares this
+                # template with an explicit ``file:``, resolve to that path —
+                # and do NOT fall back to convention when it's missing, to
+                # avoid masking typos or picking up an undeclared file. Only
+                # when the manifest is absent or doesn't list this template do
+                # we use the convention-based subdir lookup. Mirrors
+                # collect_all_layers()/resolve_content() so resolve() and
+                # resolve_with_source() agree with them instead of returning
+                # the core template (or a stray convention file).
+                entry, manifest_candidate = self._manifest_declared_template(
+                    pack_dir, template_name, template_type
+                )
+                if manifest_candidate is not None:
+                    return manifest_candidate
+                if entry is not None:
+                    # Manifest declares this template but the file is missing,
+                    # non-file (e.g. a directory), or an empty/falsey ``file``
+                    # value. The manifest is authoritative, so skip this pack's
+                    # convention fallback rather than mask a typo — mirrors
+                    # collect_all_layers().
+                    continue
                 for subdir in subdirs:
                     if subdir:
                         candidate = pack_dir / subdir / f"{template_name}{ext}"
@@ -2943,31 +3011,22 @@ class PresetResolver:
                 pack_dir = self.presets_dir / pack_id
                 # Read strategy and manifest file path from preset manifest
                 strategy = "replace"
-                manifest_file_path = None
                 manifest_has_strategy = False
-                manifest_found_entry = False
-                manifest = self._get_manifest(pack_dir)
-                if manifest:
-                    for tmpl in manifest.templates:
-                        if (tmpl.get("name") == template_name
-                                and tmpl.get("type") == template_type):
-                            strategy = tmpl.get("strategy", "replace")
-                            manifest_has_strategy = "strategy" in tmpl
-                            manifest_file_path = tmpl.get("file")
-                            manifest_found_entry = True
-                            break
-                # Use manifest file path if specified, otherwise convention-based
-                # lookup — but only when the manifest doesn't exist or doesn't
-                # list this template, so preset.yml stays authoritative.
+                entry, manifest_candidate = self._manifest_declared_template(
+                    pack_dir, template_name, template_type
+                )
+                if entry is not None:
+                    strategy = entry.get("strategy", "replace")
+                    manifest_has_strategy = "strategy" in entry
+                # Use the manifest's declared file when it's a usable regular file;
+                # only fall back to convention-based lookup when the manifest
+                # doesn't list this template at all, so preset.yml stays
+                # authoritative (a declared-but-unusable file skips convention —
+                # parity with resolve()).
                 candidate = None
-                if manifest_file_path:
-                    manifest_candidate = pack_dir / manifest_file_path
-                    if manifest_candidate.exists():
-                        candidate = manifest_candidate
-                    # Explicit file path that doesn't exist: skip convention
-                    # fallback to avoid masking typos or picking up unintended files.
-                elif not manifest_found_entry:
-                    # Manifest doesn't list this template — check convention paths
+                if manifest_candidate is not None:
+                    candidate = manifest_candidate
+                elif entry is None:
                     candidate = _find_in_subdirs(pack_dir)
                 if candidate:
                     # Legacy fallback: if manifest doesn't explicitly declare a
@@ -3038,6 +3097,8 @@ class PresetResolver:
                     "path": candidate,
                     "source": source,
                     "strategy": "replace",
+                    "extension_id": ext_id,
+                    "extension_dir": ext_dir,
                 })
 
         # Priority 4: Core templates (always "replace")
@@ -3157,10 +3218,32 @@ 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 +3266,7 @@ 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

@@ -469,7 +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/workflows/catalog.py

@@ -13,6 +13,8 @@ from __future__ import annotations
 import hashlib
 import json
 import os
+import stat
+import tempfile
 import time
 from dataclasses import dataclass
 from pathlib import Path
@@ -71,40 +73,180 @@ class WorkflowRegistry:
         self.registry_path = self.workflows_dir / self.REGISTRY_FILE
         self.data = self._load()
 
+    def _has_symlinked_parent(self) -> bool:
+        """Return True if any directory under .specify/workflows is a symlink."""
+        current = self.project_root
+        for part in (".specify", "workflows"):
+            current = current / part
+            if current.is_symlink():
+                return True
+        return False
+
     def _load(self) -> dict[str, Any]:
         """Load registry from disk or create default."""
+        default_registry: dict[str, Any] = {
+            "schema_version": self.SCHEMA_VERSION,
+            "workflows": {},
+        }
+        # Defense-in-depth: refuse to read through symlinked parents or a
+        # symlinked registry file. Unlike StepRegistry (read-only best-effort
+        # elsewhere), a fabricated empty registry here is not safe: read-only
+        # callers (notably the bundler's remove path) query is_installed()
+        # before ever writing, and would otherwise conclude an installed
+        # workflow is absent, skip removing it, then delete the bundle
+        # record -- leaving the workflow untracked but still on disk. Fail
+        # closed here just like the unreadable-file case below.
+        if self._has_symlinked_parent() or self.registry_path.is_symlink():
+            raise OSError(
+                f"Refusing to read workflow registry at {self.registry_path}: "
+                "a parent directory or the registry file itself is a symlink"
+            )
         if self.registry_path.exists():
             try:
                 with open(self.registry_path, encoding="utf-8") as f:
-                    return json.load(f)
-            except (json.JSONDecodeError, ValueError):
-                # Corrupted registry file — reset to default
-                return {"schema_version": self.SCHEMA_VERSION, "workflows": {}}
-        return {"schema_version": self.SCHEMA_VERSION, "workflows": {}}
+                    data = json.load(f)
+            except OSError as exc:
+                # The real data may still be intact on disk. Fail closed at
+                # construction rather than fabricating an empty registry that
+                # a read-only caller could mistake for "nothing installed."
+                raise OSError(
+                    f"Failed to read workflow registry at {self.registry_path}: {exc}"
+                ) from exc
+            except (
+                json.JSONDecodeError,
+                ValueError,
+                UnicodeError,
+            ) as exc:
+                raise OSError(
+                    f"Workflow registry at {self.registry_path} is corrupted: "
+                    f"{exc}"
+                ) from exc
+            # Validate shape: must be a dict with a dict "workflows" field.
+            if not isinstance(data, dict):
+                raise OSError(
+                    f"Workflow registry at {self.registry_path} is corrupted: "
+                    "top-level value must be an object"
+                )
+            if not isinstance(data.get("workflows"), dict):
+                raise OSError(
+                    f"Workflow registry at {self.registry_path} is corrupted: "
+                    "'workflows' must be an object"
+                )
+            return data
+        return default_registry
 
     def save(self) -> None:
-        """Persist registry to disk."""
+        """Persist registry to disk atomically."""
+        # Refuse to write through symlinked parents (mirrors StepRegistry.save
+        # and the CLI-level _reject_unsafe_dir guard).
+        if self._has_symlinked_parent() or self.registry_path.is_symlink():
+            raise OSError(
+                "Refusing to write workflow registry through a symlinked path."
+            )
         self.workflows_dir.mkdir(parents=True, exist_ok=True)
-        with open(self.registry_path, "w", encoding="utf-8") as f:
-            json.dump(self.data, f, indent=2)
+        # Unique, exclusive temp then replace: a failed dump cannot truncate
+        # the registry, a pre-created symlink cannot redirect the write, and
+        # concurrent CLI processes cannot collide on the same temp path.
+        fd, tmp = tempfile.mkstemp(
+            dir=str(self.registry_path.parent),
+            prefix=f".{self.registry_path.name}.",
+            suffix=".tmp",
+        )
+        try:
+            # Write through a duplicate so the exclusive mkstemp descriptor
+            # stays open for fd-based metadata updates and inode verification.
+            with os.fdopen(os.dup(fd), "w", encoding="utf-8") as f:
+                json.dump(self.data, f, indent=2)
+            # mkstemp creates the temp file at 0600. A pre-existing registry
+            # may be shared more permissively (e.g. 0640/0644); preserve its
+            # mode across the replace so a save doesn't silently lock other
+            # project users out. A brand-new registry has no prior mode to
+            # preserve, so mkstemp's secure 0600 default stands. Mirrors
+            # _utils.py's atomic_write_json (best-effort; data safety over
+            # metadata preservation).
+            try:
+                if self.registry_path.exists():
+                    existing_stat = self.registry_path.stat(
+                        follow_symlinks=False
+                    )
+                    if stat.S_ISREG(existing_stat.st_mode) and hasattr(
+                        os, "fchmod"
+                    ):
+                        os.fchmod(fd, stat.S_IMODE(existing_stat.st_mode))
+                    if stat.S_ISREG(existing_stat.st_mode) and hasattr(
+                        os, "fchown"
+                    ):
+                        try:
+                            os.fchown(
+                                fd, existing_stat.st_uid, existing_stat.st_gid
+                            )
+                        except PermissionError:
+                            pass
+            except OSError:
+                pass
+            staged_stat = os.stat(tmp, follow_symlinks=False)
+            open_stat = os.fstat(fd)
+            if (
+                not stat.S_ISREG(staged_stat.st_mode)
+                or staged_stat.st_dev != open_stat.st_dev
+                or staged_stat.st_ino != open_stat.st_ino
+            ):
+                raise OSError(
+                    "Refusing to replace workflow registry: "
+                    "staged file changed before commit"
+                )
+            os.close(fd)
+            fd = -1
+            os.replace(tmp, self.registry_path)
+        except BaseException:
+            if fd >= 0:
+                try:
+                    os.close(fd)
+                except OSError:
+                    pass
+            try:
+                os.unlink(tmp)
+            except OSError:
+                pass
+            raise
 
     def add(self, workflow_id: str, metadata: dict[str, Any]) -> None:
         """Add or update an installed workflow entry."""
         from datetime import datetime, timezone
 
-        existing = self.data["workflows"].get(workflow_id, {})
+        raw_existing = self.data["workflows"].get(workflow_id)
+        had_entry = workflow_id in self.data["workflows"]
+        # Corrupted-but-parseable registries may hold non-dict entries.
+        existing = raw_existing if isinstance(raw_existing, dict) else {}
         metadata["installed_at"] = existing.get(
             "installed_at", datetime.now(timezone.utc).isoformat()
         )
         metadata["updated_at"] = datetime.now(timezone.utc).isoformat()
         self.data["workflows"][workflow_id] = metadata
-        self.save()
+        try:
+            self.save()
+        except (OSError, TypeError, ValueError):
+            # Roll back the in-memory mutation so a later successful save
+            # cannot persist metadata for a write that failed.
+            if had_entry:
+                self.data["workflows"][workflow_id] = raw_existing
+            else:
+                del self.data["workflows"][workflow_id]
+            raise
 
     def remove(self, workflow_id: str) -> bool:
         """Remove an installed workflow entry. Returns True if found."""
         if workflow_id in self.data["workflows"]:
+            removed_entry = self.data["workflows"][workflow_id]
             del self.data["workflows"][workflow_id]
-            self.save()
+            try:
+                self.save()
+            except (OSError, TypeError, ValueError):
+                # Roll back the in-memory deletion so a save failure can't
+                # desync this instance from the untouched file on disk,
+                # mirroring add()'s rollback-on-save-failure.
+                self.data["workflows"][workflow_id] = removed_entry
+                raise
             return True
         return False
 
@@ -157,8 +299,20 @@ class WorkflowCatalog:
         """Validate that a catalog URL uses HTTPS (localhost HTTP allowed)."""
         from urllib.parse import urlparse
 
-        parsed = urlparse(url)
-        is_localhost = parsed.hostname in ("localhost", "127.0.0.1", "::1")
+        # A malformed authority (e.g. an unterminated IPv6 bracket
+        # "https://[::1") makes urlparse / hostname access raise ValueError.
+        # This validator's contract is to raise WorkflowValidationError for a
+        # bad URL, so surface that rather than leaking a raw ValueError past the
+        # command handler (which only catches WorkflowValidationError). Mirrors
+        # specify_cli.catalogs (#3435).
+        try:
+            parsed = urlparse(url)
+            hostname = parsed.hostname
+        except ValueError:
+            raise WorkflowValidationError(
+                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
         ):
@@ -166,7 +320,7 @@ class WorkflowCatalog:
                 f"Catalog URL must use HTTPS (got {parsed.scheme}://). "
                 "HTTP is only allowed for localhost."
             )
-        if not parsed.hostname:
+        if not hostname:
             raise WorkflowValidationError(
                 "Catalog URL must be a valid URL with a host."
             )
@@ -332,15 +486,26 @@ class WorkflowCatalog:
         from specify_cli.authentication.http import open_url as _open_url
 
         def _validate_catalog_url(url: str) -> None:
-            parsed = urlparse(url)
-            is_localhost = parsed.hostname in ("localhost", "127.0.0.1", "::1")
+            # A malformed authority (e.g. "https://[::1") makes urlparse /
+            # hostname access raise ValueError; treat it as a refused fetch
+            # rather than leaking a raw ValueError (this also validates the
+            # post-redirect resp.geturl(), so a hostile redirect target cannot
+            # crash the fetch either).
+            try:
+                parsed = urlparse(url)
+                hostname = parsed.hostname
+            except ValueError:
+                raise WorkflowCatalogError(
+                    f"Refusing to fetch catalog from malformed URL: {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 WorkflowCatalogError(
                     f"Refusing to fetch catalog from non-HTTPS URL: {url}"
                 )
-            if not parsed.hostname:
+            if not hostname:
                 raise WorkflowCatalogError(
                     f"Refusing to fetch catalog from URL with no hostname: {url}"
                 )
@@ -427,6 +592,7 @@ class WorkflowCatalog:
         self,
         query: str | None = None,
         tag: str | None = None,
+        author: str | None = None,
     ) -> list[dict[str, Any]]:
         """Search workflows across all configured catalogs."""
         merged = self._get_merged_workflows()
@@ -438,9 +604,9 @@ 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:
@@ -451,6 +617,10 @@ class WorkflowCatalog:
                 normalized_tags = [t.lower() for t in tags if isinstance(t, str)]
                 if tag.lower() not in normalized_tags:
                     continue
+            if author:
+                wf_author = wf_data.get("author", "")
+                if not isinstance(wf_author, str) or wf_author.lower() != author.lower():
+                    continue
             results.append(wf_data)
         return results
 
@@ -774,8 +944,20 @@ class StepCatalog:
         """Validate that a catalog URL uses HTTPS (localhost HTTP allowed)."""
         from urllib.parse import urlparse
 
-        parsed = urlparse(url)
-        is_localhost = parsed.hostname in ("localhost", "127.0.0.1", "::1")
+        # A malformed authority (e.g. an unterminated IPv6 bracket
+        # "https://[::1") makes urlparse / hostname access raise ValueError.
+        # This validator's contract is to raise StepValidationError for a bad
+        # URL, so surface that rather than leaking a raw ValueError past the
+        # command handler (which only catches StepValidationError). Mirrors
+        # specify_cli.catalogs (#3435).
+        try:
+            parsed = urlparse(url)
+            hostname = parsed.hostname
+        except ValueError:
+            raise StepValidationError(
+                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
         ):
@@ -783,7 +965,7 @@ class StepCatalog:
                 f"Catalog URL must use HTTPS (got {parsed.scheme}://). "
                 "HTTP is only allowed for localhost."
             )
-        if not parsed.hostname:
+        if not hostname:
             raise StepValidationError(
                 "Catalog URL must be a valid URL with a host."
             )
@@ -949,15 +1131,26 @@ class StepCatalog:
         from specify_cli.authentication.http import open_url as _open_url
 
         def _validate_url(url: str) -> None:
-            parsed = urlparse(url)
-            is_localhost = parsed.hostname in ("localhost", "127.0.0.1", "::1")
+            # A malformed authority (e.g. "https://[::1") makes urlparse /
+            # hostname access raise ValueError; treat it as a refused fetch
+            # rather than leaking a raw ValueError (this also validates the
+            # post-redirect resp.geturl(), so a hostile redirect target cannot
+            # crash the fetch either).
+            try:
+                parsed = urlparse(url)
+                hostname = parsed.hostname
+            except ValueError:
+                raise StepCatalogError(
+                    f"Refusing to fetch catalog from malformed URL: {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 StepCatalogError(
                     f"Refusing to fetch catalog from non-HTTPS URL: {url}"
                 )
-            if not parsed.hostname:
+            if not hostname:
                 raise StepCatalogError(
                     f"Refusing to fetch catalog from URL with no hostname: {url}"
                 )

src/specify_cli/workflows/engine.py

@@ -129,27 +129,50 @@ 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 _ID_PATTERN.match(definition.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.fullmatch(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 re.match(r"^\d+\.\d+\.\d+$", definition.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.fullmatch(r"\d+\.\d+\.\d+", definition.version):
         errors.append(
             f"Workflow version {definition.version!r} is not valid "
             f"semantic versioning (expected X.Y.Z)."
@@ -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(
@@ -387,18 +416,57 @@ class RunState:
         ID into a path so a malicious value cannot probe or read files
         outside ``.specify/workflows/runs/<run_id>/``.
         """
-        if not isinstance(run_id, str) or not cls._RUN_ID_PATTERN.match(run_id):
+        if not isinstance(run_id, str) or not cls._RUN_ID_PATTERN.fullmatch(run_id):
             raise ValueError(
                 f"Invalid run_id {run_id!r}: must be alphanumeric with "
                 "hyphens/underscores only (and must start with an "
                 "alphanumeric character)."
             )
 
