chore: bump version to 0.12.1

* chore: align CI Python matrix with devguide release lifecycle

Run the pytest matrix only on the bugfix (maintenance) releases — 3.13
and 3.14 — instead of 3.11/3.12/3.13, and point the ruff lint job at the
latest interpreter (3.14). The supported floor stays at requires-python
>= 3.11 (oldest non-EOL security release): older security versions are
supported by claim and fixed reactively rather than gated on a wide
per-commit matrix. Also add macos-latest to the OS matrix so macOS
regressions are caught.

Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: make bash scripts portable to bash 3.2 (macOS system /bin/bash)

Adding macos-latest to the CI matrix surfaced two pre-existing bash 3.2
incompatibilities (macOS ships bash 3.2 as /bin/bash):

1. update-agent-context.sh embedded Python heredocs inside $(...) command
   substitution. bash 3.2 mis-parses an apostrophe in a heredoc body
   nested in $(...), failing with "unexpected EOF while looking for
   matching `''". Removed the apostrophes from the affected $()-nested
   heredoc body and documented the constraint to prevent regressions.

2. create-new-feature-branch.sh and create-new-feature.sh used the
   bash 4+ ${word^^} uppercase parameter expansion, which errors as a
   "bad substitution" on bash 3.2 and caused short uppercase acronyms
   (e.g. "GO") to be dropped from derived branch names. Replaced with a
   portable `tr '[:lower:]' '[:upper:]'` pipeline.

Verified the full test suite passes under bash 3.2.57 and shellcheck
(--severity=error) is clean.

Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: address review feedback on bash 3.2 portability changes

- create-new-feature.sh: replace the non-portable `\b...\b` grep
  word-boundary (BSD grep treats `\b` as a backspace, so the acronym
  branch could silently fail) with `grep -qw`, matching its twin
  create-new-feature-branch.sh, and pipe the description via
  `printf '%s'` instead of `echo`.
- create-new-feature-branch.sh: switch the acronym check to
  `printf '%s'` as well so both twins are identical and avoid `echo`
  on user-provided text.
- update-agent-context.sh: reword the apostrophe-free self-seeding
  comment to be clearer and less easy to misread.

Verified under bash 3.2.57 (full bash-script suite green) and
shellcheck --severity=error.

Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

---------

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

.devcontainer/post-create.sh

@@ -56,7 +56,7 @@ run_command "npm install -g @jetbrains/junie-cli@latest"
 echo "✅ Done"
 
 echo -e "\n🤖 Installing Pi Coding Agent..."
-run_command "npm install -g @mariozechner/pi-coding-agent@latest"
+run_command "npm install -g @earendil-works/pi-coding-agent@latest"
 echo "✅ Done"
 
 echo -e "\n🤖 Installing Kiro CLI..."

.github/ISSUE_TEMPLATE/bundle_submission.yml

@@ -0,0 +1,293 @@
+name: Bundle Submission
+description: Submit your bundle metadata for community catalog validation
+title: "[Bundle]: Add "
+labels: ["enhancement", "needs-triage"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for contributing a bundle! This template captures metadata for maintainers to validate formatting, links, component resolution, and installation evidence. Maintainers do not audit, endorse, or support bundle code or installed components.
+
+        **Before submitting:**
+        - Review the [Bundles reference](https://github.com/github/spec-kit/blob/main/docs/reference/bundles.md)
+        - Ensure your bundle has a valid `bundle.yml` manifest
+        - Create a GitHub release with a versioned bundle artifact
+        - Test installation from a downloaded artifact: `specify bundle install ./your-bundle-1.0.0.zip`
+        - If you host a bundle catalog, test catalog installation with `specify bundle catalog add <catalog-url> --id <catalog-id> --policy install-allowed` and `specify bundle install <bundle-id>`
+        - If your bundle depends on components from non-default catalogs, document those catalog URLs and test installation from a clean project
+
+  - type: input
+    id: bundle-id
+    attributes:
+      label: Bundle ID
+      description: Unique bundle identifier; must start and end with a lowercase letter or digit and may contain lowercase letters, digits, dots, underscores, and hyphens between
+      placeholder: "e.g., security-governance-stack"
+    validations:
+      required: true
+
+  - type: input
+    id: bundle-name
+    attributes:
+      label: Bundle Name
+      description: Human-readable bundle name
+      placeholder: "e.g., Security Governance Stack"
+    validations:
+      required: true
+
+  - type: input
+    id: version
+    attributes:
+      label: Version
+      description: Semantic version number
+      placeholder: "e.g., 1.0.0"
+    validations:
+      required: true
+
+  - type: input
+    id: role
+    attributes:
+      label: Role or Team
+      description: Primary role, team, or persona this bundle provisions
+      placeholder: "e.g., security-engineer, product-manager, platform-team"
+    validations:
+      required: true
+
+  - type: textarea
+    id: description
+    attributes:
+      label: Description
+      description: Brief description of the stack this bundle installs
+      placeholder: Installs a security governance stack with compliance presets, review commands, and evidence workflows
+    validations:
+      required: true
+
+  - type: input
+    id: author
+    attributes:
+      label: Author
+      description: Your name or organization
+      placeholder: "e.g., Jane Doe or Acme Corp"
+    validations:
+      required: true
+
+  - type: input
+    id: repository
+    attributes:
+      label: Repository URL
+      description: GitHub repository URL for your bundle source
+      placeholder: "https://github.com/your-org/spec-kit-bundle-your-bundle"
+    validations:
+      required: true
+
+  - type: input
+    id: download-url
+    attributes:
+      label: Download URL
+      description: URL to the versioned bundle artifact generated by `specify bundle build`
+      placeholder: "https://github.com/your-org/spec-kit-bundle-your-bundle/releases/download/v1.0.0/your-bundle-1.0.0.zip"
+    validations:
+      required: true
+
+  - type: input
+    id: documentation
+    attributes:
+      label: Documentation URL
+      description: Link to documentation that explains what the bundle installs and how to use it
+      placeholder: "https://github.com/your-org/spec-kit-bundle-your-bundle/blob/main/README.md"
+    validations:
+      required: true
+
+  - type: input
+    id: license
+    attributes:
+      label: License
+      description: Open source license type
+      placeholder: "e.g., MIT, Apache-2.0"
+    validations:
+      required: true
+
+  - type: input
+    id: speckit-version
+    attributes:
+      label: Required Spec Kit Version
+      description: Minimum Spec Kit version required by the bundle
+      placeholder: "e.g., >=0.9.0"
+    validations:
+      required: true
+
+  - type: input
+    id: integration
+    attributes:
+      label: Integration Target (optional)
+      description: Integration ID if the bundle pins one; leave empty if integration-agnostic
+      placeholder: "e.g., claude, copilot, gemini"
+
+  - type: textarea
+    id: components-provided
+    attributes:
+      label: Components Provided
+      description: List the extensions, presets, workflows, and steps this bundle installs
+      placeholder: |
+        - extensions: sicario-guard@0.5.1
+        - presets: sicario-core@0.5.1, sicario-ai-governance@0.5.1
+        - workflows: evidence-review@1.0.0
+        - steps: threat-model
+    validations:
+      required: true
+
+  - type: textarea
+    id: required-catalogs
+    attributes:
+      label: Required Component Catalogs
+      description: List any non-default catalogs users must add before this bundle can resolve its components; enter "None" if every component resolves from built-in or bundled catalogs
+      placeholder: |
+        - Presets: https://github.com/your-org/your-bundle/releases/download/v1.0.0/presets.json
+        - Extensions: https://github.com/your-org/your-bundle/releases/download/v1.0.0/extensions.json
+    validations:
+      required: true
+
+  - type: textarea
+    id: tags
+    attributes:
+      label: Tags
+      description: 2-5 relevant tags (lowercase, separated by commas)
+      placeholder: "security, governance, compliance"
+    validations:
+      required: true
+
+  - type: textarea
+    id: features
+    attributes:
+      label: Key Features
+      description: List the main capabilities this bundle provides
+      placeholder: |
+        - Installs evidence-first security governance templates
+        - Adds automated bundle verification commands
+        - Pins all components to release-tested versions
+    validations:
+      required: true
+
+  - type: checkboxes
+    id: testing
+    attributes:
+      label: Testing Checklist
+      description: Confirm that your bundle has been tested
+      options:
+        - label: Validation succeeds with `specify bundle validate --path <bundle-directory>`
+          required: true
+        - label: Build succeeds with `specify bundle build --path <bundle-directory>` and produces the submitted artifact
+          required: true
+        - label: Bundle installs successfully from the built artifact
+          required: true
+        - label: The submitted distribution path was tested end to end, including bundle-ID installation from an install-allowed catalog when a catalog entry is proposed
+          required: true
+        - label: Installation was tested in a clean Spec Kit project
+          required: true
+        - label: Required component catalogs are documented and were included in testing, or no extra catalogs are required
+          required: true
+        - label: Documentation is complete and accurate
+          required: true
+
+  - type: checkboxes
+    id: requirements
+    attributes:
+      label: Submission Requirements
+      description: Verify your bundle meets all requirements
+      options:
+        - label: Valid `bundle.yml` manifest included
+          required: true
+        - label: README.md explains the bundle's intended role, installed components, and installation steps
+          required: true
+        - label: LICENSE file included
+          required: true
+        - label: GitHub release created with a version tag
+          required: true
+        - label: Bundle ID matches the manifest and follows naming conventions
+          required: true
+        - label: Every extension, preset, workflow, and step reference is pinned where the manifest requires a version
+          required: true
+
+  - type: textarea
+    id: testing-details
+    attributes:
+      label: Testing Details
+      description: Describe how you tested your bundle
+      placeholder: |
+        **Tested on:**
+        - macOS 15 with Spec Kit v0.9.0
+        - Ubuntu 24.04 with Spec Kit v0.9.0
+
+        **Test project:** [Link or description]
+
+        **Test scenarios:**
+        1. Added required catalogs
+        2. Validated bundle manifest
+        3. Built release artifact
+        4. Installed bundle in a clean project
+        5. Ran the installed commands or workflows
+    validations:
+      required: true
+
+  - type: textarea
+    id: example-usage
+    attributes:
+      label: Example Usage
+      description: Provide a simple example of installing and using your bundle
+      render: markdown
+      placeholder: |
+        ```bash
+        # Add any required component catalogs first
+        specify preset catalog add https://github.com/your-org/your-bundle/releases/download/v1.0.0/presets.json --name your-bundle --install-allowed
+        specify extension catalog add https://github.com/your-org/your-bundle/releases/download/v1.0.0/extensions.json --name your-bundle --install-allowed
+
+        # Install the downloaded bundle artifact
+        curl -L -o your-bundle-1.0.0.zip https://github.com/your-org/your-bundle/releases/download/v1.0.0/your-bundle-1.0.0.zip
+        specify bundle install ./your-bundle-1.0.0.zip
+
+        # Or test through an install-allowed bundle catalog
+        specify bundle catalog add https://github.com/your-org/your-bundle/releases/download/v1.0.0/bundles.json --id your-bundle-catalog --policy install-allowed
+        specify bundle install your-bundle
+        ```
+    validations:
+      required: true
+
+  - type: textarea
+    id: catalog-entry
+    attributes:
+      label: Proposed Catalog Entry
+      description: Provide the JSON entry that would appear under the top-level `bundles` object in a bundle catalog (helps reviewers)
+      render: json
+      placeholder: |
+        {
+          "your-bundle": {
+            "name": "Your Bundle",
+            "id": "your-bundle",
+            "version": "1.0.0",
+            "role": "security-engineer",
+            "description": "Brief description of the stack",
+            "author": "Your Name",
+            "license": "MIT",
+            "download_url": "https://github.com/your-org/your-bundle/releases/download/v1.0.0/your-bundle-1.0.0.zip",
+            "repository": "https://github.com/your-org/your-bundle",
+            "requires": {
+              "speckit_version": ">=0.9.0"
+            },
+            "provides": {
+              "extensions": 1,
+              "presets": 2,
+              "steps": 0,
+              "workflows": 1
+            },
+            "tags": ["security", "governance"],
+            "verified": false
+          }
+        }
+    validations:
+      required: true
+
+  - type: textarea
+    id: additional-context
+    attributes:
+      label: Additional Context
+      description: Any other information that would help reviewers
+      placeholder: Screenshots, demo videos, links to related projects, dependency-resolution notes, etc.