+    @staticmethod
+    def _validate_installed_origin(
+        installed_workflow_id: str | None,
+        installed_registry_root: str | None,
+    ) -> None:
+        """Validate persisted installed-workflow ownership metadata."""
+        if installed_workflow_id is not None:
+            if not isinstance(installed_workflow_id, str):
+                raise ValueError(
+                    "Invalid run state: 'installed_workflow_id' must be a "
+                    f"string or null, got {type(installed_workflow_id).__name__}"
+                )
+            if not _ID_PATTERN.fullmatch(installed_workflow_id):
+                raise ValueError(
+                    "Invalid run state: 'installed_workflow_id' must be a "
+                    "lowercase alphanumeric workflow ID with hyphens"
+                )
+        if installed_registry_root is not None:
+            if not isinstance(installed_registry_root, str):
+                raise ValueError(
+                    "Invalid run state: 'installed_registry_root' must be a "
+                    f"string or null, got {type(installed_registry_root).__name__}"
+                )
+            if not installed_registry_root or not Path(
+                installed_registry_root
+            ).is_absolute():
+                raise ValueError(
+                    "Invalid run state: 'installed_registry_root' must be "
+                    "an absolute path or null"
+                )
+            if installed_workflow_id is None:
+                raise ValueError(
+                    "Invalid run state: 'installed_registry_root' requires "
+                    "'installed_workflow_id'"
+                )
+
     def __init__(
         self,
         run_id: str | None = None,
         workflow_id: str = "",
         project_root: Path | None = None,
+        installed_workflow_id: str | None = None,
+        installed_registry_root: str | None = None,
+        installed_origin_tracked: bool = True,
     ) -> None:
         # ``run_id is None`` (omitted) → auto-generate. An explicit empty
         # string is *not* the same as "omitted" and must be validated like
@@ -410,8 +478,22 @@ class RunState:
         else:
             self.run_id = run_id
         self._validate_run_id(self.run_id)
+        self._validate_installed_origin(
+            installed_workflow_id, installed_registry_root
+        )
         self.workflow_id = workflow_id
         self.project_root = project_root or Path(".")
+        # Identifies the installed workflow (if any) this run was started
+        # from, and the project root that owns its registry — set by
+        # execute() when the source was resolved to an installed ID (see
+        # workflow_run's ownership mapping). None for a direct/non-installed
+        # YAML source. ``installed_origin_tracked`` distinguishes those
+        # explicit None values from legacy state files that predate both
+        # fields, allowing the CLI to conservatively infer same-project
+        # registry ownership before resuming.
+        self.installed_workflow_id = installed_workflow_id
+        self.installed_registry_root = installed_registry_root
+        self.installed_origin_tracked = installed_origin_tracked
         self.status = RunStatus.CREATED
         self.current_step_index = 0
         self.current_step_id: str | None = None
@@ -474,6 +556,8 @@ class RunState:
             state_data = {
                 "run_id": self.run_id,
                 "workflow_id": self.workflow_id,
+                "installed_workflow_id": self.installed_workflow_id,
+                "installed_registry_root": self.installed_registry_root,
                 "status": self.status.value,
                 "current_step_index": self.current_step_index,
                 "current_step_id": self.current_step_id,
@@ -525,11 +609,46 @@ class RunState:
 
         with open(state_path, encoding="utf-8") as f:
             state_data = json.load(f)
+        if not isinstance(state_data, dict):
+            raise ValueError("Invalid run state: expected a JSON object")
+        missing_fields = [
+            field
+            for field in ("run_id", "workflow_id", "status")
+            if field not in state_data
+        ]
+        if missing_fields:
+            raise ValueError(
+                "Invalid run state: missing required field(s): "
+                + ", ".join(missing_fields)
+            )
+
+        workflow_id = state_data["workflow_id"]
+        if not isinstance(workflow_id, str) or not _ID_PATTERN.fullmatch(
+            workflow_id
+        ):
+            raise ValueError(
+                "Invalid run state: 'workflow_id' must be a lowercase "
+                "alphanumeric workflow ID with hyphens"
+            )
+
+        has_installed_workflow_id = "installed_workflow_id" in state_data
+        has_installed_registry_root = "installed_registry_root" in state_data
+        if has_installed_workflow_id != has_installed_registry_root:
+            raise ValueError(
+                "Invalid run state: installed workflow origin fields must "
+                "either both be present or both be absent"
+            )
+
+        installed_workflow_id = state_data.get("installed_workflow_id")
+        installed_registry_root = state_data.get("installed_registry_root")
 
         state = cls(
             run_id=state_data["run_id"],
-            workflow_id=state_data["workflow_id"],
+            workflow_id=workflow_id,
             project_root=project_root,
+            installed_workflow_id=installed_workflow_id,
+            installed_registry_root=installed_registry_root,
+            installed_origin_tracked=has_installed_workflow_id,
         )
         state.status = RunStatus(state_data["status"])
         state.current_step_index = state_data.get("current_step_index", 0)
@@ -542,7 +661,16 @@ class RunState:
         if inputs_path.exists():
             with open(inputs_path, encoding="utf-8") as f:
                 inputs_data = json.load(f)
-            state.inputs = inputs_data.get("inputs", {})
+            if not isinstance(inputs_data, dict):
+                raise ValueError(
+                    "Invalid run inputs: expected a JSON object"
+                )
+            inputs = inputs_data.get("inputs", {})
+            if not isinstance(inputs, dict):
+                raise ValueError(
+                    "Invalid run inputs: 'inputs' must be a JSON object"
+                )
+            state.inputs = inputs
 
         return state
 
@@ -625,6 +753,8 @@ class WorkflowEngine:
         definition: WorkflowDefinition,
         inputs: dict[str, Any] | None = None,
         run_id: str | None = None,
+        installed_workflow_id: str | None = None,
+        installed_registry_root: Path | None = None,
     ) -> RunState:
         """Execute a workflow definition.
 
@@ -636,6 +766,12 @@ class WorkflowEngine:
             User-provided input values.
         run_id:
             Optional run ID (uses SPECKIT_WORKFLOW_RUN_ID when set, otherwise auto-generated).
+        installed_workflow_id, installed_registry_root:
+            When the run was started from an installed workflow (as opposed
+            to a direct/non-installed YAML source), identifies it and its
+            owning registry root so a later ``resume`` can re-check the
+            registry's current disabled state before continuing — see
+            ``workflow_resume``.
 
         Returns
         -------
@@ -653,6 +789,12 @@ class WorkflowEngine:
             run_id=effective_run_id,
             workflow_id=definition.id,
             project_root=self.project_root,
+            installed_workflow_id=installed_workflow_id,
+            installed_registry_root=(
+                str(installed_registry_root)
+                if installed_registry_root is not None
+                else None
+            ),
         )
 
         # Persist a copy of the workflow definition so resume can
@@ -953,7 +1095,16 @@ 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

@@ -464,9 +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:
@@ -511,6 +511,26 @@ def _coerce_number(value: Any) -> Any:
     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:
+        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.
 

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

@@ -31,6 +31,20 @@ class CommandStep(StepBase):
     def execute(self, config: dict[str, Any], context: StepContext) -> StepResult:
         command = config.get("command", "")
         input_data = config.get("input", {})
+        # validate() rejects a non-mapping input, but the engine does not
+        # auto-validate before execute(); a workflow that skipped validation can
+        # still reach here. Fail the step with the same contract error rather
+        # than silently coercing to {} and dispatching with empty args — that
+        # would change the command's meaning, hide the config error, and report
+        # COMPLETED, defeating the per-step FAILED / continue_on_error behavior.
+        if not isinstance(input_data, dict):
+            return StepResult(
+                status=StepStatus.FAILED,
+                error=(
+                    f"Command step {config.get('id', '?')!r}: 'input' must be a "
+                    f"mapping, got {type(input_data).__name__}."
+                ),
+            )
 
         # Resolve expressions in input
         resolved_input: dict[str, Any] = {}
@@ -50,8 +64,18 @@ class CommandStep(StepBase):
         # Merge options (workflow defaults ← step overrides)
         options = dict(context.default_options)
         step_options = config.get("options", {})
-        if step_options:
-            options.update(step_options)
+        # Same rationale as 'input': a malformed options fails the step rather
+        # than being silently ignored (which would let an invalid step run and
+        # apparently complete).
+        if not isinstance(step_options, dict):
+            return StepResult(
+                status=StepStatus.FAILED,
+                error=(
+                    f"Command step {config.get('id', '?')!r}: 'options' must be a "
+                    f"mapping, got {type(step_options).__name__}."
+                ),
+            )
+        options.update(step_options)
 
         # Attempt CLI dispatch
         args_str = str(resolved_input.get("args", ""))
@@ -155,4 +179,16 @@ class CommandStep(StepBase):
             errors.append(
                 f"Command step {config.get('id', '?')!r} is missing 'command' field."
             )
+        # execute() iterates input.items() and options.update(step_options); a
+        # non-mapping here would raise at run time. Validate the shape like the
+        # sibling steps (switch 'cases', fan-out 'step') so it is reported, not
+        # crashed on.
+        if "input" in config and not isinstance(config["input"], dict):
+            errors.append(
+                f"Command step {config.get('id', '?')!r}: 'input' must be a mapping."
+            )
+        if "options" in config and not isinstance(config["options"], dict):
+            errors.append(
+                f"Command step {config.get('id', '?')!r}: 'options' must be a mapping."
+            )
         return errors

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

@@ -24,6 +24,24 @@ class FanInStep(StepBase):
         if not isinstance(output_config, dict):
             output_config = {}
 
+        # The engine does not auto-validate step config, so an unvalidated run
+        # with a non-list ``wait_for`` reaches here raw. Iterating it then
+        # either crashes the whole run (a scalar like an int or None raises
+        # TypeError) or, worse, silently iterates a string's characters and
+        # yields a bogus join of empty results with a COMPLETED status — the
+        # exact "silent empty result + COMPLETED" wiring bug the engine's
+        # fan-in validation guards against. Fail this step loudly instead,
+        # mirroring the fan-out step's non-list ``items`` handling.
+        if not isinstance(wait_for, list):
+            return StepResult(
+                status=StepStatus.FAILED,
+                error=(
+                    f"Fan-in step {config.get('id', '?')!r}: 'wait_for' must be "
+                    f"a list of step IDs, got {type(wait_for).__name__}."
+                ),
+                output={"results": []},
+            )
+
         # Collect results from referenced steps
         results = []
         for step_id in wait_for:

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
 
@@ -25,15 +26,20 @@ class ShellStep(StepBase):
         run_cmd = str(run_cmd)
 
         cwd = context.project_root or "."
-        # Defensive: the engine does not auto-validate step config, so an
-        # invalid ``timeout`` (string, None, ...) would otherwise raise a
-        # TypeError from subprocess.run() and crash the whole run.  Mirror
-        # the engine's handling of unvalidated ``continue_on_error`` by
-        # only honoring well-formed values and falling back to the default.
+        # 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)
-        if isinstance(timeout, bool) or not isinstance(timeout, int) or timeout <= 0:
-            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
@@ -92,6 +98,32 @@ 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:
@@ -114,16 +146,7 @@ class ShellStep(StepBase):
                 f"Shell step {config.get('id', '?')!r}: 'output_format' must "
                 f"be 'json' when present, got {output_format!r}."
             )
-        if "timeout" in config:
-            timeout = config["timeout"]
-            # bool is an int subclass, so reject it explicitly.
-            if (
-                isinstance(timeout, bool)
-                or not isinstance(timeout, int)
-                or timeout <= 0
-            ):
-                errors.append(
-                    f"Shell step {config.get('id', '?')!r}: 'timeout' must be a "
-                    f"positive integer (seconds) when present, got {timeout!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/clarify.md

@@ -1,6 +1,6 @@
 ---
 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...

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/implement.md

@@ -43,7 +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.
@@ -145,7 +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

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]_
            ```
 

templates/commands/tasks.md

@@ -1,6 +1,6 @@
 ---
 description: Generate an actionable, dependency-ordered tasks.md for the feature based on available design artifacts.
-handoffs: 
+handoffs:
   - label: Analyze For Consistency
     agent: speckit.analyze
     prompt: Run a project analysis for consistency
@@ -51,7 +51,7 @@ 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.
@@ -161,7 +161,7 @@ Every task MUST strictly follow this format:
 4. **[Story] label**: REQUIRED for user story phase tasks only
    - Format: [US1], [US2], [US3], etc. (maps to user stories from spec.md)
    - Setup phase: NO story label
-   - Foundational phase: NO story label  
+   - Foundational phase: NO story label
    - User Story phases: MUST have story label
    - Polish phase: NO story label
 5. **Description**: Clear action with exact file path

templates/plan-template.md

@@ -4,7 +4,7 @@
 
 **Input**: Feature specification from `/specs/[###-feature-name]/spec.md`
 
-**Note**: This template is filled in by the `__SPECKIT_COMMAND_PLAN__` command. See `.specify/templates/plan-template.md` for the execution workflow.
+**Note**: This template is filled in by the `__SPECKIT_COMMAND_PLAN__` command; its definition describes the execution workflow.
 
 ## Summary
 

templates/vscode-settings.json

@@ -11,4 +11,3 @@
         ".specify/scripts/powershell/": true
     }
 }
-

tests/contract/test_bundle_cli.py

@@ -6,6 +6,7 @@ contracts/cli-commands.md (offline, discovery-only refusal, not-a-project error)
 """
 from __future__ import annotations
 
+import io
 import json
 from pathlib import Path
 from unittest.mock import patch
@@ -63,6 +64,42 @@ def test_commands_outside_project_fail_with_guidance(tmp_path: Path, monkeypatch
     assert "Spec Kit project" in result.output
 
 
+def test_remove_reports_clean_error_when_primitive_raises_raw_exception(
+    project: Path,
+):
+    """A raw exception from a primitive installer (e.g. an OSError from an
+    unreadable workflow registry surfacing through _WorkflowKindManager's
+    fail-closed construction) must not propagate uncaught through
+    `specify bundle remove` -- the command only catches BundlerError, so
+    without a conversion at the remove_bundle boundary this would exit
+    with an unhandled exception and empty/raw output instead of a clean,
+    actionable message, and no removal side effects should occur either."""
+    from specify_cli.bundler.models.manifest import BundleManifest
+    from specify_cli.bundler.models.records import load_records
+    from specify_cli.bundler.services.adapters import DefaultPrimitiveInstaller
+    from specify_cli.bundler.services.installer import install_bundle
+    from specify_cli.bundler.services.resolver import resolve_install_plan
+    from tests.bundler_helpers import FakeInstaller
+
+    manifest = BundleManifest.from_dict(valid_manifest_dict())
+    plan = resolve_install_plan(
+        manifest, speckit_version="0.11.2", active_integration="copilot"
+    )
+    install_bundle(project, plan, FakeInstaller(), manifest=manifest)
+
+    def boom(self, project_root, component):
+        raise OSError("workflow registry unreadable")
+
+    with pytest.MonkeyPatch.context() as mp:
+        mp.setattr(DefaultPrimitiveInstaller, "is_installed", boom)
+        result = runner.invoke(app, ["bundle", "remove", "demo-bundle"])
+
+    assert result.exit_code != 0
+    assert result.output.strip() != ""
+    assert result.exception is None or isinstance(result.exception, SystemExit)
+    assert {r.bundle_id for r in load_records(project)} == {"demo-bundle"}
+
+
 def test_fail_writes_error_to_stderr_not_stdout(capsys):
     """_fail must write to stderr, not stdout: every bundle command routes errors
     through it, and under --json the error would otherwise corrupt the JSON payload
@@ -175,7 +212,23 @@ def test_build_produces_artifact(project: Path):
     assert len(artifacts) == 1
 
 
-def test_info_expands_full_component_set(project: Path):
+def _mock_manifest_download(monkeypatch, source_path: Path) -> None:
+    """Mock the HTTPS manifest fetch to return a locally-authored manifest.
+
+    Catalog ``download_url``s are HTTPS-only, so ``info`` tests can no longer
+    point one at a local file. Patch ``_download_manifest`` to return the
+    manifest parsed from *source_path* (a bundle.yml or a .zip artifact),
+    exercising ``info``'s expansion without a network call.
+    """
+    from specify_cli.commands.bundle import _local_manifest_source
+
+    monkeypatch.setattr(
+        "specify_cli.commands.bundle._download_manifest",
+        lambda resolved, *, offline: _local_manifest_source(str(source_path)),
+    )
+
+
+def test_info_expands_full_component_set(project: Path, monkeypatch):
     bundle_dir = project / "src-bundle"
     bundle_dir.mkdir()
     (bundle_dir / "bundle.yml").write_text(
@@ -183,13 +236,14 @@ def test_info_expands_full_component_set(project: Path):
     )
     catalog = project / "local-catalog.json"
     entry = catalog_entry_dict(
-        "demo-bundle", download_url=str(bundle_dir / "bundle.yml")
+        "demo-bundle", download_url="https://example.com/demo-bundle.zip"
     )
     write_catalog_file(catalog, {"demo-bundle": entry})
     added = runner.invoke(
         app, ["bundle", "catalog", "add", str(catalog), "--id", "local"]
     )
     assert added.exit_code == 0, added.output
+    _mock_manifest_download(monkeypatch, bundle_dir / "bundle.yml")
 
     result = runner.invoke(app, ["bundle", "info", "demo-bundle", "--json", "--offline"])
     assert result.exit_code == 0, result.output
@@ -207,7 +261,7 @@ def test_info_expands_full_component_set(project: Path):
     assert "Trust" in text.output
 
 
-def test_info_expands_discovery_only_bundle(project: Path):
+def test_info_expands_discovery_only_bundle(project: Path, monkeypatch):
     # Discovery-only bundles must still be fully inspectable via `info`;
     # only `install` is refused for them.
     bundle_dir = project / "disc-bundle"
@@ -217,7 +271,7 @@ def test_info_expands_discovery_only_bundle(project: Path):
     )
     catalog = project / "disc-catalog.json"
     entry = catalog_entry_dict(
-        "demo-bundle", download_url=str(bundle_dir / "bundle.yml")
+        "demo-bundle", download_url="https://example.com/demo-bundle.zip"
     )
     write_catalog_file(catalog, {"demo-bundle": entry})
     config = {
@@ -230,6 +284,7 @@ def test_info_expands_discovery_only_bundle(project: Path):
     (project / ".specify" / "bundle-catalogs.yml").write_text(
         yaml.safe_dump(config), encoding="utf-8"
     )
+    _mock_manifest_download(monkeypatch, bundle_dir / "bundle.yml")
     result = runner.invoke(app, ["bundle", "info", "demo-bundle", "--json", "--offline"])
     assert result.exit_code == 0, result.output
     payload = json.loads(result.output)
@@ -237,8 +292,9 @@ def test_info_expands_discovery_only_bundle(project: Path):
     assert ("extensions", "ext-a") in components
 
 
-def test_info_resolves_local_zip_download_url(project: Path):
-    # A local .zip artifact as download_url is extracted to read bundle.yml.
+def test_info_expands_zip_sourced_bundle(project: Path, monkeypatch):
+    # A .zip artifact is extracted to read bundle.yml; info expands it. (The
+    # download itself is HTTPS-only now and mocked here — see contract note.)
     bundle_dir = project / "zip-src"
     bundle_dir.mkdir()
     (bundle_dir / "bundle.yml").write_text(
@@ -249,12 +305,15 @@ def test_info_resolves_local_zip_download_url(project: Path):
     catalog = project / "zip-catalog.json"
     write_catalog_file(
         catalog,
-        {"demo-bundle": catalog_entry_dict("demo-bundle", download_url=str(artifact))},
+        {"demo-bundle": catalog_entry_dict(
+            "demo-bundle", download_url="https://example.com/demo-bundle.zip"
+        )},
     )
     added = runner.invoke(
         app, ["bundle", "catalog", "add", str(catalog), "--id", "local"]
     )
     assert added.exit_code == 0, added.output
+    _mock_manifest_download(monkeypatch, artifact)
     result = runner.invoke(app, ["bundle", "info", "demo-bundle", "--json", "--offline"])
     assert result.exit_code == 0, result.output
     payload = json.loads(result.output)
@@ -410,25 +469,16 @@ def test_install_integration_override_cannot_bypass_clash_guard(project: Path):
 # ===== Private GitHub release asset URL resolution =====
 
 
-class FakeBundleResponse:
+class FakeBundleResponse(io.BytesIO):
     """Minimal context-manager response stub for open_url fakes."""
 
     def __init__(self, data: bytes, url: str = "https://api.github.com/repos/org/repo/releases/assets/99"):
-        self._data = data
+        super().__init__(data)
         self._url = url
 
-    def read(self) -> bytes:
-        return self._data
-
     def geturl(self) -> str:
         return self._url
 
-    def __enter__(self):
-        return self
-
-    def __exit__(self, *_):
-        return False
-
 
 def _make_catalog_config(catalog_path: Path, project: Path) -> None:
     """Write a bundle-catalogs.yml pointing at *catalog_path* in *project*."""

tests/extensions/test_extension_agent_context.py

@@ -25,6 +25,14 @@ BASH = shutil.which("bash")
 POWERSHELL = (
     shutil.which("pwsh") or shutil.which("powershell.exe") or shutil.which("powershell")
 )
+# On Windows, prefer the built-in Windows PowerShell 5.1 (.NET Framework) when a
+# test needs to exercise a 5.1-specific code path; fall back to whatever
+# POWERSHELL resolves to elsewhere.
+WINDOWS_POWERSHELL = (
+    (shutil.which("powershell.exe") or shutil.which("powershell") or POWERSHELL)
+    if os.name == "nt"
+    else POWERSHELL
+)
 
 
 def _write_ext_config(project_root: Path, **overrides: object) -> None:
@@ -279,12 +287,14 @@ def shlex_quote(value: str) -> str:
     return "'" + value.replace("'", "'\"'\"'") + "'"
 
 
-def _run_powershell_agent_context_script(project_root: Path) -> subprocess.CompletedProcess:
+def _run_powershell_agent_context_script(
+    project_root: Path, powershell: str | None = None
+) -> subprocess.CompletedProcess:
     script = EXT_DIR / "scripts" / "powershell" / "update-agent-context.ps1"
     env = _bundled_script_env(project_root)
     return subprocess.run(
         [
-            POWERSHELL,
+            powershell or POWERSHELL,
             "-NoProfile",
             "-ExecutionPolicy",
             "Bypass",
@@ -412,6 +422,29 @@ class TestBundledUpdaterPathValidation:
         assert output.count("agent-context: updated CLAUDE.md") == 1
         assert "agent-context: updated agents.md" not in output
 
+    @requires_bash
+    def test_bash_script_discovers_nested_plan(self, tmp_path):
+        """Plan discovery recurses into scoped layouts (#3024)."""
+        project = tmp_path / "project"
+        project.mkdir()
+        _install_agent_context_config(
+            project,
+            context_file="AGENTS.md",
+            context_files=[],
+        )
+        plan = project / "specs" / "scope" / "001-feature" / "plan.md"
+        plan.parent.mkdir(parents=True)
+        plan.write_text("# Plan\n", encoding="utf-8")
+
+        result = _run_bash_agent_context_script(project)
+
+        assert result.returncode == 0, result.stderr + result.stdout
+        text = (project / "AGENTS.md").read_text(encoding="utf-8")
+        # The old one-level glob (specs/*/plan.md) would find nothing here, so no
+        # "at" line would be emitted. Normalize separators before matching: on
+        # MSYS bash the emitted path may be absolute with backslashes.
+        assert "specs/scope/001-feature/plan.md" in text.replace("\\", "/")
+
     @requires_bash
     def test_bash_script_falls_back_from_invalid_speckit_python(self, tmp_path):
         project = tmp_path / "project"
@@ -484,6 +517,33 @@ class TestBundledUpdaterPathValidation:
         assert output.count("agent-context: updated CLAUDE.md") == 1
         assert "agent-context: updated agents.md" not in output
 
+    @pytest.mark.skipif(WINDOWS_POWERSHELL is None, reason="PowerShell not available")
+    def test_powershell_script_discovers_nested_plan(self, tmp_path):
+        """Plan discovery recurses into scoped layouts (#3024).
+
+        The relative-path fix this covers is specific to Windows PowerShell 5.1
+        (.NET Framework), so prefer ``powershell.exe`` over ``pwsh`` here to
+        actually exercise that failure mode on Windows.
+        """
+        project = tmp_path / "project"
+        project.mkdir()
+        _install_agent_context_config(
+            project,
+            context_file="AGENTS.md",
+            context_files=[],
+        )
+        plan = project / "specs" / "scope" / "001-feature" / "plan.md"
+        plan.parent.mkdir(parents=True)
+        plan.write_text("# Plan\n", encoding="utf-8")
+
+        result = _run_powershell_agent_context_script(
+            project, powershell=WINDOWS_POWERSHELL
+        )
+
+        assert result.returncode == 0, result.stderr + result.stdout
+        text = (project / "AGENTS.md").read_text(encoding="utf-8")
+        assert "at specs/scope/001-feature/plan.md" in text
+
     @pytest.mark.skipif(POWERSHELL is None, reason="PowerShell not available")
     def test_powershell_script_falls_back_from_invalid_speckit_python(self, tmp_path):
         project = tmp_path / "project"

tests/hooks/.specify/extensions.yml

@@ -6,7 +6,7 @@ hooks:
       extension: "test-extension"
       command: "pre_implement_test"
       description: "Test before implement hook execution"
-      
+
   after_implement:
     - id: post_test
       enabled: true

tests/hooks/TESTING.md

@@ -7,7 +7,7 @@ This directory contains a mock project to verify that LLM agents correctly ident
 1. Open a chat with an LLM (like GitHub Copilot) in this project.
 2. Ask it to generate tasks for the current directory:
    > "Please follow `/speckit.tasks` for the `./tests/hooks` directory."
-3. **Expected Behavior**: 
+3. **Expected Behavior**:
    - Before doing any generation, the LLM should notice the `AUTOMATIC Pre-Hook` in `.specify/extensions.yml` under `before_tasks`.
    - It should state it is executing `EXECUTE_COMMAND: pre_tasks_test`.
    - It should then proceed to read the `.md` docs and produce a `tasks.md`.

tests/integration/test_bundler_install_flow.py

@@ -11,7 +11,7 @@ import pytest
 
 from specify_cli.bundler import BundlerError
 from specify_cli.bundler.models.manifest import BundleManifest
-from specify_cli.bundler.models.records import load_records
+from specify_cli.bundler.models.records import load_records, records_path
 from specify_cli.bundler.services.installer import install_bundle, remove_bundle
 from specify_cli.bundler.services.resolver import resolve_install_plan
 from tests.bundler_helpers import FakeInstaller, make_project, valid_manifest_dict
@@ -97,6 +97,212 @@ def test_remove_unknown_bundle_errors(tmp_path: Path):
         remove_bundle(tmp_path, "ghost", FakeInstaller())
 
 
+def test_remove_converts_raw_installer_exception_to_bundler_error(tmp_path: Path):
+    """A raw exception from a primitive installer (e.g. an OSError from an
+    unreadable workflow registry surfacing through _WorkflowKindManager's
+    fail-closed construction) must not propagate uncaught out of
+    remove_bundle: install_bundle already converts any non-BundlerError
+    exception into a clean BundlerError, but remove_bundle had no such
+    conversion, so the CLI's `bundle remove` (which only catches
+    BundlerError) would let a raw exception through with no clean message
+    and no removal side effects should occur either."""
+    make_project(tmp_path)
+    manifest = BundleManifest.from_dict(valid_manifest_dict())
+    installer = FakeInstaller()
+    install_bundle(tmp_path, _plan(manifest), installer, manifest=manifest)
+
+    def boom(project_root, component):
+        raise OSError("workflow registry unreadable")
+
+    with pytest.MonkeyPatch.context() as mp:
+        mp.setattr(installer, "is_installed", boom)
+        with pytest.raises(BundlerError):
+            remove_bundle(tmp_path, "demo-bundle", installer)
+
+    # No removal side effects: the bundle record must still be present.
+    assert {r.bundle_id for r in load_records(tmp_path)} == {"demo-bundle"}
+
+
+def test_remove_partial_failure_message_reflects_partial_state(tmp_path: Path):
+    """A failure can occur after earlier components in the same bundle have
+    already been removed from disk. The bundle record is left unchanged
+    (save_records never runs on this path), so it still claims the bundle
+    fully installed -- but the message must not claim "No changes were
+    recorded" when components were, in fact, already removed."""
+    make_project(tmp_path)
+    manifest = BundleManifest.from_dict(valid_manifest_dict())
+    installer = FakeInstaller()
+    install_bundle(tmp_path, _plan(manifest), installer, manifest=manifest)
+
+    real_remove = installer.remove
+    calls = {"n": 0}
+
+    def remove_then_fail(project_root, component):
+        calls["n"] += 1
+        if calls["n"] == 1:
+            return real_remove(project_root, component)
+        raise OSError("disk full")
+
+    with pytest.MonkeyPatch.context() as mp:
+        mp.setattr(installer, "remove", remove_then_fail)
+        with pytest.raises(BundlerError) as exc_info:
+            remove_bundle(tmp_path, "demo-bundle", installer)
+
+    message = str(exc_info.value)
+    assert "no changes were recorded" not in message.lower()
+    assert {r.bundle_id for r in load_records(tmp_path)} == {"demo-bundle"}
+
+
+def test_remove_bundler_error_from_installer_after_partial_removal_reports_partial_state(
+    tmp_path: Path,
+):
+    """If the primitive installer itself raises BundlerError (not a raw/
+    unexpected exception) after an earlier component in the same bundle was
+    already removed, the surfaced message must still carry the same
+    partial-removal detail as the generic-exception path -- a bare
+    ``except BundlerError: raise`` would re-raise the installer's original
+    message verbatim with no mention that the project may now be partially
+    uninstalled."""
+    make_project(tmp_path)
+    manifest = BundleManifest.from_dict(valid_manifest_dict())
+    installer = FakeInstaller()
+    install_bundle(tmp_path, _plan(manifest), installer, manifest=manifest)
+
+    real_remove = installer.remove
+    calls = {"n": 0}
+
+    def remove_then_raise_bundler_error(project_root, component):
+        calls["n"] += 1
+        if calls["n"] == 1:
+            return real_remove(project_root, component)
+        raise BundlerError("kind manager refused removal")
+
+    with pytest.MonkeyPatch.context() as mp:
+        mp.setattr(installer, "remove", remove_then_raise_bundler_error)
+        with pytest.raises(BundlerError) as exc_info:
+            remove_bundle(tmp_path, "demo-bundle", installer)
+
+    message = str(exc_info.value)
+    assert "no changes were recorded" not in message.lower()
+    assert "kind manager refused removal" in message
+    assert "partially uninstalled" in message.lower()
+    assert {r.bundle_id for r in load_records(tmp_path)} == {"demo-bundle"}
+
+
+def test_remove_bundler_error_from_installer_with_zero_removed_reports_no_changes(
+    tmp_path: Path,
+):
+    """When the installer raises BundlerError before anything was actually
+    removed, the message should not misleadingly claim partial state."""
+    make_project(tmp_path)
+    manifest = BundleManifest.from_dict(valid_manifest_dict())
+    installer = FakeInstaller()
+    install_bundle(tmp_path, _plan(manifest), installer, manifest=manifest)
+
+    def boom(project_root, component):
+        raise BundlerError("kind manager unavailable")
+
+    with pytest.MonkeyPatch.context() as mp:
+        mp.setattr(installer, "is_installed", boom)
+        with pytest.raises(BundlerError) as exc_info:
+            remove_bundle(tmp_path, "demo-bundle", installer)
+
+    message = str(exc_info.value)
+    assert "no components were removed" in message.lower()
+    assert "no removal was attempted" in message.lower()
+    assert "partially uninstalled" not in message.lower()
+    assert "kind manager unavailable" in message
+    assert {r.bundle_id for r in load_records(tmp_path)} == {"demo-bundle"}
+
+
+def test_remove_zero_completed_removals_still_cautions_about_partial_changes(
+    tmp_path: Path,
+):
+    """`result.uninstalled` only records a component after its `remove()`
+    call returns successfully. If the very first `remove()` call itself
+    raises after already deleting some files, zero completed removals are
+    recorded even though the project may already be partially uninstalled --
+    the zero-count message must not claim "No components were removed" as
+    an unqualified fact; it must caution that the failing component may
+    have made partial changes before raising."""
+    make_project(tmp_path)
+    manifest = BundleManifest.from_dict(valid_manifest_dict())
+    installer = FakeInstaller()
+    install_bundle(tmp_path, _plan(manifest), installer, manifest=manifest)
+
+    def boom(project_root, component):
+        # Simulates a remove() that deletes some files before raising --
+        # from the caller's perspective this component was never recorded
+        # as completed, but disk state may already be partially changed.
+        raise OSError("disk full partway through removal")
+
+    with pytest.MonkeyPatch.context() as mp:
+        mp.setattr(installer, "remove", boom)
+        with pytest.raises(BundlerError) as exc_info:
+            remove_bundle(tmp_path, "demo-bundle", installer)
+
+    message = str(exc_info.value)
+    assert "no components were removed" in message.lower()
+    assert "partial" in message.lower()
+    assert "partially uninstalled" in message.lower()
+    assert {r.bundle_id for r in load_records(tmp_path)} == {"demo-bundle"}
+
+
+def test_remove_record_save_failure_reports_partial_state(tmp_path: Path):
+    make_project(tmp_path)
+    manifest = BundleManifest.from_dict(valid_manifest_dict())
+    installer = FakeInstaller()
+    install_bundle(tmp_path, _plan(manifest), installer, manifest=manifest)
+    record_file = records_path(tmp_path)
+    original_record = record_file.read_bytes()
+
+    def fail_dump(_data, handle, *_args, **_kwargs):
+        handle.write('{"partial":')
+        handle.flush()
+        raise OSError("disk full")
+
+    with pytest.MonkeyPatch.context() as mp:
+        mp.setattr(
+            "specify_cli.bundler.lib.yamlio.json.dump",
+            fail_dump,
+        )
+        with pytest.raises(BundlerError) as exc_info:
+            remove_bundle(tmp_path, "demo-bundle", installer)
+
+    message = str(exc_info.value)
+    assert "disk full" in message
+    assert "partially uninstalled" in message.lower()
+    assert installer.installed == set()
+    assert record_file.read_bytes() == original_record
+    assert {r.bundle_id for r in load_records(tmp_path)} == {"demo-bundle"}
+
+
+def test_remove_record_save_failure_without_remove_attempt_is_not_partial(
+    tmp_path: Path,
+):
+    make_project(tmp_path)
+    manifest = BundleManifest.from_dict(valid_manifest_dict())
+    installer = FakeInstaller()
+    install_bundle(tmp_path, _plan(manifest), installer, manifest=manifest)
+    installer.installed.clear()
+
+    def fail_save(*_args, **_kwargs):
+        raise OSError("disk full")
+
+    with pytest.MonkeyPatch.context() as mp:
+        mp.setattr(
+            "specify_cli.bundler.services.installer.save_records",
+            fail_save,
+        )
+        with pytest.raises(BundlerError) as exc_info:
+            remove_bundle(tmp_path, "demo-bundle", installer)
+
+    message = str(exc_info.value)
+    assert "no removal was attempted" in message.lower()
+    assert "partially uninstalled" not in message.lower()
+    assert {r.bundle_id for r in load_records(tmp_path)} == {"demo-bundle"}
+
+
 def test_remove_reports_uninstalled_not_installed(tmp_path: Path):
     make_project(tmp_path)
     manifest = BundleManifest.from_dict(valid_manifest_dict())
@@ -128,7 +334,7 @@ def test_remove_counts_only_components_actually_removed(tmp_path: Path):
 
     assert len(result.uninstalled) == 3
     assert (gone.kind, gone.id) not in installer.remove_calls
-    assert gone in result.skipped
+    assert gone not in result.skipped
     make_project(tmp_path)
     manifest = BundleManifest.from_dict(valid_manifest_dict())
     installer = FakeInstaller()