.github/workflows/publish-pypi.yml

@@ -35,7 +35,7 @@ jobs:
         uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
 
       - name: Set up Python
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
         with:
           python-version: "3.13"
 

.github/workflows/test.yml

@@ -19,9 +19,9 @@ jobs:
         uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
 
       - name: Set up Python
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
 
       - name: Run ruff check
         run: uvx ruff check src/
@@ -30,8 +30,8 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, windows-latest]
-        python-version: ["3.11", "3.12", "3.13"]
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ["3.13", "3.14"]
     steps:
       - name: Checkout
         uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
@@ -40,7 +40,7 @@ jobs:
         uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
         with:
           python-version: ${{ matrix.python-version }}
 

AGENTS.md

@@ -75,7 +75,6 @@ class WindsurfIntegration(MarkdownIntegration):
         "args": "$ARGUMENTS",
         "extension": ".md",
     }
-    context_file = ".windsurf/rules/specify-rules.md"
 ```
 
 **TOML agent (Gemini):**
@@ -101,7 +100,6 @@ class GeminiIntegration(TomlIntegration):
         "args": "{{args}}",
         "extension": ".toml",
     }
-    context_file = "GEMINI.md"
 ```
 
 **Skills agent (Codex):**
@@ -129,7 +127,6 @@ class CodexIntegration(SkillsIntegration):
         "args": "$ARGUMENTS",
         "extension": "/SKILL.md",
     }
-    context_file = "AGENTS.md"
 
     @classmethod
     def options(cls) -> list[IntegrationOption]:
@@ -150,7 +147,6 @@ class CodexIntegration(SkillsIntegration):
 | `key` | Class attribute | Unique identifier; for CLI-based integrations (`requires_cli: True`), must match the CLI executable name |
 | `config` | Class attribute (dict) | Agent metadata: `name`, `folder`, `commands_subdir`, `install_url`, `requires_cli` |
 | `registrar_config` | Class attribute (dict) | Command output config: `dir`, `format`, `args` placeholder, file `extension` |
-| `context_file` | Class attribute (str or None) | Path to agent context/instructions file (e.g., `"CLAUDE.md"`, `".github/copilot-instructions.md"`) |
 
 **Key design rule:** For CLI-based integrations (`requires_cli: True`), `key` must be the actual executable name (e.g., `"cursor-agent"` not `"cursor"`). This ensures `shutil.which(key)` works for CLI-tool checks without special-case mappings. IDE-based integrations (`requires_cli: False`) should use their canonical identifier (e.g., `"windsurf"`, `"copilot"`).
 
@@ -175,9 +171,11 @@ def _register_builtins() -> None:
 
 ### 4. Context file behavior
 
-Set `context_file` on the integration class. The base integration setup creates or updates the managed Spec Kit section in that file, and uninstall removes the managed section when appropriate.
+The Specify CLI carries **no agent-context state whatsoever**. Integration classes do **not** declare a `context_file`, and the CLI never creates, updates, removes, resolves, or migrates a context/instruction file (`CLAUDE.md`, `AGENTS.md`, `.github/copilot-instructions.md`, …). New integrations add nothing for context handling.
 
-The managed section is owned by the bundled `agent-context` extension (`extensions/agent-context/`). All configuration flows through the extension's own config file at `.specify/extensions/agent-context/agent-context-config.yml`:
+Managing the "Spec Kit" section in the context file is fully owned by the bundled `agent-context` extension (`extensions/agent-context/`), which is a **full opt-in**: `specify init` does not install it. A user adds/enables it through the standard extension verbs, after which the extension's own bundled scripts maintain the context section. When the extension is absent or disabled, nothing in Spec Kit touches the context file.
+
+The extension reads its own config file at `.specify/extensions/agent-context/agent-context-config.yml`:
 
 ```yaml
 # Path to the coding agent context file managed by this extension
@@ -189,10 +187,10 @@ context_markers:
   end: "<!-- SPECKIT END -->"
 ```
 
-- `context_file` is written automatically from the integration's class attribute when `specify init` or `specify integration use` is run.
-- `context_markers.{start,end}` defaults to `IntegrationBase.CONTEXT_MARKER_START` / `CONTEXT_MARKER_END`. Users who want custom markers edit `agent-context-config.yml` directly — both the Python layer (`upsert_context_section()` / `remove_context_section()`) and the bundled scripts (`extensions/agent-context/scripts/bash/update-agent-context.sh` and `.ps1`) read from this single source of truth.
+- The Specify CLI does **not** write this config. When `context_file` is empty, the extension's bundled scripts self-seed it by looking up the active integration's key in the extension's own `agent-context-defaults.json` map (`extensions/agent-context/scripts/bash/update-agent-context.sh` and `.ps1`). The CLI registry is never consulted — all agent→context-file knowledge lives inside the extension.
+- `context_markers.{start,end}` are read solely by the extension's scripts; they default to the Spec Kit markers shown above and can be customized by editing `agent-context-config.yml` directly.
 
-Users can opt out entirely with `specify extension disable agent-context`; while disabled, Spec Kit skips context-file creation, updates, and removal (the gates are inside `upsert_context_section()` and `remove_context_section()`).
+Existing projects created by older Spec Kit versions keep working: any previously written managed section or extension config is left intact and is only ever updated by the extension when run.
 
 Only add custom setup logic when the agent needs non-standard behavior. Integrations no longer require per-agent thin wrapper scripts or shared context-update dispatcher scripts — the `agent-context` extension is fully generic.
 
@@ -401,7 +399,6 @@ Implementation: Extends `YamlIntegration` (parallel to `TomlIntegration`):
 2. Extracts title and description from frontmatter
 3. Renders output as Goose recipe YAML (version, title, description, author, extensions, activities, prompt)
 4. Uses `yaml.safe_dump()` for header fields to ensure proper escaping
-5. Sets `context_file = "AGENTS.md"` so the base setup manages the Spec Kit context section there
 
 ## Branch Naming Convention
 
@@ -466,7 +463,7 @@ Disclosure is **continuous**, not a one-time event. A single AI-disclosure parag
 ## Common Pitfalls
 
 1. **Using shorthand keys for CLI-based integrations**: For CLI-based integrations (`requires_cli: True`), the `key` must match the executable name (e.g., `"cursor-agent"` not `"cursor"`). `shutil.which(key)` is used for CLI tool checks — mismatches require special-case mappings. IDE-based integrations (`requires_cli: False`) are not subject to this constraint.
-2. **Forgetting context configuration**: The bundled `agent-context` extension reads from `.specify/extensions/agent-context/agent-context-config.yml`. New integrations only need to set `context_file` on the class — markers and dispatcher scripts are managed centrally.
+2. **Reintroducing context handling into the CLI**: The opt-in `agent-context` extension owns everything about context files — including the per-agent default mapping in `agent-context-defaults.json`. Integration classes must **not** declare a `context_file`, and no CLI code should read, write, resolve, or migrate context files. All context-file logic lives in `.specify/extensions/agent-context/` and its bundled scripts.
 3. **Incorrect `requires_cli` value**: Set to `True` only for agents that have a CLI tool; set to `False` for IDE-based agents.
 4. **Wrong argument format**: Use `$ARGUMENTS` for Markdown agents, `{{args}}` for TOML agents.
 5. **Skipping registration**: The import and `_register()` call in `_register_builtins()` must both be added.

CHANGELOG.md

@@ -2,6 +2,85 @@
 
 <!-- insert new changelog below this comment -->
 
+## [0.12.1] - 2026-06-30
+
+### Changed
+
+- chore: align CI Python matrix with devguide lifecycle + fix bash 3.2 portability (#3244)
+- fix: stop check-prerequisites --paths-only from writing feature.json (#3025) (#3190)
+- docs: document integration catalog subcommands (#3206)
+- fix(scripts): use ASCII [OK] marker in initialize-repo.sh (parity with PowerShell twin) (#3231)
+- docs: document integration `search`/`info`/`scaffold` subcommands (#3174) (#3194)
+- docs: remove Cursor from `specify check` agent list (#3178) (#3193)
+- fix(goose): repoint install_url and docs to goose-docs.ai (#3171) (#3215)
+- fix(scripts): route 'Plan template not found' per --json in setup-plan.ps1 (parity with bash) (#3241)
+- fix(bundle): send command errors to stderr so --json stdout stays parseable (#3235)
+- chore: release 0.12.0, begin 0.12.1.dev0 development (#3243)
+
+## [0.12.0] - 2026-06-29
+
+### Changed
+
+- feat: make agent-context extension a full opt-in (#3097)
+- docs(workflows): add the built-in 'init' step type to the Step Types table (#3234)
+- fix(workflows): gate validate() must not crash on non-string options (#3233)
+- fix(workflows): make pipe-filter detection quote-aware in expressions (#3232)
+- fix(workflows): reject a fan-in wait_for that names an unknown step at validation (#3225)
+- fix(scripts): warn when spec template is missing in create-new-feature.ps1 (parity with bash) (#3230)
+- fix(scripts): count subdirectory-only dirs as non-empty in PowerShell (parity with bash) (#3137)
+- fix(scripts): drop HAS_GIT from PowerShell git-extension output (parity with bash) (#3195)
+- Update Product Spec Extension to v1.0.1 (#3226)
+- chore: release 0.11.10, begin 0.11.11.dev0 development (#3240)
+
+## [0.11.10] - 2026-06-29
+
+### Changed
+
+- fix(extensions): apply GHES auth and resolve release assets for `extension add --from` (#3217)
+- fix(pi): repoint install_url to @earendil-works/pi-coding-agent (#3169) (#3214)
+- fix(catalogs): reject host-less catalog URLs in base and preset validators (#3210)
+- fix: update CodeBuddy install docs URL (#3187)
+- fix(workflows): reject infinite number-input default instead of raising OverflowError (#3199)
+- fix(scripts): emit 'Copied plan template' status in setup-plan.ps1 (parity with bash) (#3198)
+- fix(workflows): make expression operator/literal parsing quote-aware (#3197)
+- fix(scripts): honor explicit -Number 0 in PowerShell create-new-feature (parity with bash) (#3196)
+- Add community bundle submission path (#3162)
+- Docs: Document /speckit.converge command (#3181)
+- chore: release 0.11.9, begin 0.11.10.dev0 development (#3189)
+
+## [0.11.9] - 2026-06-26
+
+### Changed
+
+- Docs: add cline and zcode to multi-install-safe table (#3180)
+- Docs: document missing flags --force and --refresh-shared-infra (#3179)
+- fix(claude): stop forking /speckit-analyze to prevent long-session freezes (#3188)
+- fix: derive plan path from feature.json in update-agent-context (#3069)
+- fix(catalog): companion → README docs, version-pinned download URL, v0.11.0, refreshed tags (#2954)
+- chore(deps): bump actions/setup-python from 6.2.0 to 6.3.0 (#3173)
+- Update SicarioSpec Core preset to v0.5.1 (#3165)
+- fix(extensions,presets,workflows): resolve private GHES release assets via /api/v3 (#3157)
+- Update preset composition strategy reference (#3143)
+- fix(scripts): keep PowerShell branch-name acronym match case-sensitive (parity with bash) (#3129)
+- fix(extensions): tell agent to run mandatory hooks, not just emit the directive (#2901)
+- Point sicario-core docs to preset README (#3120)
+- chore: release 0.11.8, begin 0.11.9.dev0 development (#3156)
+
+## [0.11.8] - 2026-06-24
+
+### Changed
+
+- docs: add SpecKit Assistant npm package to Community Friends (#3142)
+- Require preset-usage README with Spec Kit CLI syntax in preset submissions (#3104)
+- [extension] Update Jira Integration (Sync Engine) extension to v0.4.0 (#3152)
+- Add Spec Roadmap extension to community catalog (#3153)
+- feat(integration): update Kimi integration for Kimi Code CLI (#2979)
+- [extension] Add Golden Demo extension to community catalog (#3151)
+- docs: run /speckit.checklist after /speckit.plan in quickstart (#3108)
+- fix(workflows): preserve commas inside quoted list-literal elements (#3134)
+- ci: pin actions to commit SHAs and add shellcheck (#3126)
+- chore: release 0.11.7, begin 0.11.8.dev0 development (#3154)
+
 ## [0.11.7] - 2026-06-24
 
 ### Changed

README.md

@@ -134,13 +134,14 @@ Explore community-contributed resources on the [Spec Kit docs site](https://gith
 
 - [Extensions](https://github.github.io/spec-kit/community/extensions.html) — commands, hooks, and capabilities
 - [Presets](https://github.github.io/spec-kit/community/presets.html) — template and terminology overrides
+- [Bundles](https://github.github.io/spec-kit/community/bundles.html) — role and team stacks composed from existing components
 - [Walkthroughs](https://github.github.io/spec-kit/community/walkthroughs.html) — end-to-end SDD scenarios
 - [Friends](https://github.github.io/spec-kit/community/friends.html) — projects that extend or build on Spec Kit
 
 > [!NOTE]
 > Community contributions are independently created and maintained by their respective authors. Review source code before installation and use at your own discretion.
 
-Want to contribute? See the [Extension Publishing Guide](extensions/EXTENSION-PUBLISHING-GUIDE.md) or the [Presets Publishing Guide](presets/PUBLISHING.md).
+Want to contribute? See the [Extension Publishing Guide](extensions/EXTENSION-PUBLISHING-GUIDE.md), the [Presets Publishing Guide](presets/PUBLISHING.md), or the [Community Bundles guide](docs/community/bundles.md).
 
 ## 🤖 Supported AI Coding Agent Integrations
 
@@ -262,8 +263,10 @@ built-in). Each source carries an install policy: `install-allowed` sources can
 be installed from, while `discovery-only` sources are visible in `search`/`info`
 but refuse installation. Manage the stack with `specify bundle catalog list|add|remove`.
 
-Authors validate and package bundles locally — there is no first-class publish;
-distribution is hosting the built artifact and adding a catalog entry:
+Authors validate and package bundles locally. Distribution is hosting the built
+artifact and adding a catalog source; community bundle submissions use the
+[Bundle Submission](https://github.com/github/spec-kit/issues/new?template=bundle_submission.yml)
+issue template so required component catalogs and install evidence can be reviewed:
 
 ```bash
 specify bundle validate --path ./my-bundle      # structural + reference checks
@@ -403,7 +406,7 @@ specify init . --force --integration copilot
 specify init --here --force --integration copilot
 ```
 
-The CLI will check if you have Claude Code, Gemini CLI, Cursor CLI, Qwen CLI, opencode, Codex CLI, Qoder CLI, Tabnine CLI, Kiro CLI, Pi, Oh My Pi, Forge, Goose, Mistral Vibe, or ZCode installed. If you do not, or you prefer to get the templates without checking for the right tools, use `--ignore-agent-tools` with your command:
+The CLI will check that your selected agent's CLI tool is installed (for integrations that require a CLI), such as Claude Code, Gemini CLI, Qwen Code, opencode, Codex CLI, Qoder CLI, Tabnine CLI, Kiro CLI, Pi Coding Agent, Oh My Pi, Forge, Goose, Mistral Vibe, or ZCode. If you don't have the required tool installed, or you prefer to get the templates without checking for the right tools, use `--ignore-agent-tools` with your command:
 
 ```bash
 specify init <project_name> --integration copilot --ignore-agent-tools

docs/community/bundles.md

@@ -0,0 +1,53 @@
+# Community Bundles
+
+> [!NOTE]
+> Community bundles are independently created and maintained by their respective authors. Maintainers only verify that submission metadata is complete and correctly formatted — they do **not review, audit, endorse, or support the bundle code or the components it installs**. Review bundle manifests, component catalogs, and source repositories before installation and use at your own discretion.
+
+Bundles compose existing Spec Kit components — extensions, presets, workflows, and steps — into a single role or team stack. They are useful when a user should be able to install a tested set of components together instead of following several separate install commands.
+
+Accepted community bundle entries will be listed here once a community bundle catalog is available. To submit a bundle for review, file a [Bundle Submission](https://github.com/github/spec-kit/issues/new?template=bundle_submission.yml) issue.
+
+## What to Submit
+
+A bundle submission should include:
+
+- A public repository with a valid `bundle.yml` manifest.
+- A versioned GitHub release with a bundle artifact created by `specify bundle build`.
+- Documentation that explains the intended role, installed components, required catalogs, and expected workflow.
+- A proposed catalog entry with bundle metadata and component counts.
+- Test evidence from a clean Spec Kit project.
+
+## Component Resolution
+
+A bundle catalog entry describes where to download the bundle artifact, but the bundle's component references still need to resolve when a user installs it. References can resolve from bundled components, already installed components, or active extension, preset, workflow, and step catalogs.
+
+If your bundle depends on components that are not available from the default Spec Kit catalogs, include the required catalog URLs in the submission and in your README. Test the full install path from a clean project with those catalogs added before submitting.
+
+For example:
+
+```bash
+specify preset catalog add https://example.com/presets.json --name example-bundle --install-allowed
+specify extension catalog add https://example.com/extensions.json --name example-bundle --install-allowed
+curl -L -o example-bundle-1.0.0.zip https://example.com/example-bundle-1.0.0.zip
+specify bundle install ./example-bundle-1.0.0.zip
+
+# Or install by id from an install-allowed bundle catalog.
+specify bundle catalog add https://example.com/bundles.json --id example-bundle-catalog --policy install-allowed
+specify bundle install example-bundle
+```
+
+## Review Scope
+
+Maintainers check that:
+
+- The submission fields are complete and correctly formatted.
+- The release artifact and documentation URLs are reachable.
+- The repository contains a `bundle.yml` manifest.
+- The submission clearly identifies any required component catalogs.
+- The proposed catalog entry uses the expected bundle catalog entry shape.
+
+Maintainers do not audit the behavior of installed extensions, presets, workflows, steps, or scripts. Users should review those components before installing a community bundle.
+
+## Updating a Bundle
+
+To update a submitted bundle, file another [Bundle Submission](https://github.com/github/spec-kit/issues/new?template=bundle_submission.yml) issue with the new version, download URL, changed component list, and updated test evidence. Mention that the issue updates an existing bundle entry.

docs/community/overview.md

@@ -1,6 +1,6 @@
 # Community
 
-The Spec Kit community builds extensions, presets, walkthroughs, and companion projects that expand what you can do with Spec-Driven Development. All community contributions are independently created and maintained by their respective authors.
+The Spec Kit community builds extensions, presets, bundles, walkthroughs, and companion projects that expand what you can do with Spec-Driven Development. All community contributions are independently created and maintained by their respective authors.
 
 ## Extensions
 
@@ -14,6 +14,12 @@ Presets customize how Spec Kit behaves — overriding templates, commands, and t
 
 [Browse community presets →](presets.md)
 
+## Bundles
+
+Bundles compose extensions, presets, workflows, and steps into role or team stacks that can be installed together.
+
+[Browse community bundles →](bundles.md)
+
 ## Walkthroughs
 
 Step-by-step guides that show Spec-Driven Development in action across different scenarios, languages, and frameworks.

docs/community/presets.md

@@ -25,7 +25,7 @@ The following community-contributed presets customize how Spec Kit behaves — o
 | Pirate Speak (Full) | Transforms all Spec Kit output into pirate speak — specs become "Voyage Manifests", plans become "Battle Plans", tasks become "Crew Assignments" | 6 templates, 9 commands | — | [spec-kit-presets](https://github.com/mnriem/spec-kit-presets) |
 | Screenwriting | Spec-Driven Development for screenwriting/scriptwriting/tutorials: feature films, television (pilot, episode, limited series), and stage plays. Adapts the Spec Kit workflow to screenplay craft — slug lines, action lines, act breaks, beat sheets, and industry-standard pitch documents. Supports three-act, Save the Cat, TV pilot, network episode, cable/streaming episode, and stage-play structural frameworks. Export to Fountain, FTX, PDF | 26 templates, 32 commands, 1 script | — | [speckit-preset-screenwriting](https://github.com/adaumann/speckit-preset-screenwriting) |
 | Security Governance | Adds memory-safe-language preference, language-specific secure coding profiles, audit-ready Spec-Kit run evidence, ASVS verification, SBOM/AI-SBOM supply-chain transparency, CRA awareness, and regulatory applicability screening for NIS2, CRA, EU AI Act, and DORA | 14 templates, 3 commands | — | [spec-kit-preset-security-governance](https://github.com/hindermath/spec-kit-preset-security-governance) |
-| SicarioSpec Core | Evidence-first security operations governance that maps feature risk to controls, gates, evidence, owners, approval, and accepted-risk decisions. | 5 templates | — | [sicario-spec](https://github.com/dfirs1car1o/sicario-spec) |
+| 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) |
 | 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) |

docs/guides/evolving-specs.md

@@ -26,6 +26,7 @@ through the standard flow:
 2. Run `/speckit.plan` to define the implementation approach.
 3. Run `/speckit.tasks` to derive the work breakdown.
 4. Run `/speckit.implement` and review the resulting code and artifact diffs.
+5. Run `/speckit.converge` to verify completeness and generate tasks for remaining gaps. If tasks are appended, repeat `/speckit.implement` and `/speckit.converge` until the feature is fully complete.
 
 The previous feature directory remains intact for audit, comparison, or
 explaining how the project reached its current state. Use clear feature names or
@@ -50,6 +51,7 @@ spec:
 5. Run `/speckit.analyze` before implementation resumes to catch gaps between
    the spec, plan, and tasks.
 6. Run `/speckit.implement`, then review the code and artifact diffs together.
+7. Run `/speckit.converge` to assess completion and append any remaining work to `tasks.md`. If tasks are appended, repeat `/speckit.implement` and `/speckit.converge` until the feature is fully complete.
 
 Preserve important implementation rationale before replacing derived artifacts.
 If a plan or task list contains decisions that still matter, carry them forward

docs/installation.md

@@ -94,8 +94,15 @@ This helps verify you are running the official Spec Kit build from GitHub, not a
 After initialization, you should see the following commands available in your coding agent:
 
 - `/speckit.specify` - Create specifications
-- `/speckit.plan` - Generate implementation plans  
+- `/speckit.plan` - Generate implementation plans
 - `/speckit.tasks` - Break down into actionable tasks
+- `/speckit.implement` - Execute implementation tasks
+- `/speckit.analyze` - Validate cross-artifact consistency
+- `/speckit.clarify` - Identify and resolve ambiguities
+- `/speckit.checklist` - Generate quality checklists
+- `/speckit.constitution` - Create or update project principles
+- `/speckit.converge` - Assess codebase against artifacts and append remaining tasks
+- `/speckit.taskstoissues` - Convert tasks to issues
 
 Scripts are installed into a variant subdirectory matching the chosen script type:
 

docs/quickstart.md

@@ -13,10 +13,10 @@ This guide will help you get started with Spec-Driven Development using Spec Kit
 After installing Spec Kit and defining your project constitution, quick experiments can use the lean feature path: `/speckit.specify` -> `/speckit.plan` -> `/speckit.tasks` -> `/speckit.implement`. For production features or any work with meaningful ambiguity, treat `/speckit.clarify`, `/speckit.checklist`, and `/speckit.analyze` as regular quality gates:
 
 ```text
-/speckit.constitution -> /speckit.specify -> /speckit.clarify -> /speckit.plan -> /speckit.checklist -> /speckit.tasks -> /speckit.analyze -> /speckit.implement
+/speckit.constitution -> /speckit.specify -> /speckit.clarify -> /speckit.plan -> /speckit.checklist -> /speckit.tasks -> /speckit.analyze -> /speckit.implement -> /speckit.converge
 ```
 
-Use `/speckit.clarify` to reduce requirement ambiguity before planning, `/speckit.checklist` (after `/speckit.plan`) to generate quality checklists that validate requirements completeness, clarity, and consistency, and `/speckit.analyze` to check spec/plan/task consistency before implementation starts. You can repeat `/speckit.analyze` after implementation as an extra review, but keep the first analysis before `/speckit.implement` so gaps are caught while the plan and tasks can still be adjusted.
+Use `/speckit.clarify` to reduce requirement ambiguity before planning, `/speckit.checklist` (after `/speckit.plan`) to generate quality checklists that validate requirements completeness, clarity, and consistency, and `/speckit.analyze` to check spec/plan/task consistency before implementation starts. You can repeat `/speckit.analyze` after implementation as an extra review, but keep the first analysis before `/speckit.implement` so gaps are caught while the plan and tasks can still be adjusted. Finally, run `/speckit.converge` after implementation to verify all planned work is complete and generate tasks for any remaining gaps. If `/speckit.converge` appends new tasks, run `/speckit.implement` again (and converge again) until it reports that the feature has converged.
 
 ### Step 1: Install Specify
 
@@ -188,6 +188,14 @@ Finally, implement the solution:
 /speckit.implement
 ```
 