tests/integration/test_bundler_local_install.py

@@ -112,3 +112,62 @@ def test_install_bundled_extension_from_zip_offline(tmp_path: Path):
         assert not ExtensionManager(project).registry.is_installed("agent-context")
     finally:
         os.chdir(previous)
+
+
+def test_download_manifest_rejects_file_url(tmp_path: Path):
+    """A catalog ``file://`` download_url is rejected — catalog URLs are
+    HTTPS-only, matching extensions/presets/workflows. Disk installs go through
+    the positional path (see the local-source tests above), not download_url.
+    """
+    from types import SimpleNamespace
+
+    from specify_cli.commands.bundle import _download_manifest
+
+    manifest_path = write_manifest(tmp_path / "my bundles")
+    resolved = SimpleNamespace(
+        entry=SimpleNamespace(id="demo-bundle", download_url=manifest_path.as_uri())
+    )
+
+    with pytest.raises(BundlerError, match="bundle install"):
+        _download_manifest(resolved, offline=True)
+
+
+def test_download_manifest_rejects_bare_path(tmp_path: Path):
+    """A bare filesystem path download_url is likewise rejected."""
+    from types import SimpleNamespace
+
+    from specify_cli.commands.bundle import _download_manifest
+
+    manifest_path = write_manifest(tmp_path / "plain")
+    resolved = SimpleNamespace(
+        entry=SimpleNamespace(id="demo-bundle", download_url=str(manifest_path))
+    )
+
+    with pytest.raises(BundlerError, match="bundle install"):
+        _download_manifest(resolved, offline=True)
+
+
+def test_local_install_still_resolves_via_positional_path(tmp_path: Path):
+    """The supported local route — a positional path, not a download_url —
+    still resolves the manifest via _local_manifest_source."""
+    manifest_path = write_manifest(tmp_path / "my bundles")
+    manifest = _local_manifest_source(str(manifest_path))
+    assert manifest is not None
+    assert manifest.bundle.id == "demo-bundle"
+
+
+def test_download_manifest_rejects_non_https_url_even_offline(tmp_path: Path):
+    """A non-HTTPS download_url must report the HTTPS problem, not a misleading
+    'Network access disabled', even under --offline (scheme is validated before
+    the offline gate)."""
+    from types import SimpleNamespace
+
+    from specify_cli.commands.bundle import _download_manifest
+
+    resolved = SimpleNamespace(
+        entry=SimpleNamespace(
+            id="demo-bundle", download_url="http://example.com/bundle.zip"
+        )
+    )
+    with pytest.raises(BundlerError, match="HTTPS"):
+        _download_manifest(resolved, offline=True)

tests/integrations/test_cli.py

@@ -115,6 +115,63 @@ class TestInitIntegrationFlag:
         data = json.loads((project / ".specify" / "integration.json").read_text(encoding="utf-8"))
         assert data["integration"] == specify_cli.DEFAULT_INIT_INTEGRATION
 
+    def test_init_here_nonempty_noninteractive_errors_with_force_guidance(self, tmp_path):
+        """`init --here` on a non-empty directory with no confirmation input (empty
+        stdin) must fail fast with guidance to use --force, instead of the bare
+        'Aborted.' from an EOF on typer.confirm. CliRunner with no `input=` provides
+        empty stdin, so typer.confirm raises Abort, which the command converts to the
+        actionable error."""
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        project = tmp_path / "nonempty-here"
+        project.mkdir()
+        (project / "existing.txt").write_text("keep me", encoding="utf-8")
+        old_cwd = os.getcwd()
+        try:
+            os.chdir(project)
+            result = CliRunner().invoke(app, [
+                "init", "--here", "--integration", "copilot", "--script", "sh", "--ignore-agent-tools",
+            ], catch_exceptions=False)
+        finally:
+            os.chdir(old_cwd)
+
+        assert result.exit_code == 1, result.output
+        assert "--force" in result.output
+        # Aborted before scaffolding: the pre-existing file is untouched.
+        assert (project / "existing.txt").read_text(encoding="utf-8") == "keep me"
+
+    def test_init_here_interactive_cancel_exits_zero(self, tmp_path, monkeypatch):
+        """An interactive Ctrl+C at the merge confirmation (typer.Abort on a TTY)
+        is a normal cancellation — exit 0, "cancelled" — NOT the missing-input
+        --force error, which is reserved for non-interactive EOF. Guards the
+        regression where Abort was caught unconditionally and every cancel became
+        an exit-1 --force error."""
+        from typer.testing import CliRunner
+        from specify_cli import app
+        import specify_cli.commands.init as init_mod
+
+        # Simulate an interactive terminal so the Abort is treated as a cancel.
+        monkeypatch.setattr(init_mod, "_stdin_is_interactive", lambda: True)
+
+        project = tmp_path / "cancel-here"
+        project.mkdir()
+        (project / "existing.txt").write_text("keep me", encoding="utf-8")
+        old_cwd = os.getcwd()
+        try:
+            os.chdir(project)
+            # No input → typer.confirm raises Abort (stands in for Ctrl+C).
+            result = CliRunner().invoke(app, [
+                "init", "--here", "--integration", "copilot", "--script", "sh", "--ignore-agent-tools",
+            ], catch_exceptions=False)
+        finally:
+            os.chdir(old_cwd)
+
+        assert result.exit_code == 0, result.output
+        assert "cancelled" in result.output.lower()
+        assert "--force" not in result.output  # not the missing-input error
+        assert (project / "existing.txt").read_text(encoding="utf-8") == "keep me"
+
     def test_integration_copilot_auto_promotes(self, tmp_path):
         from typer.testing import CliRunner
         from specify_cli import app
@@ -835,7 +892,8 @@ class TestInitIntegrationFlag:
         assert (scripts_dir / "common.sh").read_text(encoding="utf-8") != custom_content
 
     def test_init_here_without_force_preserves_shared_infra(self, tmp_path):
-        """E2E: specify init --here (no --force) preserves existing shared infra files."""
+        """E2E: confirming the merge with piped "y" (no --force) preserves
+        existing shared infra files (unlike --force, which overwrites them)."""
         from typer.testing import CliRunner
         from specify_cli import app
 

tests/integrations/test_integration_base_yaml.py

@@ -201,6 +201,36 @@ class YamlIntegrationTests:
         parsed = yaml.safe_load("\n".join(yaml_lines))
         assert parsed["prompt"].rstrip("\n") == body
 
+    def test_yaml_prompt_with_control_characters_stays_valid(self):
+        """A body containing control characters must still produce parseable YAML.
+
+        YAML forbids C0 control characters (except tab and newline), DEL,
+        C1 controls, lone surrogates and U+FFFE/U+FFFF in every scalar form,
+        and YAML 1.1 treats NEL (U+0085), LS (U+2028) and PS (U+2029) as
+        line breaks that corrupt a literal block scalar's structure. The
+        renderer falls back to an escaped double-quoted scalar for such
+        bodies."""
+        for ch in (
+            "\x08", "\x0c", "\x1b", "\x7f",
+            "\x80", "\x84", "\x85", "\x86", "\x9f",
+            "\u2028", "\u2029",
+            "\ud800", "\udfff", "\ufffe", "\uffff",
+        ):
+            body = f"before{ch}after\nsecond line"
+            rendered = YamlIntegration._render_yaml("Title", "Desc", body, "src")
+            parsed = yaml.safe_load(rendered)
+            assert parsed["prompt"].rstrip("\n") == body, f"char {ch!r} round-trip"
+
+    def test_yaml_prompt_with_bare_carriage_return_stays_valid(self):
+        """A bare CR (not part of CRLF) must not break the generated YAML.
+
+        Inside a block scalar a lone \r acts as a line break, corrupting
+        the document structure."""
+        body = "line1\rstill line1\nline2"
+        rendered = YamlIntegration._render_yaml("Title", "Desc", body, "src")
+        parsed = yaml.safe_load(rendered)
+        assert parsed["prompt"].rstrip("\n") == body
+
     def test_plan_command_has_no_context_placeholder(self, tmp_path):
         """The generated plan command must not carry a context-file placeholder.
 

tests/integrations/test_integration_catalog.py

@@ -84,6 +84,20 @@ class TestCatalogURLValidation:
         with pytest.raises(IntegrationCatalogError, match="valid URL"):
             IntegrationCatalog._validate_catalog_url(url)
 
+    @pytest.mark.parametrize(
+        "url",
+        [
+            "https://[::1",                 # unclosed ipv6 bracket
+            "https://[not-an-ip]/c.json",   # bracketed non-ip host
+        ],
+    )
+    def test_malformed_url_rejected_cleanly(self, url):
+        # A malformed authority makes urlparse/hostname raise ValueError. The
+        # validator must turn that into its normal catalog error, not leak a
+        # raw ValueError to the caller.
+        with pytest.raises(IntegrationCatalogError, match="malformed"):
+            IntegrationCatalog._validate_catalog_url(url)
+
 
 # ---------------------------------------------------------------------------
 # IntegrationCatalog — active catalogs

tests/integrations/test_integration_cursor_agent.py

@@ -231,4 +231,3 @@ class TestCursorAgentCliDispatch:
 
         argv = mock_run.call_args[0][0]
         assert argv[0] == "cursor-agent"
-

tests/integrations/test_integration_devin.py

@@ -71,4 +71,4 @@ class TestDevinInitFlow:
         )
 
         assert result.exit_code == 0, f"init --integration devin failed: {result.output}"
-        assert (target / ".devin" / "skills" / "speckit-plan" / "SKILL.md").exists()
+        assert (target / ".devin" / "skills" / "speckit-plan" / "SKILL.md").exists()

tests/integrations/test_integration_forge.py

@@ -288,13 +288,13 @@ class TestForgeCommandRegistrar:
     def test_registrar_formats_extension_command_names_for_forge(self, tmp_path):
         """Verify CommandRegistrar converts dot notation to hyphens for Forge."""
         from specify_cli.agents import CommandRegistrar
-        
+
         # Create a mock extension command file
         ext_dir = tmp_path / "extension"
         ext_dir.mkdir()
         cmd_dir = ext_dir / "commands"
         cmd_dir.mkdir()
-        
+
         # Create a test command with dot notation name
         cmd_file = cmd_dir / "example.md"
         cmd_file.write_text(
@@ -304,7 +304,7 @@ class TestForgeCommandRegistrar:
             "Test content with $ARGUMENTS\n",
             encoding="utf-8"
         )
-        
+
         # Register with Forge
         registrar = CommandRegistrar()
         commands = [
@@ -313,7 +313,7 @@ class TestForgeCommandRegistrar:
                 "file": "commands/example.md"
             }
         ]
-        
+
         registered = registrar.register_commands(
             "forge",
             commands,
@@ -321,14 +321,14 @@ class TestForgeCommandRegistrar:
             ext_dir,
             tmp_path
         )
-        
+
         # Verify registration succeeded
         assert "speckit.my-extension.example" in registered
-        
+
         # Check the generated file has hyphenated name in frontmatter
         forge_cmd = tmp_path / ".forge" / "commands" / "speckit-my-extension-example.md"
         assert forge_cmd.exists()
-        
+
         content = forge_cmd.read_text(encoding="utf-8")
         # Parse frontmatter to validate name field precisely
         frontmatter, _ = registrar.parse_frontmatter(content)
@@ -339,13 +339,13 @@ class TestForgeCommandRegistrar:
     def test_registrar_formats_alias_names_for_forge(self, tmp_path):
         """Verify CommandRegistrar converts alias names to hyphens for Forge."""
         from specify_cli.agents import CommandRegistrar
-        
+
         # Create a mock extension command file
         ext_dir = tmp_path / "extension"
         ext_dir.mkdir()
         cmd_dir = ext_dir / "commands"
         cmd_dir.mkdir()
-        
+
         cmd_file = cmd_dir / "example.md"
         cmd_file.write_text(
             "---\n"
@@ -354,7 +354,7 @@ class TestForgeCommandRegistrar:
             "Test content\n",
             encoding="utf-8"
         )
-        
+
         # Register with Forge including an alias
         registrar = CommandRegistrar()
         commands = [
@@ -364,7 +364,7 @@ class TestForgeCommandRegistrar:
                 "aliases": ["speckit.my-extension.ex"]
             }
         ]
-        
+
         registrar.register_commands(
             "forge",
             commands,
@@ -372,11 +372,11 @@ class TestForgeCommandRegistrar:
             ext_dir,
             tmp_path
         )
-        
+
         # Check the alias file has hyphenated name in frontmatter
         alias_file = tmp_path / ".forge" / "commands" / "speckit-my-extension-ex.md"
         assert alias_file.exists()
-        
+
         content = alias_file.read_text(encoding="utf-8")
         # Parse frontmatter to validate alias name field precisely
         frontmatter, _ = registrar.parse_frontmatter(content)
@@ -387,13 +387,13 @@ class TestForgeCommandRegistrar:
     def test_registrar_does_not_affect_other_agents(self, tmp_path):
         """Verify format_name callback is Forge-specific and doesn't affect other agents."""
         from specify_cli.agents import CommandRegistrar
-        
+
         # Create a mock extension command file
         ext_dir = tmp_path / "extension"
         ext_dir.mkdir()
         cmd_dir = ext_dir / "commands"
         cmd_dir.mkdir()
-        
+
         cmd_file = cmd_dir / "example.md"
         cmd_file.write_text(
             "---\n"
@@ -402,7 +402,7 @@ class TestForgeCommandRegistrar:
             "Test content with $ARGUMENTS\n",
             encoding="utf-8"
         )
-        
+
         # Register with Kilo Code (standard markdown agent without inject_name)
         registrar = CommandRegistrar()
         commands = [
@@ -411,7 +411,7 @@ class TestForgeCommandRegistrar:
                 "file": "commands/example.md"
             }
         ]
-        
+
         registrar.register_commands(
             "kilocode",
             commands,
@@ -419,12 +419,12 @@ class TestForgeCommandRegistrar:
             ext_dir,
             tmp_path
         )
-        
+
         # Kilo Code uses standard markdown format without name injection.
         # The format_name callback should not be invoked for non-Forge agents.
         kilocode_cmd = tmp_path / ".kilocode" / "workflows" / "speckit.my-extension.example.md"
         assert kilocode_cmd.exists()
-        
+
         content = kilocode_cmd.read_text(encoding="utf-8")
         # Kilo Code should NOT have a name field injected
         assert "name:" not in content, (

tests/integrations/test_integration_kiro_cli.py

@@ -42,6 +42,9 @@ class TestKiroCliIntegration(MarkdownIntegrationTests):
     COMMANDS_SUBDIR = "prompts"
     REGISTRAR_DIR = ".kiro/prompts"
 
+    def test_declares_multi_install_safe(self):
+        assert get_integration(self.KEY).multi_install_safe is True
+
     def test_registrar_config(self):
         """Override base assertion: kiro-cli uses a prose fallback for args
         because Kiro CLI file-based prompts do not natively substitute

tests/integrations/test_integration_subcommand.py

@@ -2675,6 +2675,27 @@ class TestParseIntegrationOptionsEqualsForm:
         assert result_space["commands_dir"] == "./mydir"
         assert result_equals["commands_dir"] == "./mydir"
 
+    def test_unbalanced_quote_exits_cleanly(self, capsys):
+        """An unbalanced quote must exit(1) with a message, not a raw ValueError.
+
+        shlex.split() raises ValueError("No closing quotation") on an unbalanced
+        quote; the parser must translate that into the same clean typer.Exit(1)
+        UX as unknown-option / missing-value, rather than letting the traceback
+        escape (issue #3457).
+        """
+        import typer
+
+        from specify_cli.integrations._commands import _parse_integration_options
+        from specify_cli.integrations import get_integration
+
+        integration = get_integration("generic")
+        assert integration is not None
+
+        with pytest.raises(typer.Exit) as excinfo:
+            _parse_integration_options(integration, '--commands-dir "foo')
+        assert excinfo.value.exit_code == 1
+        assert "Error: Could not parse integration options: No closing quotation." in capsys.readouterr().out
+
 
 class TestUninstallNoManifestClearsInitOptions:
     def test_init_options_cleared_on_no_manifest_uninstall(self, tmp_path):

tests/integrations/test_integration_vibe.py

@@ -34,4 +34,4 @@ class TestVibeUserInvocable:
             parsed = yaml.safe_load(parts[1])
             assert parsed.get("user-invocable") is True, (
                 f"{f.parent.name}/SKILL.md is missing user-invocable: true in frontmatter"
-            )
+            )

tests/integrations/test_registry.py

@@ -272,6 +272,20 @@ class TestMultiInstallSafeContracts:
                 f"these files: {sorted(overlap)}"
             )
 
+    def test_kiro_cli_is_declared_multi_install_safe(self):
+        """kiro-cli confines itself to an isolated ``.kiro/`` root that no
+        other integration touches, so it must be declared multi-install safe
+        (issue #3471).
+
+        Before the fix, co-installing kiro-cli alongside another integration
+        left ``specify integration status`` permanently in ERROR
+        (``unsafe-multi-install``) with no way to acknowledge it. The
+        parametrized isolation/manifest contracts above already exercise
+        kiro-cli once the flag is set; this pins the declaration itself so a
+        future edit cannot silently drop it and reintroduce the error.
+        """
+        assert INTEGRATION_REGISTRY["kiro-cli"].multi_install_safe is True
+
 
 class TestCatalogParity:
     """The discovery catalog must list every registered integration."""

tests/test_authentication.py

@@ -315,6 +315,20 @@ class TestFindEntriesForUrl:
     def test_empty_url_returns_empty(self):
         assert find_entries_for_url("", [_github_entry()]) == []
 