+### Step 8: Converge
+
+Run the `/speckit.converge` command after implementation to assess the current codebase against the feature's artifacts and append any remaining unbuilt work as new tasks to `tasks.md`. If the command appends new tasks, run `/speckit.implement` again to complete them, and repeat the converge step until the feature is fully complete.
+
+```bash
+/speckit.converge
+```
+
 > [!TIP]
 > **Phased Implementation**: For large projects like Taskify, consider implementing in phases (e.g., Phase 1: Basic project/task structure, Phase 2: Kanban functionality, Phase 3: Comments and assignments). This prevents context saturation and allows for validation at each stage.
 

docs/reference/authentication.md

@@ -69,6 +69,33 @@ Either `token` or `token_env` must be set for `bearer` and `basic-pat` schemes.
 }
 ```
 
+### GitHub Enterprise Server (GHES)
+
+To use a private catalog or extension hosted on a GitHub Enterprise Server
+instance, add a `github` entry listing your GHES host(s). The same entry
+authenticates both catalog JSON fetches **and** private release-asset
+downloads — Specify recognizes the listed hosts as GitHub Enterprise and
+resolves release downloads through the GHES REST API (`/api/v3`).
+
+```json
+{
+  "providers": [
+    {
+      "hosts": ["ghes.example.com", "raw.ghes.example.com", "codeload.ghes.example.com"],
+      "provider": "github",
+      "auth": "bearer",
+      "token_env": "GH_ENTERPRISE_TOKEN"
+    }
+  ]
+}
+```
+
+List the **bare** web host (e.g. `ghes.example.com`) — release-download URLs
+live there. If your instance uses subdomain isolation, also list the `raw.`
+and `codeload.` subdomains your catalog/extension URLs use. A
+`*.ghes.example.com` wildcard matches subdomains but **not** the bare host,
+so always include the bare host explicitly.
+
 ### Azure DevOps (`azure-devops`)
 
 | Scheme | Header | Use for |

docs/reference/bundles.md

@@ -119,6 +119,12 @@ specify bundle build
 
 Produces a single versioned, distributable `.zip` artifact from a bundle directory. The artifact embeds the manifest and can be installed directly with `specify bundle install <artifact.zip>`.
 
+## Publish a Bundle
+
+Bundle authors validate and package bundles locally, then host the generated artifact and catalog metadata where users can access it. A bundle catalog entry points at the bundle artifact, but the components declared inside `bundle.yml` still resolve through bundled components, installed components, or active extension, preset, workflow, and step catalogs.
+
+If your bundle references components from non-default catalogs, document those catalog URLs and test the install path from a clean project with those catalogs added. Community bundle submissions should include that dependency-resolution evidence in the [Bundle Submission](https://github.com/github/spec-kit/issues/new?template=bundle_submission.yml) issue.
+
 ## Manage Catalog Sources
 
 Bundles are discovered through a priority-ordered stack of catalog sources (project, user, and built-in scopes).

docs/reference/extensions.md

@@ -26,6 +26,7 @@ specify extension add <name>
 | --------------- | -------------------------------------------------------- |
 | `--dev`         | Install from a local directory (for development)         |
 | `--from <url>`  | Install from a custom URL instead of the catalog         |
+| `--force`       | Overwrite if already installed                           |
 | `--priority <N>`| Resolution priority (default: 10; lower = higher precedence) |
 
 Installs an extension from the catalog, a URL, or a local directory. Extension commands are automatically registered with the currently installed AI coding agent integration.

docs/reference/integrations.md

@@ -19,7 +19,7 @@ The Specify CLI supports a wide range of AI coding agents. When you run `specify
 | [Forge](https://forgecode.dev/)                                                      | `forge`          |                                                                                                                                           |
 | [Gemini CLI](https://github.com/google-gemini/gemini-cli)                            | `gemini`         |                                                                                                                                           |
 | [GitHub Copilot](https://code.visualstudio.com/)                                     | `copilot`        |                                                                                                                                           |
-| [Goose](https://block.github.io/goose/)                                              | `goose`          | Uses YAML recipe format in `.goose/recipes/`                                                                                              |
+| [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                                                                                                                           |
 | [iFlow CLI](https://docs.iflow.cn/en/cli/quickstart)                                 | `iflow`          |                                                                                                                                           |
@@ -54,6 +54,27 @@ Shows all available integrations, which one is currently installed, and whether
 When multiple integrations are installed, the list marks the default integration separately from the other installed integrations.
 The list also shows whether each built-in integration is declared multi-install safe.
 
+## Search Available Integrations
+
+```bash
+specify integration search [query]
+```
+
+| Option     | Description        |
+| ---------- | ------------------ |
+| `--tag`    | Filter by tag      |
+| `--author` | Filter by author   |
+
+Searches the active catalog stack for integrations matching the query. Without a query, lists all available integrations. Must be run inside a Spec Kit project.
+
+## Integration Info
+
+```bash
+specify integration info <integration_id>
+```
+
+Shows catalog details for a single integration, including its description, author, license, tags, source catalog, repository (when available), and whether it is currently active. Must be run inside a Spec Kit project.
+
 ## Install an Integration
 
 ```bash
@@ -100,6 +121,7 @@ specify integration switch <key>
 | ------------------------ | ------------------------------------------------------------------------ |
 | `--script sh\|ps`        | Script type: `sh` (bash/zsh) or `ps` (PowerShell)                        |
 | `--force`                | Force removal of modified files during uninstall; when the target is already installed, overwrite managed shared templates while changing the default |
+| `--refresh-shared-infra` | Also overwrite shared infrastructure files even if you customized them (otherwise customizations are preserved) |
 | `--integration-options`  | Options for the target integration when it is not already installed      |
 
 If the target integration is not already installed, equivalent to running `uninstall` followed by `install` in a single step. In this mode, `--force` controls whether modified files from the removed integration are deleted. If the target integration is already installed, `switch` only changes the default integration, like `use`; in this mode, `--force` controls whether managed shared templates are overwritten while the default changes. `--integration-options` is rejected for already-installed targets because changing integration options requires reinstalling managed files; run `upgrade <key> --integration-options ...` first, then `use <key>`.
@@ -151,6 +173,47 @@ is `null` when no installed integration set can be evaluated, such as when the
 integration state is missing, unreadable, lacks a valid recorded integration
 list, or records no installed integrations.
 
+## Catalog Management
+
+Integration catalogs control where the discovery commands (`search` and `info`) look for integrations. Catalogs are checked in priority order.
+
+### List Catalogs
+
+```bash
+specify integration catalog list
+```
+
+Shows the active catalog sources. Project-level sources (when configured) are removable by index; otherwise the active sources are shown as non-removable.
+
+### Add a Catalog
+
+```bash
+specify integration catalog add <url>
+```
+
+| Option          | Description                   |
+| --------------- | ----------------------------- |
+| `--name <name>` | Optional name for the catalog |
+
+Adds a custom catalog URL to the project's `.specify/integration-catalogs.yml`. The URL must use HTTPS (except `http://localhost`, `http://127.0.0.1`, or `http://[::1]` for local testing).
+
+### Remove a Catalog
+
+```bash
+specify integration catalog remove <index>
+```
+
+Removes a project catalog source by its 0-based index in `catalog list`.
+
+### Catalog Resolution Order
+
+Catalogs are resolved in this order (first match wins):
+
+1. **Environment variable** — `SPECKIT_INTEGRATION_CATALOG_URL` overrides all catalogs
+2. **Project config** — `.specify/integration-catalogs.yml`
+3. **User config** — `~/.specify/integration-catalogs.yml`
+4. **Built-in defaults** — official catalog + community catalog
+
 ## Integration-Specific Options
 
 Some integrations accept additional options via `--integration-options`:
@@ -166,6 +229,18 @@ Example:
 specify integration install generic --integration-options="--commands-dir .myagent/cmds"
 ```
 
+## Scaffold a New Integration
+
+```bash
+specify integration scaffold <key>
+```
+
+Creates a minimal built-in integration package and a matching test skeleton in the Spec Kit repository, then prints the next steps for wiring it up. Run this command from the Spec Kit repository root. The `<key>` must be lowercase kebab-case (for example, `my-agent`).
+
+| Option   | Description                                                       |
+| -------- | ---------------------------------------------------------------- |
+| `--type` | Scaffold template to use: `markdown` (default), `skills`, `toml`, or `yaml` |
+
 ## FAQ
 
 ### Can I install multiple integrations in the same project?
@@ -184,6 +259,7 @@ The currently declared multi-install safe integrations are:
 | --- | --------- |
 | `auggie` | `.augment/commands`, `.augment/rules/specify-rules.md` |
 | `claude` | `.claude/skills`, `CLAUDE.md` |
+| `cline` | `.clinerules/workflows`, `.clinerules/specify-rules.md` |
 | `codebuddy` | `.codebuddy/commands`, `CODEBUDDY.md` |
 | `codex` | `.agents/skills`, `AGENTS.md` |
 | `cursor-agent` | `.cursor/skills`, `.cursor/rules/specify-rules.mdc` |
@@ -199,6 +275,7 @@ The currently declared multi-install safe integrations are:
 | `tabnine` | `.tabnine/agent/commands`, `TABNINE.md` |
 | `trae` | `.trae/skills`, `.trae/rules/project_rules.md` |
 | `windsurf` | `.windsurf/workflows`, `.windsurf/rules/specify-rules.md` |
+| `zcode` | `.zcode/skills`, `ZCODE.md` |
 
 Integrations that share a context file or command directory with another integration, require dynamic install paths such as `--commands-dir`, or merge shared tool settings are not declared safe by default. They can still be installed alongside another integration with `--force`.
 

docs/reference/presets.md

@@ -137,9 +137,11 @@ catalogs:
 
 ## File Resolution
 
-Presets can provide command files, template files (like `plan-template.md`), and script files. These are resolved at runtime using a **replace** strategy — the first match in the priority stack wins and is used entirely. Each file is looked up independently, so different files can come from different layers.
+Presets can provide command files, template files (like `plan-template.md`), and script files. Each file name is evaluated independently against the priority stack, so different files can come from different layers.
 
-> **Note:** Additional composition strategies (`append`, `prepend`, `wrap`) are planned for a future release.
+Templates and scripts are looked up from the stack when Spec Kit needs them. Commands use the same stack for replacement and composition, but are materialized into detected agent directories instead of being re-resolved by agents. During preset install, Spec Kit registers command files for the preset being installed; post-install and post-removal reconciliation then recomputes and writes the effective command content for affected command names based on the active stack. Agents do not re-resolve the stack each time they run a command.
+
+By default, files use a **replace** strategy: the first match in the priority stack wins and is used entirely. Templates and commands can also use composition strategies: **prepend** places preset content before lower-priority content, **append** places it after lower-priority content, and **wrap** replaces `{CORE_TEMPLATE}` with lower-priority content. Scripts support **replace** and **wrap**; script wrappers use `$CORE_SCRIPT` as the placeholder.
 
 The resolution stack, from highest to lowest precedence:
 
@@ -148,8 +150,6 @@ The resolution stack, from highest to lowest precedence:
 3. **Installed extensions** — sorted by priority
 4. **Spec Kit core** — `.specify/templates/`
 
-Commands are registered at install time (not resolved through the stack at runtime).
-
 ### Resolution Stack
 
 ```mermaid
@@ -215,7 +215,7 @@ Run `specify preset resolve <name>` to trace the resolution stack and see which
 
 ### What's the difference between disabling and removing a preset?
 
-**Disabling** (`specify preset disable`) keeps the preset installed but excludes its files from the resolution stack. Commands the preset registered remain available in your AI coding agent. This is useful for temporarily testing behavior without a preset, or comparing output with and without it. Re-enable anytime with `specify preset enable`.
+**Disabling** (`specify preset disable`) keeps the preset installed but excludes it from future template and script resolution. Previously registered commands remain available in your AI coding agent until preset removal, so use removal when you need command changes to stop taking effect. Disabling is useful for temporarily testing template/script behavior without a preset, or comparing template/script output with and without it. Re-enable anytime with `specify preset enable`.
 
 **Removing** (`specify preset remove`) fully uninstalls the preset — deletes its files, unregisters its commands from your AI coding agent, and removes it from the registry.
 

docs/reference/workflows.md

@@ -262,6 +262,7 @@ specify workflow run speckit -i spec="Build a kanban board with drag-and-drop ta
 | `command`    | Invoke a Spec Kit command (e.g., `speckit.plan`) |
 | `prompt`     | Send an arbitrary prompt to the AI coding agent  |
 | `shell`      | Execute a shell command and capture output       |
+| `init`       | Bootstrap a project (like `specify init`)        |
 | `gate`       | Pause for human approval before continuing       |
 | `if`         | Conditional branching (then/else)                |
 | `switch`     | Multi-branch dispatch on an expression           |

docs/toc.yml

@@ -66,6 +66,8 @@
       href: community/extensions.md
     - name: Presets
       href: community/presets.md
+    - name: Bundles
+      href: community/bundles.md
     - name: Walkthroughs
       href: community/walkthroughs.md
     - name: Friends

extensions/agent-context/README.md

@@ -6,15 +6,17 @@ It owns the lifecycle of the managed section delimited by the configurable start
 
 ## Why an extension?
 
-Not every Spec Kit user wants Spec Kit to write into the coding agent's context file. Extracting this behavior into a dedicated extension lets users:
+Not every Spec Kit user wants Spec Kit to write into the coding agent's context file. Keeping this behavior in a dedicated, **opt-in** extension lets users:
 
-- **Opt out** entirely with `specify extension disable agent-context` — Spec Kit will then never create or modify the agent context file.
-- **Customize the markers** by editing `.specify/extensions/agent-context/agent-context-config.yml` — both the Python layer and the bundled scripts honor the same `context_markers` value.
+- **Choose whether to install it at all** — `specify init` does not install it. Add it explicitly when you want Spec Kit to manage the agent context file; if it is absent or disabled, Spec Kit never creates or modifies that file.
+- **Customize the markers** by editing `.specify/extensions/agent-context/agent-context-config.yml` — the bundled scripts honor the `context_markers` value.
 - **Synchronize multiple agent anchors** by setting `context_files` when a project intentionally uses more than one coding agent context file, such as `AGENTS.md` and `CLAUDE.md`.
-- **Refresh on demand** with `/speckit.agent-context.update`, or automatically through the hooks declared in `extension.yml` (`after_specify`, `after_plan`).
+- **Refresh on demand** by running the `speckit.agent-context.update` command in your agent, or automatically through the hooks declared in `extension.yml` (`after_specify`, `after_plan`). Invoke it using your agent's slash-command separator — `/speckit.agent-context.update` for dot-separator agents or `/speckit-agent-context-update` for hyphen-separator agents (e.g. Forge, Cline).
 
 ## Commands
 
+The command ID below is canonical. When invoking it as a slash command, use your agent's separator: `/speckit.agent-context.update` for dot-separator agents or `/speckit-agent-context-update` for hyphen-separator agents (e.g. Forge, Cline).
+
 | Command | Description |
 |---------|-------------|
 | `speckit.agent-context.update` | Refresh the managed section in the agent context file with the current plan path. |
@@ -40,7 +42,7 @@ context_markers:
   end: "<!-- SPECKIT END -->"
 ```
 
-- `context_file` — the project-relative path to the coding agent context file, written by `specify init` and `specify integration install`.
+- `context_file` — the project-relative path to the coding agent context file. When empty, the bundled update scripts self-seed it by looking up the active integration's key in this extension's own `agent-context-defaults.json` map. The Specify CLI is never consulted.
 - `context_files` — optional project-relative paths to multiple coding agent context files. When non-empty, the list takes precedence over `context_file`. Absolute paths, backslash separators, and `..` path segments are rejected.
 - `context_markers.start` / `.end` — the delimiters around the managed section. Edit these to use custom markers.
 
@@ -62,5 +64,4 @@ pip install pyyaml
 specify extension disable agent-context
 ```
 
-When disabled, Spec Kit skips context file creation, updates, and removal (the gates are inside `upsert_context_section()` and `remove_context_section()`).
-Disabled projects also ignore stale `context_files` values during command rendering so disabling the extension remains a complete opt-out.
+When disabled (or never installed), Spec Kit performs no agent context file creation, updates, or removal — the extension's bundled scripts are the only code that ever touches the managed section. The Specify CLI carries no agent-context state at all: it never reads this config, never resolves a context file, and the `__CONTEXT_FILE__` placeholder (if present in any template) is left untouched. All context-file knowledge — including the per-agent default mapping in `agent-context-defaults.json` — lives entirely within this extension, so disabling it is a complete opt-out.

extensions/agent-context/agent-context-defaults.json

@@ -0,0 +1,42 @@
+{
+  "_comment": "Default coding agent context file per integration, owned by the agent-context extension. Used to self-seed agent-context-config.yml when it declares no context_file/context_files. Keyed by the Spec Kit integration key recorded in .specify/init-options.json. This mapping is independent of the Specify CLI by design.",
+  "agents": {
+    "agy": "AGENTS.md",
+    "amp": "AGENTS.md",
+    "auggie": ".augment/rules/specify-rules.md",
+    "bob": "AGENTS.md",
+    "claude": "CLAUDE.md",
+    "cline": ".clinerules/specify-rules.md",
+    "codebuddy": "CODEBUDDY.md",
+    "codex": "AGENTS.md",
+    "copilot": ".github/copilot-instructions.md",
+    "cursor-agent": ".cursor/rules/specify-rules.mdc",
+    "devin": "AGENTS.md",
+    "firebender": ".firebender/rules/specify-rules.mdc",
+    "forge": "AGENTS.md",
+    "gemini": "GEMINI.md",
+    "generic": "AGENTS.md",
+    "goose": "AGENTS.md",
+    "hermes": "AGENTS.md",
+    "iflow": "IFLOW.md",
+    "junie": ".junie/AGENTS.md",
+    "kilocode": ".kilocode/rules/specify-rules.md",
+    "kimi": "AGENTS.md",
+    "kiro-cli": "AGENTS.md",
+    "lingma": ".lingma/rules/specify-rules.md",
+    "omp": "AGENTS.md",
+    "opencode": "AGENTS.md",
+    "pi": "AGENTS.md",
+    "qodercli": "QODER.md",
+    "qwen": "QWEN.md",
+    "roo": ".roo/rules/specify-rules.md",
+    "rovodev": "AGENTS.md",
+    "shai": "SHAI.md",
+    "tabnine": "TABNINE.md",
+    "trae": ".trae/rules/project_rules.md",
+    "vibe": "AGENTS.md",
+    "windsurf": ".windsurf/rules/specify-rules.md",
+    "zcode": "ZCODE.md",
+    "zed": "AGENTS.md"
+  }
+}

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

@@ -10,9 +10,9 @@
 #
 # Usage: update-agent-context.sh [plan_path]
 #
-# When `plan_path` is omitted, the script picks the most recently modified
-# `specs/*/plan.md` if any exist, otherwise emits the section without a
-# concrete plan path.
+# When `plan_path` is omitted, the script derives it from `.specify/feature.json`
+# (written by /speckit-specify). Falls back to the most recently modified
+# `specs/*/plan.md` only when feature.json is absent or its plan does not exist yet.
 
 set -euo pipefail
 
@@ -59,7 +59,14 @@ case "$(uname -s 2>/dev/null || true)" in
 esac
 
 # Parse extension config once; emit context files as JSON, followed by marker strings.
-if ! _raw_opts="$("$_python" - "$EXT_CONFIG" "$_case_insensitive_context_files" <<'PY'
+#
+# NOTE (bash 3.2 / macOS portability): the embedded Python heredocs below run
+# inside $(...) command substitution. bash 3.2 (the system /bin/bash on macOS)
+# mis-parses a single-quote/apostrophe in a heredoc body nested in $(...),
+# failing with "unexpected EOF while looking for matching `''". Keep these
+# $(...)-nested heredoc bodies free of apostrophes (use double quotes in Python
+# string literals and avoid contractions in comments).
+if ! _raw_opts="$("$_python" - "$EXT_CONFIG" "$_case_insensitive_context_files" "$PROJECT_ROOT" <<'PY'
 import json
 import sys
 try:
@@ -95,24 +102,67 @@ def get_str(obj, *keys):
 context_files = []
 seen_context_files = set()
 case_insensitive = sys.argv[2] == "1" or sys.platform.startswith(("win32", "cygwin"))
+def add_context_file(value):
+    if not isinstance(value, str):
+        return
+    candidate = value.strip()
+    if not candidate:
+        return
+    key = candidate.casefold() if case_insensitive else candidate
+    if key in seen_context_files:
+        return
+    context_files.append(candidate)
+    seen_context_files.add(key)
 raw_files = data.get("context_files")
 if isinstance(raw_files, list):
     for value in raw_files:
-        if not isinstance(value, str):
-            continue
-        candidate = value.strip()
-        if not candidate:
-            continue
-        key = candidate.casefold() if case_insensitive else candidate
-        if key in seen_context_files:
-            continue
-        context_files.append(candidate)
-        seen_context_files.add(key)
+        add_context_file(value)
 if not context_files:
-    raw_file = get_str(data, "context_file")
-    candidate = raw_file.strip()
-    if candidate:
-        context_files.append(candidate)
+    add_context_file(get_str(data, "context_file"))
+if not context_files:
+    # Self-seed: the agent-context extension manages its own lifecycle, so when
+    # its config declares no target, it derives one from the active integration
+    # recorded in init-options.json, mapped through the bundled
+    # agent-context-defaults.json file. This is independent of the Specify CLI
+    # by design; nothing here imports specify_cli.
+    project_root = sys.argv[3] if len(sys.argv) > 3 else "."
+    integration_key = ""
+    try:
+        with open(
+            f"{project_root}/.specify/init-options.json", "r", encoding="utf-8"
+        ) as fh:
+            opts = json.load(fh)
+        if isinstance(opts, dict):
+            value = opts.get("integration") or opts.get("ai") or ""
+            integration_key = value if isinstance(value, str) else ""
+    except Exception:
+        integration_key = ""
+    if integration_key:
+        defaults_path = (
+            f"{project_root}/.specify/extensions/agent-context/"
+            "agent-context-defaults.json"
+        )
+        mapping = {}
+        try:
+            with open(defaults_path, "r", encoding="utf-8") as fh:
+                loaded = json.load(fh)
+            agents = loaded.get("agents", {}) if isinstance(loaded, dict) else {}
+            mapping = agents if isinstance(agents, dict) else {}
+        except Exception:
+            print(
+                "agent-context: unable to read %s; cannot self-seed the context "
+                "file. Set context_file in the extension config." % defaults_path,
+                file=sys.stderr,
+            )
+            mapping = {}
+        add_context_file(mapping.get(integration_key, "") or "")
+        if not context_files:
+            print(
+                "agent-context: no default context file is known for integration "
+                "%s. Set context_file in the extension config to choose one."
+                % integration_key,
+                file=sys.stderr,
+            )
 print(json.dumps(context_files))
 print(get_str(data, "context_markers", "start"))
 print(get_str(data, "context_markers", "end"))
@@ -202,23 +252,78 @@ unset _cf_parts _seg
 