+    @pytest.mark.parametrize(
+        "url",
+        [
+            "https://[::1",                 # unterminated ipv6 bracket
+            "https://[not-an-ip]/file",     # bracketed non-ip host
+        ],
+    )
+    def test_malformed_url_returns_empty(self, url):
+        # A malformed authority makes urlparse/hostname raise ValueError.
+        # Since no entry can match such a URL, this must return no matches
+        # (like a host-less URL) rather than leaking a raw ValueError out of
+        # the shared HTTP client.
+        assert find_entries_for_url(url, [_github_entry()]) == []
+
     def test_empty_entries_returns_empty(self):
         assert find_entries_for_url("https://github.com/org/repo", []) == []
 

tests/test_extension_registration.py

@@ -17,7 +17,7 @@ class TestExtensionRegistration:
         """Standard registration: Adding an extension should add it to the list."""
         executor = HookExecutor(project_dir)
         executor.register_extension("test-ext")
-        
+
         config = executor.get_project_config()
         assert "installed" in config
         assert config["installed"] == ["test-ext"]
@@ -28,7 +28,7 @@ class TestExtensionRegistration:
         executor.register_extension("zebra-ext")
         executor.register_extension("apple-ext")
         executor.register_extension("middle-ext")
-        
+
         config = executor.get_project_config()
         assert config["installed"] == ["apple-ext", "middle-ext", "zebra-ext"]
 
@@ -37,7 +37,7 @@ class TestExtensionRegistration:
         executor = HookExecutor(project_dir)
         executor.register_extension("test-ext")
         executor.register_extension("test-ext")
-        
+
         config = executor.get_project_config()
         assert config["installed"] == ["test-ext"]
         assert len(config["installed"]) == 1
@@ -47,9 +47,9 @@ class TestExtensionRegistration:
         executor = HookExecutor(project_dir)
         executor.register_extension("ext-1")
         executor.register_extension("ext-2")
-        
+
         executor.unregister_extension("ext-1")
-        
+
         config = executor.get_project_config()
         assert config["installed"] == ["ext-2"]
 
@@ -57,10 +57,10 @@ class TestExtensionRegistration:
         """Safe Removal: Unregistering a non-existent extension should do nothing."""
         executor = HookExecutor(project_dir)
         executor.register_extension("ext-1")
-        
+
         # Should not raise or change the list
         executor.unregister_extension("ext-nonexistent")
-        
+
         config = executor.get_project_config()
         assert config["installed"] == ["ext-1"]
 
@@ -87,27 +87,27 @@ class TestExtensionRegistration:
         manifest_path = tmp_path / "extension.yml"
         with open(manifest_path, "w") as f:
             yaml.dump(manifest_data, f)
-        
+
         manifest = ExtensionManifest(manifest_path)
         executor = HookExecutor(project_dir)
-        
+
         # This should call register_extension internally
         executor.register_hooks(manifest)
-        
+
         config = executor.get_project_config()
         assert "hook-ext" in config["installed"]
 
     def test_missing_installed_key_initialization(self, project_dir):
         """Graceful Initialization: If 'installed' key is missing, it should be created."""
         executor = HookExecutor(project_dir)
-        
+
         # Manually create a config without 'installed'
         config_path = project_dir / ".specify" / "extensions.yml"
         config_path.write_text(yaml.dump({"settings": {"auto_execute_hooks": True}}))
-        
+
         # This should detect the missing key and initialize it
         executor.register_extension("new-ext")
-        
+
         config = executor.get_project_config()
         assert "installed" in config
         assert config["installed"] == ["new-ext"]
@@ -135,20 +135,20 @@ class TestExtensionRegistration:
         manifest_path = tmp_path / "extension.yml"
         with open(manifest_path, "w") as f:
             yaml.dump(manifest_data, f)
-        
+
         manifest = ExtensionManifest(manifest_path)
         executor = HookExecutor(project_dir)
-        
+
         # Register hooks first
         executor.register_hooks(manifest)
-        
+
         config = executor.get_project_config()
         assert "hook-ext" in config["installed"]
         assert "after_tasks" in config["hooks"]
-        
+
         # Now unregister hooks
         executor.unregister_hooks("hook-ext")
-        
+
         config = executor.get_project_config()
         assert "hook-ext" not in config["installed"]
         # unregister_hooks() removes the empty hook array entirely, so the key is absent
@@ -157,16 +157,16 @@ class TestExtensionRegistration:
     def test_unregister_hooks_no_hooks_key(self, project_dir):
         """Resilience: unregister_hooks should work even if config has no 'hooks' key."""
         executor = HookExecutor(project_dir)
-        
+
         # Register extension without hooks
         executor.register_extension("ext-no-hooks")
-        
+
         config = executor.get_project_config()
         assert "ext-no-hooks" in config["installed"]
-        
+
         # Unregister should not crash even if no hooks key exists
         executor.unregister_hooks("ext-no-hooks")
-        
+
         config = executor.get_project_config()
         assert "ext-no-hooks" not in config["installed"]
 
@@ -175,12 +175,12 @@ class TestExtensionRegistration:
         # Create a corrupted config (root is a list)
         config_path = project_dir / ".specify" / "extensions.yml"
         config_path.write_text(yaml.dump(["corrupted", "list"]))
-        
+
         executor = HookExecutor(project_dir)
-        
+
         # Should not raise even with corrupted config
         executor.unregister_hooks("non-existent")
-        
+
         # Config should remain as-is or be handled gracefully
         config = executor.get_project_config()
         # If it's corrupted, it's returned as-is or handled by defensive logic
@@ -223,30 +223,30 @@ class TestExtensionRegistration:
                 "after_tasks": {"command": "speckit.ext-2.run"}
             }
         }
-        
+
         manifest_path_1 = tmp_path / "extension1.yml"
         manifest_path_2 = tmp_path / "extension2.yml"
         with open(manifest_path_1, "w") as f:
             yaml.dump(manifest_data_1, f)
         with open(manifest_path_2, "w") as f:
             yaml.dump(manifest_data_2, f)
-        
+
         manifest1 = ExtensionManifest(manifest_path_1)
         manifest2 = ExtensionManifest(manifest_path_2)
         executor = HookExecutor(project_dir)
-        
+
         # Register both extensions
         executor.register_hooks(manifest1)
         executor.register_hooks(manifest2)
-        
+
         config = executor.get_project_config()
         assert "ext-1" in config["installed"]
         assert "ext-2" in config["installed"]
         assert len(config["hooks"]["after_tasks"]) == 2
-        
+
         # Unregister first extension
         executor.unregister_hooks("ext-1")
-        
+
         config = executor.get_project_config()
         assert "ext-1" not in config["installed"]
         assert "ext-2" in config["installed"]
@@ -346,9 +346,9 @@ class TestExtensionRegistration:
         manifest_path = tmp_path / "extension.yml"
         with open(manifest_path, "w") as f:
             yaml.dump(manifest_data, f)
-        
+
         manifest = ExtensionManifest(manifest_path)
-        
+
         # Should not raise TypeError when trying to append to None
         executor.register_hooks(manifest)
 
@@ -378,16 +378,16 @@ class TestExtensionRegistration:
         """Review Feedback: register_extension should support and preserve dict entries."""
         executor = HookExecutor(project_dir)
         config_path = project_dir / ".specify" / "extensions.yml"
-        
+
         # Setup config with a pinned extension (dict)
         pinned_ext = {"id": "pinned-ext", "version": "1.0.0"}
         config_path.write_text(yaml.dump({
             "installed": [pinned_ext, "string-ext"]
         }))
-        
+
         # Register a new extension
         executor.register_extension("new-ext")
-        
+
         config = executor.get_project_config()
         # Should contain all three, sorted by id: new-ext, pinned-ext, string-ext
         assert config["installed"] == ["new-ext", pinned_ext, "string-ext"]
@@ -396,15 +396,15 @@ class TestExtensionRegistration:
         """Review Feedback: unregister_extension should support removing matching dict entries."""
         executor = HookExecutor(project_dir)
         config_path = project_dir / ".specify" / "extensions.yml"
-        
+
         pinned_ext = {"id": "to-remove", "version": "1.0.0"}
         config_path.write_text(yaml.dump({
             "installed": [pinned_ext, "other-ext"]
         }))
-        
+
         # Unregister by ID
         executor.unregister_extension("to-remove")
-        
+
         config = executor.get_project_config()
         assert config["installed"] == ["other-ext"]
 
@@ -412,14 +412,14 @@ class TestExtensionRegistration:
         """Hardening: unregister_extension should handle non-list installed key."""
         executor = HookExecutor(project_dir)
         config_path = project_dir / ".specify" / "extensions.yml"
-        
+
         config_path.write_text(yaml.dump({
             "installed": "not-a-list"
         }))
-        
+
         # Should not crash and should normalize to []
         executor.unregister_extension("any-ext")
-        
+
         config = executor.get_project_config()
         assert config["installed"] == []
     def test_register_hooks_mixed_type_hook_list(self, project_dir, tmp_path):
@@ -458,7 +458,7 @@ class TestExtensionRegistration:
 
         config = executor.get_project_config()
         hooks = config["hooks"]["after_tasks"]
-        
+
         # Should have 2 valid dict hooks, and 0 non-dict items
         assert len(hooks) == 2
         assert all(isinstance(h, dict) for h in hooks)
@@ -469,12 +469,12 @@ class TestExtensionRegistration:
         """Hardening: unregister_extension should handle scalar root config."""
         executor = HookExecutor(project_dir)
         config_path = project_dir / ".specify" / "extensions.yml"
-        
+
         config_path.write_text(yaml.dump(123))
-        
+
         # Should not crash and should normalize to {}
         executor.unregister_extension("any-ext")
-        
+
         config = executor.get_project_config()
         assert isinstance(config, dict)
         assert config["installed"] == []
@@ -483,15 +483,15 @@ class TestExtensionRegistration:
         """Regression: unregister_hooks() must handle scalar hook event values."""
         executor = HookExecutor(project_dir)
         config_path = project_dir / ".specify" / "extensions.yml"
-        
+
         config_path.write_text(yaml.dump({
             "installed": ["some-ext"],
             "hooks": {"after_tasks": 123}
         }))
-        
+
         # Should not raise TypeError when iterating
         executor.unregister_hooks("some-ext")
-        
+
         config = executor.get_project_config()
         assert "some-ext" not in config["installed"]
         assert "after_tasks" not in config["hooks"]

tests/test_extension_skills.py

@@ -911,6 +911,65 @@ class TestExtensionSkillRegistration:
         assert ".specify/scripts/bash/resolve-skill.sh" not in content
         assert ".specify/scripts/bash/ensure-skills.sh" not in content
 
+    def test_skill_registration_rewrites_extension_subdir_paths(self, project_dir, temp_dir):
+        """Auto-registered skills should resolve extension-relative subdir
+        references (agents/, knowledge-base/) to their installed location,
+        matching the rewrite already applied by register_commands() (#2101)."""
+        _create_init_options(project_dir, ai="claude", ai_skills=True)
+        skills_dir = _create_skills_dir(project_dir, ai="claude")
+
+        ext_dir = temp_dir / "path-ext"
+        ext_dir.mkdir()
+        manifest_data = {
+            "schema_version": "1.0",
+            "extension": {
+                "id": "path-ext",
+                "name": "Path Extension",
+                "version": "1.0.0",
+                "description": "Test",
+            },
+            "requires": {"speckit_version": ">=0.1.0"},
+            "provides": {
+                "commands": [
+                    {
+                        "name": "speckit.path-ext.run",
+                        "file": "commands/run.md",
+                        "description": "Run command",
+                    }
+                ]
+            },
+        }
+        with open(ext_dir / "extension.yml", "w") as f:
+            yaml.safe_dump(manifest_data, f)
+
+        (ext_dir / "commands").mkdir()
+        (ext_dir / "agents" / "control").mkdir(parents=True)
+        (ext_dir / "agents" / "control" / "commander.md").write_text("# Commander\n")
+        (ext_dir / "knowledge-base").mkdir()
+        (ext_dir / "knowledge-base" / "agent-scores.yaml").write_text("scores: {}\n")
+        (ext_dir / "templates").mkdir()
+        (ext_dir / "templates" / "kill-report.md").write_text("# Kill Report\n")
+
+        (ext_dir / "commands" / "run.md").write_text(
+            "---\n"
+            "description: Run command\n"
+            "---\n\n"
+            "Read agents/control/commander.md and knowledge-base/agent-scores.yaml.\n"
+            "Use templates/kill-report.md as the report template.\n"
+        )
+
+        manager = ExtensionManager(project_dir)
+        manager.install_from_directory(ext_dir, "0.1.0", register_commands=False)
+
+        content = (skills_dir / "speckit-path-ext-run" / "SKILL.md").read_text()
+        assert ".specify/extensions/path-ext/agents/control/commander.md" in content
+        assert ".specify/extensions/path-ext/knowledge-base/agent-scores.yaml" in content
+        # extension's own templates/ dir must resolve under the extension,
+        # not the project-level .specify/templates/
+        assert ".specify/extensions/path-ext/templates/kill-report.md" in content
+        assert "Read agents/control" not in content
+        assert "and knowledge-base/" not in content
+
     def test_missing_command_file_skipped(self, skills_project, temp_dir):
         """Commands with missing source files should be skipped gracefully."""
         project_dir, skills_dir = skills_project

tests/test_extension_update_hardening.py

@@ -20,28 +20,28 @@ def test_extension_update_corrupted_config_root(project_dir, monkeypatch):
     """Regression: extension update must handle corrupted extensions.yml (root is scalar)."""
     # chdir into project_dir so _require_specify_project() succeeds
     monkeypatch.chdir(project_dir)
-    
+
     # Corrupt extensions.yml
     config_path = project_dir / ".specify" / "extensions.yml"
     config_path.write_text(yaml.dump(123))
-    
+
     # Mock ExtensionManager to return an installed extension for resolution
-    
+
     monkeypatch.setattr(ExtensionManager, "list_installed", lambda self: [{"id": "test-ext", "name": "Test Ext", "version": "1.0.0"}])
     monkeypatch.setattr(ExtensionRegistry, "get", lambda self, ext_id: {"version": "1.0.0", "enabled": True})
     monkeypatch.setattr(ExtensionCatalog, "get_extension_info", lambda self, ext_id: {"id": "test-ext", "name": "Test Ext", "version": "1.1.0", "download_url": "https://example.com/ext.zip"})
-    
+
     # Mock download_extension to avoid network calls; use tmp_path so the test is hermetic
     # and returns a Path so zip_path.exists() / zip_path.unlink() work without AttributeError
     mock_zip = project_dir / "mock.zip"
     monkeypatch.setattr(ExtensionCatalog, "download_extension", lambda self, ext_id: mock_zip)
-    
+
     # Mock confirmation to true
     monkeypatch.setattr("typer.confirm", lambda _: True)
-    
+
     # Run update
     result = runner.invoke(app, ["extension", "update", "test-ext"], obj={"project_root": project_dir})
-    
+
     # extension_update() catches exceptions internally and exits with code 1 on failure.
     assert result.exit_code == 1
     assert "AttributeError" not in result.output
@@ -50,13 +50,13 @@ def test_extension_update_corrupted_config_root(project_dir, monkeypatch):
 def test_extension_update_corrupted_hooks_value(project_dir, monkeypatch):
     """Regression: extension update must handle non-dict 'hooks' in extensions.yml."""
     monkeypatch.chdir(project_dir)
-    
+
     config_path = project_dir / ".specify" / "extensions.yml"
     config_path.write_text(yaml.dump({
         "installed": ["test-ext"],
         "hooks": ["not", "a", "dict"]
     }))
-    
+
     monkeypatch.setattr(ExtensionManager, "list_installed", lambda self: [{"id": "test-ext", "name": "Test Ext", "version": "1.0.0"}])
     monkeypatch.setattr(ExtensionRegistry, "get", lambda self, ext_id: {"version": "1.0.0", "enabled": True})
     monkeypatch.setattr(ExtensionCatalog, "get_extension_info", lambda self, ext_id: {"id": "test-ext", "name": "Test Ext", "version": "1.1.0", "download_url": "https://example.com/ext.zip"})
@@ -64,9 +64,9 @@ def test_extension_update_corrupted_hooks_value(project_dir, monkeypatch):
     mock_zip = project_dir / "mock.zip"
     monkeypatch.setattr(ExtensionCatalog, "download_extension", lambda self, ext_id: mock_zip)
     monkeypatch.setattr("typer.confirm", lambda _: True)
-    
+
     result = runner.invoke(app, ["extension", "update", "test-ext"], obj={"project_root": project_dir})
-    
+
     # extension_update() catches exceptions internally and exits with code 1 on failure.
     assert result.exit_code == 1
     assert "AttributeError" not in result.output
@@ -75,33 +75,33 @@ def test_extension_update_corrupted_hooks_value(project_dir, monkeypatch):
 def test_extension_update_rollback_corrupted_config(project_dir, monkeypatch):
     """Regression: extension update rollback must handle corrupted extensions.yml."""
     monkeypatch.chdir(project_dir)
-    
+
     config_path = project_dir / ".specify" / "extensions.yml"
     # Write config with hooks: null; get_project_config() normalizes this to {}
     # so the backup captures {} and the restored config will have hooks: {}.
     config_path.write_text(yaml.dump({"installed": ["test-ext"], "hooks": None}))
-    
+
     # Mock update process to fail after backup
     monkeypatch.setattr(ExtensionManager, "list_installed", lambda self: [{"id": "test-ext", "name": "Test Ext", "version": "1.0.0"}])
     monkeypatch.setattr(ExtensionRegistry, "get", lambda self, ext_id: {"version": "1.0.0", "enabled": True})
-    
+
     # Force failure in download_extension to trigger rollback
     def mock_download_fail(*args, **kwargs):
         # Corrupt the config BEFORE rollback is triggered
         config_path.write_text(yaml.dump("CORRUPTED"))
         raise Exception("Download failed")
-        
+
     monkeypatch.setattr(ExtensionCatalog, "get_extension_info", lambda self, ext_id: {"id": "test-ext", "name": "Test Ext", "version": "1.1.0", "download_url": "https://example.com/ext.zip"})
     monkeypatch.setattr(ExtensionCatalog, "download_extension", mock_download_fail)
     monkeypatch.setattr("typer.confirm", lambda _: True)
-    
+
     result = runner.invoke(app, ["extension", "update", "test-ext"], obj={"project_root": project_dir})
-    
+
     # Should handle Exception and NOT crash with AttributeError during rollback
     assert result.exit_code == 1
     assert "Download failed" in result.output
     assert not isinstance(result.exception, AttributeError)
-    
+
     # Verify hooks key was preserved (normalized to {} if it was null/corrupted)
     restored_config = yaml.safe_load(config_path.read_text())
     assert isinstance(restored_config, dict)

tests/test_extensions.py

@@ -2376,6 +2376,185 @@ Run {SCRIPT}
         assert ".specify/scripts/powershell/setup-plan.ps1 -Json" in content
         assert ".specify/scripts/bash/setup-plan.sh" not in content
 