 PLAN_PATH="${1:-}"
 if [[ -z "$PLAN_PATH" ]]; then
-  # Pick the most recently modified plan.md one level deep (specs/<feature>/plan.md).
-  # Use find + sort by modification time to avoid ls/head fragility with
-  # spaces in paths or SIGPIPE from pipefail.
-  _plan_abs="$("$_python" - "$PROJECT_ROOT" <<'PY'
-import sys, os
+  # Prefer .specify/feature.json (written by /speckit-specify) over mtime heuristic.
+  _feature_json="$PROJECT_ROOT/.specify/feature.json"
+  if [[ -f "$_feature_json" ]]; then
+    _feature_dir="$("$_python" - "$_feature_json" <<'PY'
+import sys, json
+try:
+    with open(sys.argv[1], encoding="utf-8") as fh:
+        d = json.load(fh)
+    val = d.get("feature_directory", "")
+    print(val if isinstance(val, str) else "")
+except Exception:
+    print("")
+PY
+)"
+    # Normalize backslashes (written by PS on Windows) to forward slashes before path ops.
+    _feature_dir="$(printf '%s' "$_feature_dir" | tr '\\' '/')"
+    _feature_dir="${_feature_dir%/}"
+    if [[ -n "$_feature_dir" ]]; then
+      # feature_directory may be relative or absolute (absolute paths outside PROJECT_ROOT
+      # are preserved as-is by _persist_feature_json in common.sh).
+      # Also match drive-qualified paths (C:/...) written by PowerShell on Windows.
+      if [[ "$_feature_dir" == /* ]] || [[ "$_feature_dir" =~ ^[A-Za-z]:/ ]]; then
+        _candidate="$_feature_dir/plan.md"
+      else
+        _candidate="$PROJECT_ROOT/$_feature_dir/plan.md"
+      fi
+      if [[ -f "$_candidate" ]]; then
+        # Resolve symlinks before comparing so paths like /var/… vs /private/var/…
+        # (macOS) are treated as equivalent. Mirrors the mtime-fallback approach.
+        PLAN_PATH="$("$_python" - "$PROJECT_ROOT" "$_candidate" <<'PY'
+import sys
 from pathlib import Path
-specs = Path(sys.argv[1]) / "specs"
+root = Path(sys.argv[1]).resolve()
+cand = Path(sys.argv[2]).resolve()
+try:
+    print(cand.relative_to(root).as_posix())
+except ValueError:
+    # Outside project root: emit the resolved path in POSIX form.
+    # as_posix() converts backslashes correctly on native Windows Python.
+    print(cand.as_posix())
+PY
+)"
+      fi
+    fi
+  fi
+
+  # Fall back to mtime only when feature.json is absent or its plan does not exist yet.
+  # Python emits a project-relative POSIX path directly to avoid bash prefix-strip
+  # issues with backslash paths on Windows (Git bash / MSYS2).
+  if [[ -z "$PLAN_PATH" ]]; then
+    _plan_rel="$("$_python" - "$PROJECT_ROOT" <<'PY'
+import sys
+from pathlib import Path
+root = Path(sys.argv[1]).resolve()
+specs = root / "specs"
 plans = sorted(
     specs.glob("*/plan.md"),
     key=lambda p: p.stat().st_mtime,
     reverse=True,
 )
-print(plans[0] if plans else "")
+if plans:
+    try:
+        print(plans[0].relative_to(root).as_posix())
+    except ValueError:
+        print("")
+else:
+    print("")
 PY
 )"
-  if [[ -n "$_plan_abs" ]]; then
-    PLAN_PATH="${_plan_abs#"$PROJECT_ROOT/"}"
+    if [[ -n "$_plan_rel" ]]; then
+      PLAN_PATH="$_plan_rel"
+    fi
   fi
 fi
 
@@ -240,11 +345,58 @@ for CONTEXT_FILE in "${CONTEXT_FILES[@]}"; do
   mkdir -p "$(dirname "$CTX_PATH")"
 
   "$_python" - "$CTX_PATH" "$MARKER_START" "$MARKER_END" "$TMP_SECTION" <<'PY'
-import sys, os
+import os
+import re
+import sys
+
 ctx_path, start, end, section_path = sys.argv[1:5]
 with open(section_path, "r", encoding="utf-8") as fh:
     section = fh.read().rstrip("\n") + "\n"
 
+
+def ensure_mdc_frontmatter(content):
+    """Ensure ``.mdc`` content has YAML frontmatter with ``alwaysApply: true``.
+
+    Cursor only auto-loads ``.mdc`` rule files that carry frontmatter with
+    ``alwaysApply: true``. Prepend it when missing, or repair the value while
+    preserving any existing frontmatter comments/formatting.
+    """
+    leading_ws = len(content) - len(content.lstrip())
+    leading = content[:leading_ws]
+    stripped = content[leading_ws:]
+
+    if not stripped.startswith("---"):
+        return "---\nalwaysApply: true\n---\n\n" + content
+
+    match = re.match(
+        r"^(---[ \t]*\r?\n)(.*?)(\r?\n---[ \t]*)(\r?\n|$)(.*)",
+        stripped,
+        re.DOTALL,
+    )
+    if not match:
+        return "---\nalwaysApply: true\n---\n\n" + content
+
+    opening, fm_text, closing, sep, rest = match.groups()
+    newline = "\r\n" if "\r\n" in opening else "\n"
+
+    if re.search(r"(?m)^[ \t]*alwaysApply[ \t]*:[ \t]*true[ \t]*(?:#.*)?$", fm_text):
+        return content
+
+    if re.search(r"(?m)^[ \t]*alwaysApply[ \t]*:", fm_text):
+        fm_text = re.sub(
+            r"(?m)^([ \t]*)alwaysApply[ \t]*:.*?([ \t]*(?:#.*)?)$",
+            r"\1alwaysApply: true\2",
+            fm_text,
+            count=1,
+        )
+    elif fm_text.strip():
+        fm_text = fm_text + newline + "alwaysApply: true"
+    else:
+        fm_text = "alwaysApply: true"
+
+    return f"{leading}{opening}{fm_text}{closing}{sep}{rest}"
+
+
 if os.path.exists(ctx_path):
     with open(ctx_path, "r", encoding="utf-8-sig") as fh:
         content = fh.read()
@@ -274,6 +426,8 @@ else:
     new_content = section
 
 new_content = new_content.replace("\r\n", "\n").replace("\r", "\n")
+if ctx_path.casefold().endswith(".mdc"):
+    new_content = ensure_mdc_frontmatter(new_content)
 with open(ctx_path, "wb") as fh:
     fh.write(new_content.encode("utf-8"))
 PY

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

@@ -9,6 +9,10 @@
 #   .specify/extensions/agent-context/agent-context-config.yml
 #
 # Usage: update-agent-context.ps1 [plan_path]
+#
+# When `plan_path` is omitted, the script derives it from `.specify/feature.json`
+# (written by /speckit-specify). Falls back to the most recently modified
+# `specs/*/plan.md` only when feature.json is absent or its plan does not exist yet.
 
 [CmdletBinding()]
 param(
@@ -16,6 +20,56 @@ param(
     [string]$PlanPath
 )
 
+function Add-MdcFrontmatter {
+    <#
+        Ensure .mdc content has YAML frontmatter with alwaysApply: true.
+
+        Cursor only auto-loads .mdc rule files that carry frontmatter with
+        alwaysApply: true. Prepend it when missing, or repair the value while
+        preserving any existing frontmatter comments/formatting.
+    #>
+    param([Parameter(Mandatory = $true)][AllowEmptyString()][string]$Content)
+
+    $leading = ''
+    $stripped = $Content
+    $m = [regex]::Match($Content, '^\s*')
+    if ($m.Success) {
+        $leading = $m.Value
+        $stripped = $Content.Substring($m.Length)
+    }
+
+    if (-not $stripped.StartsWith('---')) {
+        return "---`nalwaysApply: true`n---`n`n" + $Content
+    }
+
+    $fm = [regex]::Match($stripped, '^(---[ \t]*\r?\n)(.*?)(\r?\n---[ \t]*)(\r?\n|$)(.*)', [System.Text.RegularExpressions.RegexOptions]::Singleline)
+    if (-not $fm.Success) {
+        return "---`nalwaysApply: true`n---`n`n" + $Content
+    }
+
+    $opening = $fm.Groups[1].Value
+    $fmText  = $fm.Groups[2].Value
+    $closing = $fm.Groups[3].Value
+    $sep     = $fm.Groups[4].Value
+    $rest    = $fm.Groups[5].Value
+    $newline = if ($opening.Contains("`r`n")) { "`r`n" } else { "`n" }
+
+    if ([regex]::IsMatch($fmText, '(?m)^[ \t]*alwaysApply[ \t]*:[ \t]*true[ \t]*(?:#.*)?$')) {
+        return $Content
+    }
+
+    if ([regex]::IsMatch($fmText, '(?m)^[ \t]*alwaysApply[ \t]*:')) {
+        $alwaysApplyRegex = [regex]'(?m)^([ \t]*)alwaysApply[ \t]*:.*?([ \t]*(?:#.*)?)$'
+        $fmText = $alwaysApplyRegex.Replace($fmText, '${1}alwaysApply: true${2}', 1)
+    } elseif ($fmText.Trim()) {
+        $fmText = $fmText + $newline + 'alwaysApply: true'
+    } else {
+        $fmText = 'alwaysApply: true'
+    }
+
+    return "$leading$opening$fmText$closing$sep$rest"
+}
+
 function Get-ConfigValue {
     param(
         [AllowNull()][object]$Object,
@@ -126,14 +180,26 @@ if (-not (Test-Path -LiteralPath $ExtConfig)) {
 $Options = $null
 if (Get-Command ConvertFrom-Yaml -ErrorAction SilentlyContinue) {
     try {
-        $Options = Get-Content -LiteralPath $ExtConfig -Raw | ConvertFrom-Yaml -ErrorAction Stop
+        $Options = Get-Content -LiteralPath $ExtConfig -Raw -Encoding UTF8 | ConvertFrom-Yaml -ErrorAction Stop
     } catch {
-        # fall through to Python fallback
+        # fall through to ConvertFrom-Json fallback
     }
 }
 
 if ($null -eq $Options) {
-    # ConvertFrom-Yaml unavailable or failed; fall back to Python+PyYAML.
+    # ConvertFrom-Yaml unavailable or failed; try ConvertFrom-Json (no external deps,
+    # works when the config file is valid JSON, which is a subset of YAML).
+    try {
+        $raw = Get-Content -LiteralPath $ExtConfig -Raw -Encoding UTF8
+        $Options = $raw | ConvertFrom-Json -ErrorAction Stop
+        if (-not (Test-ConfigObject -Object $Options)) { $Options = $null }
+    } catch {
+        $Options = $null
+    }
+}
+
+if ($null -eq $Options) {
+    # ConvertFrom-Yaml/Json unavailable or failed; fall back to Python+PyYAML.
     $pythonCmd = $null
     $pythonCandidates = @()
     if ($env:SPECKIT_PYTHON) {
@@ -234,6 +300,43 @@ foreach ($ContextFile in $ContextFiles) {
     }
 }
 $ContextFiles = $dedupedContextFiles
+if ($ContextFiles.Count -eq 0) {
+    # Self-seed: the agent-context extension owns its lifecycle, so when its
+    # own config declares no target it derives one from the active integration
+    # recorded in init-options.json, using the extension's OWN bundled mapping
+    # (agent-context-defaults.json). Independent of the Specify CLI by design.
+    $initOptionsPath = Join-Path $ProjectRoot '.specify/init-options.json'
+    if (Test-Path -LiteralPath $initOptionsPath) {
+        try {
+            $initOpts = Get-Content -LiteralPath $initOptionsPath -Raw | ConvertFrom-Json -ErrorAction Stop
+            $integrationKey = $null
+            if ($initOpts.PSObject.Properties['integration'] -and $initOpts.integration) {
+                $integrationKey = [string]$initOpts.integration
+            } elseif ($initOpts.PSObject.Properties['ai'] -and $initOpts.ai) {
+                $integrationKey = [string]$initOpts.ai
+            }
+            if ($integrationKey) {
+                $defaultsPath = Join-Path $ProjectRoot '.specify/extensions/agent-context/agent-context-defaults.json'
+                if (Test-Path -LiteralPath $defaultsPath) {
+                    $defaults = Get-Content -LiteralPath $defaultsPath -Raw | ConvertFrom-Json -ErrorAction Stop
+                    $derived = $null
+                    if ($defaults.PSObject.Properties['agents'] -and $defaults.agents.PSObject.Properties[$integrationKey]) {
+                        $derived = [string]$defaults.agents.PSObject.Properties[$integrationKey].Value
+                    }
+                    if ($derived -and -not [string]::IsNullOrWhiteSpace($derived)) {
+                        $ContextFiles += $derived.Trim()
+                    } else {
+                        Write-Warning ("agent-context: no default context file is known for integration '{0}'; set 'context_file' in the extension config to choose one." -f $integrationKey)
+                    }
+                } else {
+                    Write-Warning ("agent-context: unable to read {0}; cannot self-seed the context file. Set 'context_file' in the extension config." -f $defaultsPath)
+                }
+            }
+        } catch {
+            # Non-fatal: fall through to the nothing-to-do guard below.
+        }
+    }
+}
 if ($ContextFiles.Count -eq 0) {
     Write-Warning 'agent-context: context_files/context_file not set in extension config; nothing to do.'
     exit 0
@@ -280,21 +383,69 @@ if ($cm) {
 }
 
 if (-not $PlanPath) {
-    # Discover plan.md exactly one level deep (specs/<feature>/plan.md),
-    # matching the bash glob specs/*/plan.md. Wrap in try/catch so access errors under
-    # $ErrorActionPreference = 'Stop' don't abort the script.
-    try {
-        $specsDir = Join-Path $ProjectRoot 'specs'
-        $candidate = Get-ChildItem -Path $specsDir -Directory -ErrorAction SilentlyContinue |
-            ForEach-Object { Get-Item -LiteralPath (Join-Path $_.FullName 'plan.md') -ErrorAction SilentlyContinue } |
-            Where-Object { $_ } |
-            Sort-Object LastWriteTime -Descending |
-            Select-Object -First 1
-        if ($candidate) {
-            $PlanPath = [System.IO.Path]::GetRelativePath($ProjectRoot, $candidate.FullName).Replace('\','/')
+    # Prefer .specify/feature.json (written by /speckit-specify) over mtime heuristic.
+    $FeatureJson = Join-Path $ProjectRoot '.specify/feature.json'
+    if (Test-Path -LiteralPath $FeatureJson) {
+        try {
+            $fj = Get-Content -LiteralPath $FeatureJson -Raw -Encoding UTF8 | ConvertFrom-Json
+            $featureDir = $fj.feature_directory
+            if ($featureDir -isnot [string] -or -not $featureDir) {
+                $featureDir = $null
+            } else {
+                $featureDir = $featureDir.TrimEnd('\', '/')
+            }
+            if ($featureDir) {
+                # Join-Path on Unix does not treat absolute ChildPath as "wins"; check explicitly.
+                if ([System.IO.Path]::IsPathRooted($featureDir)) {
+                    $candidatePlan = Join-Path $featureDir 'plan.md'
+                } else {
+                    $candidatePlan = Join-Path (Join-Path $ProjectRoot $featureDir) 'plan.md'
+                }
+                if (Test-Path -LiteralPath $candidatePlan) {
+                    # Resolve ./ .. segments before relativizing (mirrors bash Path.resolve()).
+                    # GetFullPath is available in .NET Framework 4.x (PS 5.1 compatible).
+                    $resolvedPlan = [System.IO.Path]::GetFullPath($candidatePlan)
+                    $resolvedDir  = [System.IO.Path]::GetDirectoryName($resolvedPlan)
+                    $normRoot = $ProjectRoot.TrimEnd('\', '/') + [System.IO.Path]::DirectorySeparatorChar
+                    $normDir  = $resolvedDir.TrimEnd('\', '/') + [System.IO.Path]::DirectorySeparatorChar
+                    $cmp = if ([System.Environment]::OSVersion.Platform -eq [System.PlatformID]::Win32NT) { [System.StringComparison]::OrdinalIgnoreCase } else { [System.StringComparison]::Ordinal }
+                    if ($normDir.StartsWith($normRoot, $cmp)) {
+                        $relDir = $normDir.Substring($normRoot.Length).TrimEnd('\', '/')
+                        $PlanPath = if ($relDir) { $relDir.Replace('\', '/') + '/plan.md' } else { 'plan.md' }
+                    } else {
+                        $PlanPath = $resolvedPlan.Replace('\', '/')
+                    }
+                }
+            }
+        } catch {
+            # Non-fatal: fall through to mtime heuristic.
+        }
+    }
+
+    # Fall back to mtime only when feature.json is absent or its plan does not exist yet.
+    if (-not $PlanPath) {
+        try {
+            $specsDir = Join-Path $ProjectRoot 'specs'
+            $candidate = Get-ChildItem -Path $specsDir -Directory -ErrorAction SilentlyContinue |
+                ForEach-Object { Get-Item -LiteralPath (Join-Path $_.FullName 'plan.md') -ErrorAction SilentlyContinue } |
+                Where-Object { $_ } |
+                Sort-Object LastWriteTime -Descending |
+                Select-Object -First 1
+            if ($candidate) {
+                # GetRelativePath is .NET 5+ only; strip prefix manually for PS 5.1 compat.
+                # Use case-insensitive comparison on Windows only (matches common.ps1 pattern).
+                $fullPath = $candidate.FullName.Replace('\', '/')
+                $normRoot = $ProjectRoot.Replace('\', '/').TrimEnd('/') + '/'
+                $cmp = if ([System.Environment]::OSVersion.Platform -eq [System.PlatformID]::Win32NT) { [System.StringComparison]::OrdinalIgnoreCase } else { [System.StringComparison]::Ordinal }
+                if ($fullPath.StartsWith($normRoot, $cmp)) {
+                    $PlanPath = $fullPath.Substring($normRoot.Length)
+                } else {
+                    $PlanPath = $fullPath
+                }
+            }
+        } catch {
+            # Non-fatal: continue without a plan path.
         }
-    } catch {
-        # Non-fatal: continue without a plan path.
     }
 }
 
@@ -347,6 +498,9 @@ foreach ($ContextFile in $ContextFiles) {
     }
 
     $newContent = $newContent.Replace("`r`n", "`n").Replace("`r", "`n")
+    if ($ContextFile -match '\.mdc$') {
+        $newContent = Add-MdcFrontmatter -Content $newContent
+    }
     [System.IO.File]::WriteAllText($CtxPath, $newContent, (New-Object System.Text.UTF8Encoding($false)))
 
     Write-Host "agent-context: updated $ContextFile"

extensions/catalog.community.json

@@ -1,6 +1,6 @@
 {
   "schema_version": "1.0",
-  "updated_at": "2026-06-24T00:00:00Z",
+  "updated_at": "2026-06-29T00:00:00Z",
   "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/extensions/catalog.community.json",
   "extensions": {
     "aide": {
@@ -772,40 +772,40 @@
     "companion": {
       "name": "SpecKit Companion",
       "id": "companion",
-      "description": "Live spec-driven progress for SpecKit Companion — lifecycle capture, status, resume, and a turbo pipeline profile.",
+      "description": "Live spec-driven progress for SpecKit Companion — lifecycle capture, status, resume, and composable commands you can customize with hooks and recipes.",
       "author": "alfredoperez",
-      "version": "0.3.0",
-      "download_url": "https://github.com/alfredoperez/speckit-companion/releases/download/speckit-ext-v0.3.0/companion-0.3.0.zip",
+      "version": "0.11.0",
+      "download_url": "https://github.com/alfredoperez/speckit-companion/releases/download/speckit-ext-v0.11.0/companion-0.11.0.zip",
       "repository": "https://github.com/alfredoperez/speckit-companion",
       "homepage": "https://github.com/alfredoperez/speckit-companion/tree/main/speckit-extension",
-      "documentation": "https://github.com/alfredoperez/speckit-companion/blob/main/speckit-extension/docs/",
+      "documentation": "https://github.com/alfredoperez/speckit-companion/blob/main/speckit-extension/README.md",
       "changelog": "https://github.com/alfredoperez/speckit-companion/blob/main/speckit-extension/CHANGELOG.md",
       "license": "MIT",
       "category": "visibility",
       "effect": "read-write",
       "requires": {
-        "speckit_version": ">=0.8.5",
+        "speckit_version": ">=0.9.5",
         "tools": [
           { "name": "python3", "required": false }
         ]
       },
       "provides": {
-        "commands": 10,
+        "commands": 13,
         "hooks": 4
       },
       "tags": [
-        "tracking",
-        "companion",
-        "progress",
         "vscode",
-        "lifecycle",
-        "resume"
+        "progress",
+        "status",
+        "resume",
+        "configurable",
+        "extensible"
       ],
       "verified": false,
       "downloads": 0,
       "stars": 0,
       "created_at": "2026-06-11T00:00:00Z",
-      "updated_at": "2026-06-11T00:00:00Z"
+      "updated_at": "2026-06-24T00:00:00Z"
     },
     "conduct": {
       "name": "Conduct Extension",
@@ -2501,8 +2501,8 @@
       "id": "product",
       "description": "Generates PRFAQ, Lean PRD, stakeholder summaries, and technical designs from engineering specs.",
       "author": "d0whc3r",
-      "version": "0.8.3",
-      "download_url": "https://github.com/d0whc3r/spec-kit-product/releases/download/v0.8.3/product-0.8.3.zip",
+      "version": "1.0.1",
+      "download_url": "https://github.com/d0whc3r/spec-kit-product/releases/download/v1.0.1/product-1.0.1.zip",
       "repository": "https://github.com/d0whc3r/spec-kit-product",
       "homepage": "https://d0whc3r.github.io/spec-kit-product/",
       "documentation": "https://github.com/d0whc3r/spec-kit-product/wiki",
@@ -2514,7 +2514,7 @@
         "speckit_version": ">=0.2.0"
       },
       "provides": {
-        "commands": 4,
+        "commands": 3,
         "hooks": 3
       },
       "tags": [
@@ -2538,7 +2538,7 @@
       "downloads": 0,
       "stars": 0,
       "created_at": "2026-05-26T00:00:00Z",
-      "updated_at": "2026-06-01T00:00:00Z"
+      "updated_at": "2026-06-29T00:00:00Z"
     },
     "product-forge": {
       "name": "Product Forge",

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

@@ -288,7 +288,7 @@ generate_branch_name() {
         if ! echo "$word" | grep -qiE "$stop_words"; then
             if [ ${#word} -ge 3 ]; then
                 meaningful_words+=("$word")
-            elif echo "$description" | grep -qw -- "${word^^}"; then
+            elif printf '%s' "$description" | grep -qw -- "$(printf '%s' "$word" | tr '[:lower:]' '[:upper:]')"; then
                 meaningful_words+=("$word")
             fi
         fi

extensions/git/scripts/bash/initialize-repo.sh

@@ -51,4 +51,4 @@ _git_out=$(git init -q 2>&1) || { echo "[specify] Error: git init failed: $_git_
 _git_out=$(git add . 2>&1) || { echo "[specify] Error: git add failed: $_git_out" >&2; exit 1; }
 _git_out=$(git commit --allow-empty -q -m "$COMMIT_MSG" 2>&1) || { echo "[specify] Error: git commit failed: $_git_out" >&2; exit 1; }
 
-echo "✓ Git repository initialized" >&2
+echo "[OK] Git repository initialized" >&2