+    @staticmethod
+    def _make_subdir_extension(temp_dir, ext_id="echelon", aliases=None):
+        """Create an extension whose command body references bundled subdirs."""
+        import yaml
+
+        ext_dir = temp_dir / ext_id
+        ext_dir.mkdir()
+        (ext_dir / "commands").mkdir()
+        (ext_dir / "agents" / "control").mkdir(parents=True)
+        (ext_dir / "knowledge-base").mkdir()
+        (ext_dir / "templates").mkdir()
+        (ext_dir / "specs" / "001-internal").mkdir(parents=True)
+
+        command = {
+            "name": f"speckit.{ext_id}.run",
+            "file": "commands/run.md",
+            "description": "Run",
+        }
+        if aliases:
+            command["aliases"] = aliases
+        manifest_data = {
+            "schema_version": "1.0",
+            "extension": {
+                "id": ext_id,
+                "name": "Echelon",
+                "version": "1.0.0",
+                "description": "Test",
+            },
+            "requires": {"speckit_version": ">=0.1.0"},
+            "provides": {"commands": [command]},
+        }
+        with open(ext_dir / "extension.yml", "w") as f:
+            yaml.dump(manifest_data, f)
+
+        (ext_dir / "commands" / "run.md").write_text(
+            "---\ndescription: Run\n---\n\n"
+            "Read agents/control/commander.md for instructions.\n"
+            "Load knowledge-base/agent-scores.yaml for calibration.\n"
+            "Use templates/kill-report.md as output format.\n"
+            "Artifacts go to specs/001-internal/plan.md.\n"
+            "See commands/run.md for the source.\n"
+        )
+        return ext_dir
+
+    def test_codex_skill_registration_rewrites_extension_subdir_paths(
+        self, project_dir, temp_dir
+    ):
+        """Extension-relative subdir refs must point at the installed location."""
+        ext_dir = self._make_subdir_extension(temp_dir)
+
+        skills_dir = project_dir / ".agents" / "skills"
+        skills_dir.mkdir(parents=True)
+
+        manifest = ExtensionManifest(ext_dir / "extension.yml")
+        registrar = CommandRegistrar()
+        registrar.register_commands_for_agent("codex", manifest, ext_dir, project_dir)
+
+        content = (skills_dir / "speckit-echelon-run" / "SKILL.md").read_text()
+        assert ".specify/extensions/echelon/agents/control/commander.md" in content
+        assert ".specify/extensions/echelon/knowledge-base/agent-scores.yaml" in content
+        assert ".specify/extensions/echelon/templates/kill-report.md" in content
+        assert "Read agents/" not in content
+        # specs/ refs point at the user's project artifacts, never the extension
+        assert "to specs/001-internal/plan.md" in content
+        assert ".specify/extensions/echelon/specs/" not in content
+        # commands/ refs are slash-command sources, not runtime reads
+        assert "See commands/run.md" in content
+
+    def test_skill_registration_rewrites_extension_subdir_paths_in_aliases(
+        self, project_dir, temp_dir
+    ):
+        """Alias skills reuse the rewritten body."""
+        ext_dir = self._make_subdir_extension(
+            temp_dir, ext_id="ext-alias-paths", aliases=["speckit.ext-alias-paths.go"]
+        )
+
+        skills_dir = project_dir / ".agents" / "skills"
+        skills_dir.mkdir(parents=True)
+
+        manifest = ExtensionManifest(ext_dir / "extension.yml")
+        registrar = CommandRegistrar()
+        registrar.register_commands_for_agent("codex", manifest, ext_dir, project_dir)
+
+        alias_content = (
+            skills_dir / "speckit-ext-alias-paths-go" / "SKILL.md"
+        ).read_text()
+        assert (
+            ".specify/extensions/ext-alias-paths/agents/control/commander.md"
+            in alias_content
+        )
+        assert "Read agents/" not in alias_content
+
+    def test_markdown_registration_rewrites_extension_subdir_paths(
+        self, project_dir, temp_dir
+    ):
+        """Markdown-format agents get the same rewrite via the shared path."""
+        ext_dir = self._make_subdir_extension(temp_dir, ext_id="ext-md-paths")
+
+        amp_dir = project_dir / ".agents" / "commands"
+        amp_dir.mkdir(parents=True)
+
+        manifest = ExtensionManifest(ext_dir / "extension.yml")
+        registrar = CommandRegistrar()
+        registrar.register_commands_for_agent("amp", manifest, ext_dir, project_dir)
+
+        content = (amp_dir / "speckit.ext-md-paths.run.md").read_text()
+        assert ".specify/extensions/ext-md-paths/agents/control/commander.md" in content
+        assert "Read agents/" not in content
+
+    def test_rewrite_extension_paths_only_rewrites_existing_subdirs(self, temp_dir):
+        """Only directories present in the extension are rewritten."""
+        from specify_cli.agents import CommandRegistrar as AgentCommandRegistrar
+
+        ext_dir = temp_dir / "ext-existing"
+        (ext_dir / "agents").mkdir(parents=True)
+        (ext_dir / ".hidden").mkdir()
+
+        text = (
+            "Read agents/one.md then knowledge-base/two.md.\n"
+            "Also ./agents/three.md but not /agents/abs.md.\n"
+            "Keep .hidden/secret.md alone.\n"
+        )
+        rewritten = AgentCommandRegistrar.rewrite_extension_paths(
+            text, "ext-existing", ext_dir
+        )
+
+        assert ".specify/extensions/ext-existing/agents/one.md" in rewritten
+        assert "Also .specify/extensions/ext-existing/agents/three.md" in rewritten
+        # absolute paths keep their meaning
+        assert "not /agents/abs.md" in rewritten
+        # knowledge-base/ does not exist in this extension: left untouched
+        assert "then knowledge-base/two.md" in rewritten
+        assert ".hidden/secret.md" in rewritten
+        assert ".specify/extensions/ext-existing/.hidden/" not in rewritten
+
+    def test_rewrite_extension_paths_handles_regex_special_replacement_text(
+        self, temp_dir
+    ):
+        """subdir/extension_id containing regex-replacement-special characters
+        (e.g. backslash / group references) must not raise or be misinterpreted
+        by re.sub's replacement template (#2101).
+
+        The subdir name uses brackets rather than a backslash: on Windows,
+        "\\" is a path separator, so a subdir literally named "assets\\q"
+        would create nested directories "assets/q" instead of a single
+        directory, and iterdir() would then only discover "assets" - never
+        exercising the intended replacement text. extension_id isn't used to
+        create a directory, so it's free to contain a real backslash/"\\1"
+        to verify the callable replacement treats it literally.
+        """
+        from specify_cli.agents import CommandRegistrar as AgentCommandRegistrar
+
+        ext_dir = temp_dir / "ext-backslash"
+        weird_subdir = "assets[q]"
+        (ext_dir / weird_subdir).mkdir(parents=True)
+        # sanity-check the cross-platform assumption above
+        assert [p.name for p in ext_dir.iterdir()] == [weird_subdir]
+
+        text = f"Read {weird_subdir}/file.md but not /{weird_subdir}/abs.md.\n"
+        rewritten = AgentCommandRegistrar.rewrite_extension_paths(
+            text, "ext\\1", ext_dir
+        )
+
+        assert f".specify/extensions/ext\\1/{weird_subdir}/file.md" in rewritten
+        # absolute paths are still left untouched
+        assert f"/{weird_subdir}/abs.md" in rewritten
+
+    def test_rewrite_extension_paths_missing_dir_returns_text(self, temp_dir):
+        """A missing extension directory leaves the text unchanged."""
+        from specify_cli.agents import CommandRegistrar as AgentCommandRegistrar
+
+        text = "Read agents/one.md."
+        assert (
+            AgentCommandRegistrar.rewrite_extension_paths(
+                text, "gone", temp_dir / "does-not-exist"
+            )
+            == text
+        )
+
     def test_register_commands_for_copilot(self, extension_dir, project_dir):
         """Test registering commands for Copilot agent with .agent.md extension."""
         # Create .github/agents directory (Copilot project)
@@ -6424,6 +6603,42 @@ class TestExtensionPriorityCLI:
         plain = strip_ansi(result.output)
         assert "already has priority 5" in plain
 
+    def test_set_priority_repairs_corrupted_bool(self, extension_dir, project_dir):
+        """A corrupted boolean priority must be repaired, not skipped.
+
+        ``isinstance(True, int)`` is True and ``True == 1`` in Python, so a
+        stored ``True`` priority would short-circuit the ``already has
+        priority 1`` skip path and never get rewritten to a real int —
+        contradicting the comment that promises corrupted values are
+        repaired. The guard must exclude bools (like normalize_priority).
+        """
+        from typer.testing import CliRunner
+        from unittest.mock import patch
+        from specify_cli import app
+
+        runner = CliRunner()
+
+        manager = ExtensionManager(project_dir)
+        manager.install_from_directory(
+            extension_dir, "0.1.0", register_commands=False, priority=5
+        )
+        # Inject a corrupted boolean priority (True == 1).
+        manager.registry.update("test-ext", {"priority": True})
+
+        with patch.object(Path, "cwd", return_value=project_dir):
+            result = runner.invoke(app, ["extension", "set-priority", "test-ext", "1"])
+
+        assert result.exit_code == 0, result.output
+        plain = strip_ansi(result.output)
+        # The corrupted bool must be repaired, not reported as already-set.
+        assert "already has priority" not in plain
+        assert "priority changed" in plain
+
+        # The stored value is now a real int, not a bool.
+        reloaded = ExtensionManager(project_dir).registry.get("test-ext")
+        assert reloaded["priority"] == 1
+        assert not isinstance(reloaded["priority"], bool)
+
     def test_set_priority_invalid_value(self, extension_dir, project_dir):
         """Test set-priority rejects invalid priority values."""
         from typer.testing import CliRunner
@@ -7628,3 +7843,188 @@ class TestConfigManagerNonMappingYaml:
         (ext_dir / "jira-config.yml").write_text("just a string\n", encoding="utf-8")
         executor = HookExecutor(tmp_path)
         assert executor._evaluate_condition("config.x is set", "jira") is False
+
+
+class TestConfigManagerEnvPrefixCollision:
+    """Prefix-colliding env vars must not crash or clobber nested config."""
+
+    def test_scalar_then_nested_yields_nested(self, tmp_path, monkeypatch):
+        """SPECKIT_X_CONNECTION=x then SPECKIT_X_CONNECTION_URL=y.
+
+        The scalar-first order previously raised TypeError ('str' object
+        does not support item assignment) when the walk indexed into 'x'.
+        """
+        monkeypatch.setenv("SPECKIT_TESTEXT_CONNECTION", "x")
+        monkeypatch.setenv("SPECKIT_TESTEXT_CONNECTION_URL", "y")
+        cm = ConfigManager(tmp_path, "testext")
+        assert cm._get_env_config() == {"connection": {"url": "y"}}
+
+    def test_nested_then_scalar_does_not_clobber(self, tmp_path, monkeypatch):
+        """Reverse order previously returned {'connection': 'x'}, losing url."""
+        monkeypatch.setenv("SPECKIT_TESTEXT_CONNECTION_URL", "y")
+        monkeypatch.setenv("SPECKIT_TESTEXT_CONNECTION", "x")
+        cm = ConfigManager(tmp_path, "testext")
+        assert cm._get_env_config() == {"connection": {"url": "y"}}
+
+    def test_colliding_env_does_not_disable_hook_condition(self, tmp_path, monkeypatch):
+        """`config.connection.url is set` must stay True under colliding env.
+
+        Before the fix the TypeError propagated into should_execute_hook's
+        blanket `except Exception: return False`, silently disabling the hook.
+        """
+        ext_dir = tmp_path / ".specify" / "extensions" / "testext"
+        ext_dir.mkdir(parents=True)
+        (ext_dir / "testext-config.yml").write_text(
+            "connection:\n  url: https://example.com\n", encoding="utf-8"
+        )
+        monkeypatch.setenv("SPECKIT_TESTEXT_CONNECTION", "x")
+        monkeypatch.setenv("SPECKIT_TESTEXT_CONNECTION_URL", "y")
+        executor = HookExecutor(tmp_path)
+        # Exercise the public API: before the fix the TypeError was swallowed
+        # by should_execute_hook's `except Exception: return False`, so the
+        # hook was silently disabled (False); after the fix it returns True.
+        assert executor.should_execute_hook(
+            {"condition": "config.connection.url is set", "extension": "testext"}
+        ) is True
+
+    def test_malformed_env_names_ignored(self, tmp_path, monkeypatch):
+        """A name with no key (SPECKIT_X_) or empty parts (consecutive
+        underscores) must not create an entry under an empty key."""
+        monkeypatch.setenv("SPECKIT_TESTEXT_", "orphan")  # no key at all
+        monkeypatch.setenv("SPECKIT_TESTEXT_A__B", "z")   # empty middle part
+        cm = ConfigManager(tmp_path, "testext")
+        cfg = cm._get_env_config()
+        assert "" not in cfg
+        assert cfg == {"a": {"b": "z"}}
+
+
+class TestConfigManagerCrossExtensionEnvLeak:
+    """Cross-extension env-var leak: a longer, co-installed sibling ID must
+    own its own env vars instead of leaking them into a shorter-prefix sibling.
+
+    Before the fix, ``SPECKIT_GIT_HOOKS_URL`` (intended for a ``git-hooks``
+    extension) also surfaced inside the ``git`` extension's config as
+    ``{'hooks': {'url': ...}}`` because ``SPECKIT_GIT_`` is a strict prefix of
+    ``SPECKIT_GIT_HOOKS_``.
+    """
+
+    def _install(self, project_root, ext_id):
+        extensions_dir = project_root / ".specify" / "extensions"
+        (extensions_dir / ext_id).mkdir(parents=True)
+        # Register in the extension registry — the registry is the source of
+        # truth for "installed" (a bare directory can be a config-only leftover
+        # from ``ExtensionManager.remove(..., keep_config=True)``).
+        ExtensionRegistry(extensions_dir).add(ext_id, {})
+
+    def test_sibling_owns_longer_prefix_env(self, tmp_path, monkeypatch):
+        """SPECKIT_GIT_HOOKS_URL belongs to git-hooks when co-installed with git."""
+        self._install(tmp_path, "git")
+        self._install(tmp_path, "git-hooks")
+        monkeypatch.setenv("SPECKIT_GIT_URL", "for_git")
+        monkeypatch.setenv("SPECKIT_GIT_HOOKS_URL", "for_git_hooks")
+
+        git_cfg = ConfigManager(tmp_path, "git")._get_env_config()
+        gh_cfg = ConfigManager(tmp_path, "git-hooks")._get_env_config()
+
+        # 'git' must NOT see the git-hooks var — no cross-extension leak.
+        assert git_cfg == {"url": "for_git"}
+        # 'git-hooks' still receives its own var (unchanged behaviour).
+        assert gh_cfg == {"url": "for_git_hooks"}
+
+    def test_no_sibling_installed_keeps_legacy_absorption(self, tmp_path, monkeypatch):
+        """Without a longer-prefix sibling installed, the legacy behaviour is
+        preserved: ``SPECKIT_GIT_HOOKS_URL`` is absorbed as a nested key of
+        the ``git`` extension. This keeps the fix strictly to the *collision*
+        case and avoids surprising users who deliberately set a nested key
+        via env with no sibling to disambiguate against.
+        """
+        self._install(tmp_path, "git")
+        monkeypatch.setenv("SPECKIT_GIT_HOOKS_URL", "for_git_hooks")
+
+        cfg = ConfigManager(tmp_path, "git")._get_env_config()
+        assert cfg == {"hooks": {"url": "for_git_hooks"}}
+
+    def test_non_prefix_sibling_ignored(self, tmp_path, monkeypatch):
+        """A sibling whose ID does not extend our own is not a collision.
+
+        e.g. current='git' and sibling='not-git' — 'not-git' normalized to
+        'NOT_GIT' does not start with 'GIT_', so its presence must not
+        influence git's env-var interpretation.
+        """
+        self._install(tmp_path, "git")
+        self._install(tmp_path, "not-git")
+        monkeypatch.setenv("SPECKIT_GIT_HOOKS_URL", "for_git_hooks")
+
+        cfg = ConfigManager(tmp_path, "git")._get_env_config()
+        assert cfg == {"hooks": {"url": "for_git_hooks"}}
+
+    def test_boundary_prevents_false_positive(self, tmp_path, monkeypatch):
+        """Sibling ID 'hook' (not 'hooks') must NOT eat env keys starting
+        with 'hooks'. The trailing-underscore boundary in the sibling prefix
+        prevents this false positive.
+        """
+        self._install(tmp_path, "git")
+        self._install(tmp_path, "git-hook")
+        monkeypatch.setenv("SPECKIT_GIT_HOOKS_URL", "for_git_key_hooks")
+
+        # git-hook's prefix is 'HOOK_', which does not match 'HOOKS_URL',
+        # so 'git' keeps the env var (single-installed semantics).
+        cfg = ConfigManager(tmp_path, "git")._get_env_config()
+        assert cfg == {"hooks": {"url": "for_git_key_hooks"}}
+
+    def test_missing_extensions_dir_does_not_crash(self, tmp_path, monkeypatch):
+        """A ConfigManager built against a project without ``.specify/extensions``
+        (fresh project, ad-hoc test harness) must still evaluate env config
+        rather than raising from the sibling scan.
+        """
+        # Note: no _install call — extensions dir intentionally absent.
+        monkeypatch.setenv("SPECKIT_TESTEXT_URL", "v")
+
+        cfg = ConfigManager(tmp_path, "testext")._get_env_config()
+        assert cfg == {"url": "v"}
+
+    def test_config_only_leftover_not_treated_as_sibling(self, tmp_path, monkeypatch):
+        """A directory left behind by ``remove(..., keep_config=True)`` must
+        NOT be treated as an installed sibling.
+
+        ``ExtensionManager.remove(keep_config=True)`` preserves the extension
+        directory (config files remain, dormant, for a possible reinstall) but
+        removes the registry entry. The sibling scan is sourced from the
+        registry, so a leftover ``git-hooks/`` directory without a registry
+        entry must not silently discard ``SPECKIT_GIT_HOOKS_*`` from ``git``.
+        """
+        self._install(tmp_path, "git")
+        # Simulate ``remove('git-hooks', keep_config=True)``: dir present,
+        # config file preserved, but no registry entry.
+        gh_dir = tmp_path / ".specify" / "extensions" / "git-hooks"
+        gh_dir.mkdir(parents=True)
+        (gh_dir / "git-hooks-config.yml").write_text("url: leftover\n")
+        # Sanity: git-hooks is NOT registered.
+        registry = ExtensionRegistry(tmp_path / ".specify" / "extensions")
+        assert "git-hooks" not in registry.keys()
+
+        monkeypatch.setenv("SPECKIT_GIT_HOOKS_URL", "for_git")
+
+        cfg = ConfigManager(tmp_path, "git")._get_env_config()
+        # git absorbs the var (no registered sibling owns it).
+        assert cfg == {"hooks": {"url": "for_git"}}
+
+    def test_non_utf8_registry_does_not_crash(self, tmp_path, monkeypatch):
+        """A registry file with invalid text encoding must NOT propagate
+        ``UnicodeDecodeError`` out of the sibling scan and abort every
+        config read. ``ExtensionRegistry._load()`` catches ``JSONDecodeError``
+        / ``FileNotFoundError`` only, so ``_sibling_extension_ids`` must
+        additionally swallow ``UnicodeError`` and degrade to the documented
+        pre-fix behaviour.
+        """
+        extensions_dir = tmp_path / ".specify" / "extensions"
+        extensions_dir.mkdir(parents=True)
+        # Write bytes that are not valid UTF-8 to the registry file.
+        (extensions_dir / ExtensionRegistry.REGISTRY_FILE).write_bytes(
+            b"\xff\xfe invalid utf-8 registry \xc3\x28"
+        )
+        monkeypatch.setenv("SPECKIT_TESTEXT_URL", "v")
+
+        # Must not raise; must fall back to the "no siblings" path.
+        cfg = ConfigManager(tmp_path, "testext")._get_env_config()
+        assert cfg == {"url": "v"}

tests/test_github_http.py

@@ -152,6 +152,44 @@ class TestResolveGitHubReleaseAssetApiUrl:
         )
         assert result is None
 
+    def test_metadata_lookup_is_bounded_and_redirect_validated(self):
+        """Release metadata reads stay bounded and use the caller's policy."""
+        captured = {}
+
+        class OversizedResponse:
+            def read(self, amount=None):
+                captured["read_amount"] = amount
+                return b"x" * amount
+
+            def __enter__(self):
+                return self
+
+            def __exit__(self, *args):
+                return False
+
+        def redirect_validator(old_url, new_url):
+            return None
+
+        def fake_open(
+            url,
+            timeout=None,
+            extra_headers=None,
+            redirect_validator=None,
+        ):
+            captured["redirect_validator"] = redirect_validator
+            return OversizedResponse()
+
+        result = resolve_github_release_asset_api_url(
+            "https://github.com/org/repo/releases/download/v1/pack.zip",
+            fake_open,
+            redirect_validator=redirect_validator,
+            max_metadata_bytes=8,
+        )
+
+        assert result is None
+        assert captured["read_amount"] == 9
+        assert captured["redirect_validator"] is redirect_validator
+
     def test_tag_with_special_characters_is_url_encoded(self):
         """Tags with reserved characters (e.g. '/') are encoded in the API URL."""
         captured_urls = []

tests/test_merge.py

@@ -10,12 +10,12 @@ def test_merge_json_files_type_mismatch_preservation(tmp_path):
     existing_file = tmp_path / "settings.json"
     # User might have overridden a setting with a simple string or different type
     existing_file.write_text('{"chat.editor.fontFamily": "CustomFont"}')
-    
+
     # Template might expect a dict for the same key (hypothetically)
     new_settings = {
         "chat.editor.fontFamily": {"font": "TemplateFont"}
     }
-    
+
     merged = merge_json_files(existing_file, new_settings)
     # Result is None because user settings were preserved and nothing else changed
     assert merged is None
@@ -32,7 +32,7 @@ def test_merge_json_files_deep_nesting(tmp_path):
         }
     }
     """)
-    
+
     new_settings = {
         "a": {
             "b": {
@@ -41,7 +41,7 @@ def test_merge_json_files_deep_nesting(tmp_path):
             "e": 3      # New mid-level key
         }
     }
-    
+
     merged = merge_json_files(existing_file, new_settings)
     assert merged["a"]["b"]["c"] == 1
     assert merged["a"]["b"]["d"] == 2
@@ -51,7 +51,7 @@ def test_merge_json_files_empty_existing(tmp_path):
     """Merging into an empty/new file."""
     existing_file = tmp_path / "empty.json"
     existing_file.write_text("{}")
-    
+
     new_settings = {"a": 1}
     merged = merge_json_files(existing_file, new_settings)
     assert merged == {"a": 1}
@@ -74,7 +74,7 @@ def test_merge_vscode_realistic_scenario(tmp_path):
         } // User comment
     }
     """)
-    
+
     template_settings = {
         "chat.promptFilesRecommendations": {
             "speckit.specify": True,
@@ -84,14 +84,14 @@ def test_merge_vscode_realistic_scenario(tmp_path):
             ".specify/scripts/bash/": True
         }
     }
-    
+
     merged = merge_json_files(existing_file, template_settings)
-    
+
     # Check preservation
     assert merged["editor.fontSize"] == 12
     assert merged["files.exclude"]["**/.git"] is True
     assert merged["chat.promptFilesRecommendations"]["existing.tool"] is True
-    
+
     # Check additions
     assert merged["chat.promptFilesRecommendations"]["speckit.specify"] is True
     assert merged["chat.tools.terminal.autoApprove"][".specify/scripts/bash/"] is True
@@ -104,7 +104,7 @@ def test_merge_json_files_with_bom(tmp_path):
     content = '{"a": 1}'
     # Prepend UTF-8 BOM
     existing_file.write_bytes(b'\xef\xbb\xbf' + content.encode('utf-8'))
-    
+
     new_settings = {"b": 2}
     merged = merge_json_files(existing_file, new_settings)
     assert merged == {"a": 1, "b": 2}
@@ -113,7 +113,7 @@ def test_merge_json_files_not_a_dictionary_template(tmp_path):
     """If for some reason new_content is not a dict, PRESERVE existing settings by returning None."""
     existing_file = tmp_path / "ok.json"
     existing_file.write_text('{"a": 1}')
-    
+
     # Secure fallback: return None to skip writing and avoid clobbering
     assert merge_json_files(existing_file, ["not", "a", "dict"]) is None
 
@@ -121,7 +121,7 @@ def test_merge_json_files_unparseable_existing(tmp_path):
     """If the existing file is unparseable JSON, return None to avoid overwriting it."""
     bad_file = tmp_path / "bad.json"
     bad_file.write_text('{"a": 1, missing_value}') # Invalid JSON
-    
+
     assert merge_json_files(bad_file, {"b": 2}) is None
 
 
@@ -129,11 +129,11 @@ def test_merge_json_files_list_preservation(tmp_path):
     """Verify that existing list values are preserved and NOT merged or overwritten."""
     existing_file = tmp_path / "list.json"
     existing_file.write_text('{"my.list": ["user_item"]}')
-    
+
     template_settings = {
         "my.list": ["template_item"]
     }
-    
+
     merged = merge_json_files(existing_file, template_settings)
     # The polite merge policy says: keep existing values if they exist and aren't both dicts.
     # Since nothing changed, it returns None.
@@ -143,12 +143,12 @@ def test_merge_json_files_no_changes(tmp_path):
     """If the merge doesn't introduce any new keys or changes, return None to skip rewrite."""
     existing_file = tmp_path / "no_change.json"
     existing_file.write_text('{"a": 1, "b": {"c": 2}}')
-    
+
     template_settings = {
         "a": 1,          # Already exists
         "b": {"c": 2}    # Already exists nested
     }
-    
+
     # Should return None because result == existing
     assert merge_json_files(existing_file, template_settings) is None
 
@@ -156,11 +156,11 @@ def test_merge_json_files_type_mismatch_no_op(tmp_path):
     """If a key exists with different type and we preserve it, it might still result in no change."""
     existing_file = tmp_path / "mismatch_no_op.json"
     existing_file.write_text('{"a": "user_string"}')
-    
+
     template_settings = {
         "a": {"key": "template_dict"} # Mismatch, will be ignored
     }
-    
+
     # Should return None because we preserved the user's string and nothing else changed
     assert merge_json_files(existing_file, template_settings) is None
 

tests/test_presets.py

@@ -884,6 +884,186 @@ class TestPresetResolver:
         assert result is not None
         assert "Custom Spec Template" in result.read_text()
 
+    def _install_pack_with_manifest_file(self, project_dir, *, extra_file=False):
+        """Create a pack whose manifest declares a NON-convention file: path.
+
+        Returns the pack dir under the project. The declared file lives at
+        custom/spec.md (not the convention templates/spec-template.md).
+        """
+        presets_dir = project_dir / ".specify" / "presets"
+        pack_dir = presets_dir / "mypack"
+        (pack_dir / "custom").mkdir(parents=True)
+        (pack_dir / "custom" / "spec.md").write_text(
+            "# Manifest-declared Spec\n", encoding="utf-8"
+        )
+        if extra_file:
+            # An undeclared convention-path file the manifest points away from.
+            (pack_dir / "templates").mkdir()
+            (pack_dir / "templates" / "spec-template.md").write_text(
+                "# Stray Convention Spec\n", encoding="utf-8"
+            )
+        manifest = {
+            "schema_version": "1.0",
+            "preset": {
+                "id": "mypack",
+                "name": "My Pack",
+                "version": "1.0.0",
+                "description": "declares a non-convention file path",
+            },
+            "requires": {"speckit_version": ">=0.1.0"},
+            "provides": {
+                "templates": [
+                    {
+                        "type": "template",
+                        "name": "spec-template",
+                        "file": "custom/spec.md",
+                        "strategy": "replace",
+                    }
+                ]
+            },
+        }
+        with open(pack_dir / "preset.yml", "w") as f:
+            yaml.dump(manifest, f)
+        PresetRegistry(presets_dir).add(
+            "mypack", {"version": "1.0.0", "priority": 10}
+        )
+        return pack_dir
+
+    def test_resolve_uses_manifest_declared_file_path(self, project_dir):
+        """resolve() must honor a manifest-declared non-convention file: path.
+
+        Previously the tier-2 loop was convention-only, so it returned the
+        core template and resolve_with_source() misattributed source='core',
+        diverging from collect_all_layers()/resolve_content().
+        """
+        pack_dir = self._install_pack_with_manifest_file(project_dir)
+        resolver = PresetResolver(project_dir)
+
+        result = resolver.resolve("spec-template")
+        assert result == pack_dir / "custom" / "spec.md"
+        assert "Manifest-declared Spec" in result.read_text()
+
+        sourced = resolver.resolve_with_source("spec-template")
+        assert sourced is not None
+        assert "mypack" in sourced["source"]
+        # resolve() must agree with collect_all_layers()'s top layer.
+        layers = resolver.collect_all_layers("spec-template")
+        assert Path(layers[0]["path"]) == pack_dir / "custom" / "spec.md"
+
+    def test_resolve_manifest_file_wins_over_undeclared_convention_file(
+        self, project_dir
+    ):
+        """A stray convention-path file must not shadow the manifest's file:."""
+        pack_dir = self._install_pack_with_manifest_file(
+            project_dir, extra_file=True
+        )
+        resolver = PresetResolver(project_dir)
+        result = resolver.resolve("spec-template")
+        assert result == pack_dir / "custom" / "spec.md"
+        assert "Manifest-declared Spec" in result.read_text()
+
+    def test_resolve_skips_convention_when_manifest_file_missing(self, project_dir):
+        """When the manifest declares a file: that does not exist, resolve()
+        must NOT fall back to a convention file in the same pack (that would
+        mask a typo) — it skips the pack and resolves core instead."""
+        presets_dir = project_dir / ".specify" / "presets"
+        pack_dir = presets_dir / "mypack"
+        # Manifest declares custom/spec.md (MISSING); a convention file exists
+        # in the pack and must NOT be used.
+        (pack_dir / "templates").mkdir(parents=True)
+        (pack_dir / "templates" / "spec-template.md").write_text(
+            "# Stray Convention Spec\n", encoding="utf-8"
+        )
+        manifest = {
+            "schema_version": "1.0",
+            "preset": {
+                "id": "mypack",
+                "name": "My Pack",
+                "version": "1.0.0",
+                "description": "declares a missing file path",
+            },
+            "requires": {"speckit_version": ">=0.1.0"},
+            "provides": {
+                "templates": [
+                    {
+                        "type": "template",
+                        "name": "spec-template",
+                        "file": "custom/spec.md",
+                        "strategy": "replace",
+                    }
+                ]
+            },
+        }
+        with open(pack_dir / "preset.yml", "w") as f:
+            yaml.dump(manifest, f)
+        PresetRegistry(presets_dir).add(
+            "mypack", {"version": "1.0.0", "priority": 10}
+        )
+
+        resolver = PresetResolver(project_dir)
+        result = resolver.resolve("spec-template")
+        assert result is not None
+        content = result.read_text()
+        assert "Stray Convention Spec" not in content  # pack convention skipped
+        assert "Core Spec Template" in content  # fell through to core
+
+    def test_resolve_skips_convention_when_manifest_file_is_directory(
+        self, project_dir
+    ):
+        """When the manifest's file: path resolves to a DIRECTORY (not a regular
+        file), resolve()/collect_all_layers() must treat it as missing — exists()
+        would accept it and downstream read_text() on a directory would crash.
+        The pack is skipped (no convention fallback), so core wins."""
+        presets_dir = project_dir / ".specify" / "presets"
+        pack_dir = presets_dir / "mypack"
+        # Declared file: custom/spec.md is created as a DIRECTORY.
+        (pack_dir / "custom" / "spec.md").mkdir(parents=True)
+        # A convention file also exists and must NOT be used.
+        (pack_dir / "templates").mkdir(parents=True)
+        (pack_dir / "templates" / "spec-template.md").write_text(
+            "# Stray Convention Spec\n", encoding="utf-8"
+        )
+        manifest = {
+            "schema_version": "1.0",
+            "preset": {
+                "id": "mypack",
+                "name": "My Pack",
+                "version": "1.0.0",
+                "description": "declares a file: that is actually a directory",
+            },
+            "requires": {"speckit_version": ">=0.1.0"},
+            "provides": {
+                "templates": [
+                    {
+                        "type": "template",
+                        "name": "spec-template",
+                        "file": "custom/spec.md",
+                        "strategy": "replace",
+                    }
+                ]
+            },
+        }
+        with open(pack_dir / "preset.yml", "w") as f:
+            yaml.dump(manifest, f)
+        PresetRegistry(presets_dir).add(
+            "mypack", {"version": "1.0.0", "priority": 10}
+        )
+
+        resolver = PresetResolver(project_dir)
+        result = resolver.resolve("spec-template")
+        assert result is not None
+        assert result.is_file()  # never a directory
+        content = result.read_text()
+        assert "Stray Convention Spec" not in content  # pack convention skipped
+        assert "Core Spec Template" in content  # fell through to core
+        # collect_all_layers() must agree: the directory is not a layer.
+        layers = resolver.collect_all_layers("spec-template")
+        assert all(Path(layer["path"]).is_file() for layer in layers)
+        assert all(
+            Path(layer["path"]) != pack_dir / "custom" / "spec.md"
+            for layer in layers
+        )
+
     def test_resolve_override_takes_priority_over_pack(self, project_dir, pack_dir):
         """Test that overrides take priority over installed packs."""
         # Install the pack
@@ -2620,7 +2800,7 @@ class TestSelfTestPreset:
         assert manifest.id == "self-test"
         assert manifest.name == "Self-Test Preset"
         assert manifest.version == "1.0.0"
-        assert len(manifest.templates) == 8  # 6 templates + 2 commands
+        assert len(manifest.templates) == 7  # 5 templates + 2 commands
 
     def test_self_test_provides_all_core_templates(self):
         """Verify the self-test preset provides an override for every core template."""
@@ -3663,6 +3843,8 @@ class TestPresetSkills:
 
         extension_dir = project_dir / ".specify" / "extensions" / "fakeext"
         (extension_dir / "commands").mkdir(parents=True, exist_ok=True)
+        (extension_dir / "agents" / "control").mkdir(parents=True, exist_ok=True)
+        (extension_dir / "agents" / "control" / "commander.md").write_text("# Commander\n")
         (extension_dir / "commands" / "cmd.md").write_text(
             "---\n"
             "description: Extension fakeext cmd\n"
@@ -3671,6 +3853,7 @@ class TestPresetSkills:
             "---\n\n"
             "extension:fakeext\n"
             "Run {SCRIPT}\n"
+            "Read agents/control/commander.md for context.\n"
         )
         extension_manifest = {
             "schema_version": "1.0",
@@ -3736,8 +3919,92 @@ class TestPresetSkills:
         assert "source: extension:fakeext" in content
         assert "extension:fakeext" in content
         assert '.specify/scripts/bash/setup-plan.sh --json "$ARGUMENTS"' in content
+        # Extension-relative subdir references must resolve to their
+        # installed location on restore too (#2101), not just on first
+        # registration.
+        assert ".specify/extensions/fakeext/agents/control/commander.md" in content
+        assert "Read agents/control" not in content
         assert "# Fakeext Cmd Skill" in content
 
+    def test_skill_composed_over_extension_base_rewrites_subdir_paths(
+        self, project_dir, temp_dir
+    ):
+        """When a preset composes (append) over an extension-provided base
+        command, the resulting skill (read from the .composed output) must
+        still resolve the extension's own subdir references (#2101), not
+        just when the extension wins outright (replace)."""
+        self._write_init_options(project_dir, ai="codex")
+        skills_dir = project_dir / ".agents" / "skills"
+        self._create_skill(skills_dir, "speckit-fakeext-cmd", body="original extension skill")
+
+        extension_dir = project_dir / ".specify" / "extensions" / "fakeext"
+        (extension_dir / "commands").mkdir(parents=True, exist_ok=True)
+        (extension_dir / "agents" / "control").mkdir(parents=True, exist_ok=True)
+        (extension_dir / "agents" / "control" / "commander.md").write_text("# Commander\n")
+        (extension_dir / "commands" / "cmd.md").write_text(
+            "---\ndescription: Extension fakeext cmd\n---\n\n"
+            "Read agents/control/commander.md for context.\n"
+        )
+        extension_manifest = {
+            "schema_version": "1.0",
+            "extension": {
+                "id": "fakeext",
+                "name": "Fake Extension",
+                "version": "1.0.0",
+                "description": "Test",
+            },
+            "requires": {"speckit_version": ">=0.1.0"},
+            "provides": {
+                "commands": [
+                    {
+                        "name": "speckit.fakeext.cmd",
+                        "file": "commands/cmd.md",
+                        "description": "Fake extension command",
+                    }
+                ]
+            },
+        }
+        with open(extension_dir / "extension.yml", "w") as f:
+            yaml.dump(extension_manifest, f)
+
+        preset_dir = temp_dir / "ext-base-append-skill"
+        preset_dir.mkdir()
+        (preset_dir / "commands").mkdir()
+        (preset_dir / "commands" / "speckit.fakeext.cmd.md").write_text(
+            "---\ndescription: Preset overlay\n---\n\n## Extra\n"
+        )
+        preset_manifest = {
+            "schema_version": "1.0",
+            "preset": {
+                "id": "ext-base-append-skill",
+                "name": "Ext Base Append Skill",
+                "version": "1.0.0",
+                "description": "Test",
+            },
+            "requires": {"speckit_version": ">=0.1.0"},
+            "provides": {
+                "templates": [
+                    {
+                        "type": "command",
+                        "name": "speckit.fakeext.cmd",
+                        "file": "commands/speckit.fakeext.cmd.md",
+                        "strategy": "append",
+                    }
+                ]
+            },
+        }
+        with open(preset_dir / "preset.yml", "w") as f:
+            yaml.dump(preset_manifest, f)
+
+        manager = PresetManager(project_dir)
+        manager.install_from_directory(preset_dir, "0.1.5")
+
+        skill_file = skills_dir / "speckit-fakeext-cmd" / "SKILL.md"
+        content = skill_file.read_text()
+        assert ".specify/extensions/fakeext/agents/control/commander.md" in content
+        assert "Read agents/control" not in content
+        assert "## Extra" in content
+
     def test_preset_remove_skips_skill_dir_without_skill_file(self, project_dir, temp_dir):
         """Preset removal should not delete arbitrary directories missing SKILL.md."""
         self._write_init_options(project_dir, ai="codex")
@@ -4060,6 +4327,40 @@ class TestPresetSetPriority:
         plain = strip_ansi(result.output)
         assert "already has priority 5" in plain
 
+    def test_set_priority_repairs_corrupted_bool(self, project_dir, pack_dir):
+        """A corrupted boolean priority must be repaired, not skipped.
+
+        ``isinstance(True, int)`` is True and ``True == 1`` in Python, so a
+        stored ``True`` priority would short-circuit the ``already has
+        priority 1`` skip path and never get rewritten to a real int —
+        contradicting the comment that promises corrupted values are
+        repaired. The guard must exclude bools (like normalize_priority).
+        """
+        from typer.testing import CliRunner
+        from unittest.mock import patch
+        from specify_cli import app
+
+        runner = CliRunner()
+
+        manager = PresetManager(project_dir)
+        manager.install_from_directory(pack_dir, "0.1.5", priority=5)
+        # Inject a corrupted boolean priority (True == 1).
+        manager.registry.update("test-pack", {"priority": True})
+
+        with patch.object(Path, "cwd", return_value=project_dir):
+            result = runner.invoke(app, ["preset", "set-priority", "test-pack", "1"])
+
+        assert result.exit_code == 0, result.output
+        plain = strip_ansi(result.output)
+        # The corrupted bool must be repaired, not reported as already-set.
+        assert "already has priority" not in plain
+        assert "priority changed" in plain
+
+        # The stored value is now a real int, not a bool.
+        reloaded = PresetManager(project_dir).registry.get("test-pack")
+        assert reloaded["priority"] == 1
+        assert not isinstance(reloaded["priority"], bool)
+
     def test_set_priority_invalid_value(self, project_dir, pack_dir):
         """Test set-priority rejects invalid priority values."""
         from typer.testing import CliRunner
@@ -4715,26 +5016,13 @@ class TestPresetAddFromUrlResolution:
 
         captured_urls = []
 
-        class FakeResponse:
-            def __init__(self, data):
-                self._data = data
-
-            def read(self):
-                return self._data
-
-            def __enter__(self):
-                return self
-
-            def __exit__(self, *a):
-                return False
-
         def fake_open_url(url, timeout=None, extra_headers=None, redirect_validator=None):
             captured_urls.append((url, extra_headers))
             if "releases/tags/" in url:
-                return FakeResponse(json.dumps({
+                return io.BytesIO(json.dumps({
                     "assets": [{"name": "preset.zip", "url": "https://api.github.com/repos/org/repo/releases/assets/42"}]
                 }).encode())
-            return FakeResponse(zip_bytes)
+            return io.BytesIO(zip_bytes)
 
         runner = CliRunner()
         with patch.object(Path, "cwd", return_value=project_dir), \
@@ -4773,22 +5061,9 @@ class TestPresetAddFromUrlResolution:
 
         captured_urls = []
 
-        class FakeResponse:
-            def __init__(self, data):
-                self._data = data
-
-            def read(self):
-                return self._data
-
-            def __enter__(self):
-                return self
-
-            def __exit__(self, *a):
-                return False
-
         def fake_open_url(url, timeout=None, extra_headers=None, redirect_validator=None):
             captured_urls.append((url, extra_headers))
-            return FakeResponse(zip_bytes)
+            return io.BytesIO(zip_bytes)
 
         runner = CliRunner()
         with patch.object(Path, "cwd", return_value=project_dir), \
@@ -4830,26 +5105,13 @@ class TestPresetAddFromUrlResolution:
 
         captured_urls = []
 
-        class FakeResponse:
-            def __init__(self, data):
-                self._data = data
-
-            def read(self):
-                return self._data
-
-            def __enter__(self):
-                return self
-
-            def __exit__(self, *a):
-                return False
-
         def fake_open_url(url, timeout=None, extra_headers=None, redirect_validator=None):
             captured_urls.append((url, extra_headers))
             if "releases/tags/" in url:
-                return FakeResponse(json.dumps({
+                return io.BytesIO(json.dumps({
                     "assets": [{"name": "preset.zip", "url": "https://ghes.example/api/v3/repos/org/repo/releases/assets/42"}]
                 }).encode())
-            return FakeResponse(zip_bytes)
+            return io.BytesIO(zip_bytes)
 
         runner = CliRunner()
         with patch.object(Path, "cwd", return_value=project_dir), \
@@ -5938,6 +6200,86 @@ class TestResolveContent:
         content = resolver.resolve_content("spec-template")
         assert content == "# Replaced content\n"
 
+    @pytest.mark.parametrize("strategy", ["append", "prepend", "wrap"])
+    def test_resolve_content_rewrites_extension_base_subdir_paths(
+        self, project_dir, temp_dir, strategy
+    ):
+        """Composing over an extension-provided base command must resolve the
+        extension's own subdir references (agents/, knowledge-base/) to their
+        installed location (#2101), not just when the extension wins outright.
+        """
+        extension_dir = project_dir / ".specify" / "extensions" / "fakeext"
+        (extension_dir / "commands").mkdir(parents=True, exist_ok=True)
+        (extension_dir / "agents" / "control").mkdir(parents=True, exist_ok=True)
+        (extension_dir / "agents" / "control" / "commander.md").write_text("# Commander\n")
+        (extension_dir / "commands" / "cmd.md").write_text(
+            "---\ndescription: Extension fakeext cmd\n---\n\n"
+            "Read agents/control/commander.md for context.\n"
+        )
+        extension_manifest = {
+            "schema_version": "1.0",
+            "extension": {
+                "id": "fakeext",
+                "name": "Fake Extension",
+                "version": "1.0.0",
+                "description": "Test",
+            },
+            "requires": {"speckit_version": ">=0.1.0"},
+            "provides": {
+                "commands": [
+                    {
+                        "name": "speckit.fakeext.cmd",
+                        "file": "commands/cmd.md",
+                        "description": "Fake extension command",
+                    }
+                ]
+            },
+        }
+        with open(extension_dir / "extension.yml", "w") as f:
+            yaml.dump(extension_manifest, f)
+
+        preset_dir = temp_dir / f"ext-base-{strategy}"
+        preset_dir.mkdir()
+        (preset_dir / "commands").mkdir()
+        overlay_body = (
+            "{CORE_TEMPLATE}\n## Extra\n" if strategy == "wrap" else "## Extra\n"
+        )
+        (preset_dir / "commands" / "speckit.fakeext.cmd.md").write_text(
+            f"---\ndescription: Preset overlay\n---\n\n{overlay_body}"
+        )
+        preset_manifest = {
+            "schema_version": "1.0",
+            "preset": {
+                "id": f"ext-base-{strategy}",
+                "name": "Ext Base",
+                "version": "1.0.0",
+                "description": "Test",
+            },
+            "requires": {"speckit_version": ">=0.1.0"},
+            "provides": {
+                "templates": [
+                    {
+                        "type": "command",
+                        "name": "speckit.fakeext.cmd",
+                        "file": "commands/speckit.fakeext.cmd.md",
+                        "strategy": strategy,
+                    }
+                ]
+            },
+        }
+        with open(preset_dir / "preset.yml", "w") as f:
+            yaml.dump(preset_manifest, f)
+
+        manager = PresetManager(project_dir)
+        manager.install_from_directory(preset_dir, "0.1.5")
+
+        resolver = PresetResolver(project_dir)
+        content = resolver.resolve_content("speckit.fakeext.cmd", "command")
+        assert content is not None
+        assert ".specify/extensions/fakeext/agents/control/commander.md" in content
+        assert "Read agents/control" not in content
+        assert "## Extra" in content
+
 
 class TestCollectAllLayers:
     """Test PresetResolver.collect_all_layers() method."""
@@ -6018,6 +6360,172 @@ class TestCollectAllLayers:
 class TestRemoveReconciliation:
     """Test that removing a preset re-registers the next layer's command."""
 
+    def test_remove_restores_extension_command_subdir_paths_for_non_skill_agent(
+        self, project_dir, temp_dir
+    ):
+        """When a preset override of an extension command is removed, the
+        reconciled non-skill-agent command file should have the extension's
+        own subdir references rewritten to their installed location (#2101),
+        not left as bare, unresolvable paths."""
+        gemini_dir = project_dir / ".gemini" / "commands"
+        gemini_dir.mkdir(parents=True)
+
+        extension_dir = project_dir / ".specify" / "extensions" / "fakeext"
+        (extension_dir / "commands").mkdir(parents=True, exist_ok=True)
+        (extension_dir / "agents" / "control").mkdir(parents=True, exist_ok=True)
+        (extension_dir / "agents" / "control" / "commander.md").write_text("# Commander\n")
+        (extension_dir / "commands" / "cmd.md").write_text(
+            "---\ndescription: Extension fakeext cmd\n---\n\n"
+            "Read agents/control/commander.md for context.\n"
+        )
+        extension_manifest = {
+            "schema_version": "1.0",
+            "extension": {
+                "id": "fakeext",
+                "name": "Fake Extension",
+                "version": "1.0.0",
+                "description": "Test",
+            },
+            "requires": {"speckit_version": ">=0.1.0"},
+            "provides": {
+                "commands": [
+                    {
+                        "name": "speckit.fakeext.cmd",
+                        "file": "commands/cmd.md",
+                        "description": "Fake extension command",
+                    }
+                ]
+            },
+        }
+        with open(extension_dir / "extension.yml", "w") as f:
+            yaml.dump(extension_manifest, f)
+
+        manager = PresetManager(project_dir)
+
+        preset_dir = temp_dir / "ext-cmd-override"
+        preset_dir.mkdir()
+        (preset_dir / "commands").mkdir()
+        (preset_dir / "commands" / "speckit.fakeext.cmd.md").write_text(
+            "---\ndescription: Override fakeext cmd\n---\n\npreset override content\n"
+        )
+        preset_manifest = {
+            "schema_version": "1.0",
+            "preset": {
+                "id": "ext-cmd-override",
+                "name": "Ext Cmd Override",
+                "version": "1.0.0",
+                "description": "Test",
+            },
+            "requires": {"speckit_version": ">=0.1.0"},
+            "provides": {
+                "templates": [
+                    {
+                        "type": "command",
+                        "name": "speckit.fakeext.cmd",
+                        "file": "commands/speckit.fakeext.cmd.md",
+                    }
+                ]
+            },
+        }
+        with open(preset_dir / "preset.yml", "w") as f:
+            yaml.dump(preset_manifest, f)
+
+        manager.install_from_directory(preset_dir, "0.1.5")
+
+        cmd_files = list(gemini_dir.glob("*fakeext*"))
+        assert cmd_files, "Command file should exist in gemini dir"
+        assert "preset override content" in cmd_files[0].read_text()
+
+        manager.remove("ext-cmd-override")
+
+        cmd_files = list(gemini_dir.glob("*fakeext*"))
+        assert cmd_files, "Command file should still exist after removal"
+        content = cmd_files[0].read_text()
+        assert "preset override content" not in content
+        assert ".specify/extensions/fakeext/agents/control/commander.md" in content
+        assert "Read agents/control" not in content
+
+    def test_install_composes_extension_command_and_rewrites_subdir_paths_for_non_skill_agent(
+        self, project_dir, temp_dir
+    ):
+        """When a preset overlays (append) an extension-provided base command,
+        the initial composed non-skill-agent command file must have the
+        extension's own subdir references rewritten to their installed
+        location (#2101), matching the live repro: extension body
+        'Read agents/control/commander.md', preset appends to
+        speckit.fakeext.cmd, generated Gemini content retains the bare path."""
+        gemini_dir = project_dir / ".gemini" / "commands"
+        gemini_dir.mkdir(parents=True)
+
+        extension_dir = project_dir / ".specify" / "extensions" / "fakeext"
+        (extension_dir / "commands").mkdir(parents=True, exist_ok=True)
+        (extension_dir / "agents" / "control").mkdir(parents=True, exist_ok=True)
+        (extension_dir / "agents" / "control" / "commander.md").write_text("# Commander\n")
+        (extension_dir / "commands" / "cmd.md").write_text(
+            "---\ndescription: Extension fakeext cmd\n---\n\n"
+            "Read agents/control/commander.md for context.\n"
+        )
+        extension_manifest = {
+            "schema_version": "1.0",
+            "extension": {
+                "id": "fakeext",
+                "name": "Fake Extension",
+                "version": "1.0.0",
+                "description": "Test",
+            },
+            "requires": {"speckit_version": ">=0.1.0"},
+            "provides": {
+                "commands": [
+                    {
+                        "name": "speckit.fakeext.cmd",
+                        "file": "commands/cmd.md",
+                        "description": "Fake extension command",
+                    }
+                ]
+            },
+        }
+        with open(extension_dir / "extension.yml", "w") as f:
+            yaml.dump(extension_manifest, f)
+
+        preset_dir = temp_dir / "ext-cmd-append"
+        preset_dir.mkdir()
+        (preset_dir / "commands").mkdir()
+        (preset_dir / "commands" / "speckit.fakeext.cmd.md").write_text(
+            "---\ndescription: Append fakeext cmd\n---\n\n## Extra\n"
+        )
+        preset_manifest = {
+            "schema_version": "1.0",
+            "preset": {
+                "id": "ext-cmd-append",
+                "name": "Ext Cmd Append",
+                "version": "1.0.0",
+                "description": "Test",
+            },
+            "requires": {"speckit_version": ">=0.1.0"},
+            "provides": {
+                "templates": [
+                    {
+                        "type": "command",
+                        "name": "speckit.fakeext.cmd",
+                        "file": "commands/speckit.fakeext.cmd.md",
+                        "strategy": "append",
+                    }
+                ]
+            },
+        }
+        with open(preset_dir / "preset.yml", "w") as f:
+            yaml.dump(preset_manifest, f)
+
+        manager = PresetManager(project_dir)
+        manager.install_from_directory(preset_dir, "0.1.5")
+
+        cmd_files = list(gemini_dir.glob("*fakeext*"))
+        assert cmd_files, "Command file should exist in gemini dir"
+        content = cmd_files[0].read_text()
+        assert ".specify/extensions/fakeext/agents/control/commander.md" in content
+        assert "Read agents/control" not in content
+        assert "## Extra" in content
+
     def test_remove_restores_lower_priority_command(
         self, project_dir, temp_dir, valid_pack_data
     ):