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

@@ -252,7 +252,10 @@ function Get-BranchName {
         if ($stopWords -contains $word) { continue }
         if ($word.Length -ge 3) {
             $meaningfulWords += $word
-        } elseif ($Description -match "\b$($word.ToUpper())\b") {
+        } elseif ($Description -cmatch "\b$($word.ToUpper())\b") {
+            # Case-sensitive (-cmatch) to mirror the bash twin's `grep -qw -- "${word^^}"`:
+            # keep a short word only when its UPPERCASE form appears in the original
+            # (an acronym). -match is case-insensitive and would keep every short word.
             $meaningfulWords += $word
         }
     }
@@ -397,8 +400,10 @@ if ($Json) {
     $obj = [PSCustomObject]@{
         BRANCH_NAME = $branchName
         FEATURE_NUM = $featureNum
-        HAS_GIT = $hasGit
     }
+    # $hasGit is computed for branch-creation logic only; it is intentionally not
+    # emitted so this output contract matches the bash twin: BRANCH_NAME and
+    # FEATURE_NUM, plus DRY_RUN (added just below) on dry runs.
     if ($DryRun) {
         $obj | Add-Member -NotePropertyName 'DRY_RUN' -NotePropertyValue $true
     }
@@ -406,7 +411,6 @@ if ($Json) {
 } else {
     Write-Output "BRANCH_NAME: $branchName"
     Write-Output "FEATURE_NUM: $featureNum"
-    Write-Output "HAS_GIT: $hasGit"
     if (-not $DryRun) {
         Write-Output "SPECIFY_FEATURE environment variable set to: $branchName"
     }

presets/catalog.community.json

@@ -1,6 +1,6 @@
 {
   "schema_version": "1.0",
-  "updated_at": "2026-06-22T00:00:00Z",
+  "updated_at": "2026-06-25T00:00:00Z",
   "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/presets/catalog.community.json",
   "presets": {
     "a11y-governance": {
@@ -567,13 +567,13 @@
     "sicario-core": {
       "name": "SicarioSpec Core",
       "id": "sicario-core",
-      "version": "0.4.0",
-      "description": "Evidence-first security operations governance that maps feature risk to controls, gates, evidence, owners, approval, and accepted-risk decisions.",
+      "version": "0.5.1",
+      "description": "Baseline secure-by-default Spec Kit governance profile.",
       "author": "SicarioSpec Contributors",
       "repository": "https://github.com/dfirs1car1o/sicario-spec",
-      "download_url": "https://github.com/dfirs1car1o/sicario-spec/releases/download/v0.4.0/sicario-core-0.4.0.zip",
+      "download_url": "https://github.com/dfirs1car1o/sicario-spec/releases/download/v0.5.1/sicario-core-0.5.1.zip",
       "homepage": "https://github.com/dfirs1car1o/sicario-spec",
-      "documentation": "https://github.com/dfirs1car1o/sicario-spec/blob/main/README.md",
+      "documentation": "https://github.com/dfirs1car1o/sicario-spec/blob/main/presets/sicario-core/README.md",
       "license": "MIT",
       "requires": {
         "speckit_version": ">=0.9.0"
@@ -583,14 +583,13 @@
         "commands": 0
       },
       "tags": [
-        "security",
         "governance",
         "security-ops",
         "secure-by-default",
         "evidence"
       ],
       "created_at": "2026-06-22T00:00:00Z",
-      "updated_at": "2026-06-22T00:00:00Z"
+      "updated_at": "2026-06-25T00:00:00Z"
     },
     "spec2cloud": {
       "name": "Spec2Cloud",

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "specify-cli"
-version = "0.11.8.dev0"
+version = "0.12.1"
 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"

scripts/bash/check-prerequisites.sh

@@ -78,8 +78,14 @@ done
 SCRIPT_DIR="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 source "$SCRIPT_DIR/common.sh"
 
-# Get feature paths
-_paths_output=$(get_feature_paths) || { echo "ERROR: Failed to resolve feature paths" >&2; exit 1; }
+# Get feature paths.
+# In --paths-only mode this is pure resolution, so pass --no-persist to opt out
+# of the feature.json write side effect (issue #3025).
+if $PATHS_ONLY; then
+    _paths_output=$(get_feature_paths --no-persist) || { echo "ERROR: Failed to resolve feature paths" >&2; exit 1; }
+else
+    _paths_output=$(get_feature_paths) || { echo "ERROR: Failed to resolve feature paths" >&2; exit 1; }
+fi
 eval "$_paths_output"
 unset _paths_output
 

scripts/bash/common.sh

@@ -152,6 +152,15 @@ _persist_feature_json() {
 }
 
 get_feature_paths() {
+    # Read-only callers (e.g. check-prerequisites.sh --paths-only) pass
+    # --no-persist so pure path resolution never writes .specify/feature.json,
+    # which would dirty the working tree or overwrite a pinned value (issue #3025).
+    local no_persist=false
+    if [[ "${1:-}" == "--no-persist" ]]; then
+        no_persist=true
+        shift
+    fi
+
     # Split decl/assignment so a SPECIFY_INIT_DIR validation failure in
     # get_repo_root propagates as a hard error instead of being masked by `local`.
     local repo_root
@@ -168,8 +177,11 @@ get_feature_paths() {
         feature_dir="$SPECIFY_FEATURE_DIRECTORY"
         # Normalize relative paths to absolute under repo root
         [[ "$feature_dir" != /* ]] && feature_dir="$repo_root/$feature_dir"
-        # Persist to feature.json so future sessions without the env var still work
-        _persist_feature_json "$repo_root" "$SPECIFY_FEATURE_DIRECTORY"
+        # Persist to feature.json so future sessions without the env var still
+        # work — unless the caller opted out for read-only resolution (#3025).
+        if [[ "$no_persist" != true ]]; then
+            _persist_feature_json "$repo_root" "$SPECIFY_FEATURE_DIRECTORY"
+        fi
     elif [[ -f "$repo_root/.specify/feature.json" ]]; then
         local _fd
         _fd=$(read_feature_json_feature_directory "$repo_root")

scripts/bash/create-new-feature.sh

@@ -152,7 +152,7 @@ generate_branch_name() {
         if ! echo "$word" | grep -qiE "$stop_words"; then
             if [ ${#word} -ge 3 ]; then
                 meaningful_words+=("$word")
-            elif echo "$description" | grep -q "\b${word^^}\b"; then
+            elif printf '%s' "$description" | grep -qw -- "$(printf '%s' "$word" | tr '[:lower:]' '[:upper:]')"; then
                 # Keep short words if they appear as uppercase in original (likely acronyms)
                 meaningful_words+=("$word")
             fi

scripts/powershell/check-prerequisites.ps1

@@ -56,8 +56,14 @@ EXAMPLES:
 # Source common functions
 . "$PSScriptRoot/common.ps1"
 
-# Get feature paths
-$paths = Get-FeaturePathsEnv
+# Get feature paths.
+# In -PathsOnly mode this is pure resolution, so pass -NoPersist to opt out of
+# the feature.json write side effect (issue #3025).
+if ($PathsOnly) {
+    $paths = Get-FeaturePathsEnv -NoPersist
+} else {
+    $paths = Get-FeaturePathsEnv
+}
 
 # If paths-only mode, output paths and exit (no validation)
 if ($PathsOnly) {

scripts/powershell/common.ps1

@@ -143,6 +143,13 @@ function Save-FeatureJson {
 }
 
 function Get-FeaturePathsEnv {
+    # Read-only callers (e.g. check-prerequisites.ps1 -PathsOnly) pass -NoPersist
+    # so pure path resolution never writes .specify/feature.json, which would
+    # dirty the working tree or overwrite a pinned value (issue #3025).
+    param(
+        [switch]$NoPersist
+    )
+
     $repoRoot = Get-RepoRoot
     $currentBranch = Get-CurrentBranch
 
@@ -157,8 +164,11 @@ function Get-FeaturePathsEnv {
         if (-not [System.IO.Path]::IsPathRooted($featureDir)) {
             $featureDir = Join-Path $repoRoot $featureDir
         }
-        # Persist to feature.json so future sessions without the env var still work
-        Save-FeatureJson -RepoRoot $repoRoot -FeatureDirectory $env:SPECIFY_FEATURE_DIRECTORY
+        # Persist to feature.json so future sessions without the env var still
+        # work - unless the caller opted out for read-only resolution (#3025).
+        if (-not $NoPersist) {
+            Save-FeatureJson -RepoRoot $repoRoot -FeatureDirectory $env:SPECIFY_FEATURE_DIRECTORY
+        }
     } elseif (Test-Path $featureJson) {
         $featureJsonRaw = Get-Content -LiteralPath $featureJson -Raw
         try {
@@ -209,7 +219,13 @@ function Test-FileExists {
 
 function Test-DirHasFiles {
     param([string]$Path, [string]$Description)
-    if ((Test-Path -Path $Path -PathType Container) -and (Get-ChildItem -Path $Path -ErrorAction SilentlyContinue | Where-Object { -not $_.PSIsContainer } | Select-Object -First 1)) {
+    # A directory counts as non-empty when Get-ChildItem returns any entry
+    # (files or subdirectories) -- matching the JSON contracts checks in
+    # check-prerequisites.ps1 / setup-tasks.ps1, and treating a directory whose
+    # only contents are subdirectories (e.g. contracts/v1/openapi.yaml) as
+    # non-empty like bash check_dir. Filtering out subdirectories would
+    # mis-report such a directory as empty.
+    if ((Test-Path -Path $Path -PathType Container) -and (Get-ChildItem -Path $Path -ErrorAction SilentlyContinue | Select-Object -First 1)) {
         Write-Output "  [OK] $Description"
         return $true
     } else {

scripts/powershell/create-new-feature.ps1

@@ -142,8 +142,10 @@ if ($ShortName) {
     $branchSuffix = Get-BranchName -Description $featureDesc
 }
 
-# Warn if -Number and -Timestamp are both specified
-if ($Timestamp -and $Number -ne 0) {
+# Warn if -Number and -Timestamp are both specified. Use ContainsKey (not
+# `-ne 0`) so an explicit `-Number 0` is also detected, matching the bash twin's
+# `[ -n "$BRANCH_NUMBER" ]` check.
+if ($Timestamp -and $PSBoundParameters.ContainsKey('Number')) {
     Write-Warning "[specify] Warning: -Number is ignored when -Timestamp is used"
     $Number = 0
 }
@@ -153,8 +155,10 @@ if ($Timestamp) {
     $featureNum = Get-Date -Format 'yyyyMMdd-HHmmss'
     $branchName = "$featureNum-$branchSuffix"
 } else {
-    # Determine branch number from existing feature directories
-    if ($Number -eq 0) {
+    # Determine branch number from existing feature directories. Auto-detect only
+    # when -Number was not supplied; an explicit value (including 0) is honored,
+    # matching the bash twin's `[ -z "$BRANCH_NUMBER" ]` check.
+    if (-not $PSBoundParameters.ContainsKey('Number')) {
         $Number = (Get-HighestNumberFromSpecs -SpecsDir $specsDir) + 1
     }
 
@@ -207,6 +211,10 @@ if (-not $DryRun) {
             $utf8NoBom = New-Object System.Text.UTF8Encoding($false)
             [System.IO.File]::WriteAllText($specFile, $content, $utf8NoBom)
         } else {
+            # Match the bash twin (create-new-feature.sh): warn on stderr that no
+            # spec template was found before creating an empty spec file, so the
+            # missing-template signal is not silently swallowed on Windows.
+            [Console]::Error.WriteLine("Warning: Spec template not found; created empty spec file")
             New-Item -ItemType File -Path $specFile -Force | Out-Null
         }
     }

scripts/powershell/setup-plan.ps1

@@ -40,8 +40,22 @@ if (Test-Path $paths.IMPL_PLAN -PathType Leaf) {
         $content = [System.IO.File]::ReadAllText($template)
         $utf8NoBom = New-Object System.Text.UTF8Encoding($false)
         [System.IO.File]::WriteAllText($paths.IMPL_PLAN, $content, $utf8NoBom)
+        # Emit the copy status like the bash twin (setup-plan.sh); route to stderr
+        # in -Json mode so stdout stays pure JSON, matching the sibling messages.
+        if ($Json) {
+            [Console]::Error.WriteLine("Copied plan template to $($paths.IMPL_PLAN)")
+        } else {
+            Write-Output "Copied plan template to $($paths.IMPL_PLAN)"
+        }
     } else {
-        Write-Warning "Plan template not found"
+        # Match the bash twin's wording and stream routing (stderr in -Json so
+        # stdout stays pure JSON, stdout otherwise), consistent with the sibling
+        # "Copied plan template" message above.
+        if ($Json) {
+            [Console]::Error.WriteLine("Warning: Plan template not found")
+        } else {
+            Write-Output "Warning: Plan template not found"
+        }
         # Create a basic plan file if template doesn't exist
         New-Item -ItemType File -Path $paths.IMPL_PLAN -Force | Out-Null
     }

src/specify_cli/__init__.py

@@ -262,85 +262,9 @@ def ensure_executable_scripts(project_path: Path, tracker: StepTracker | None =
                 console.print(f"  - {f}")
 
 # ---------------------------------------------------------------------------
-# Agent-context extension config helpers
+# Skills directory helpers
 # ---------------------------------------------------------------------------
 
-_AGENT_CTX_EXT_CONFIG = (
-    Path(".specify") / "extensions" / "agent-context" / "agent-context-config.yml"
-)
-
-
-def _load_agent_context_config(project_root: Path) -> dict[str, Any]:
-    """Load the agent-context extension config, returning defaults on failure."""
-    from .integrations.base import IntegrationBase
-
-    defaults: dict[str, Any] = {
-        "context_file": "",
-        "context_files": [],
-        "context_markers": {
-            "start": IntegrationBase.CONTEXT_MARKER_START,
-            "end": IntegrationBase.CONTEXT_MARKER_END,
-        },
-    }
-    path = project_root / _AGENT_CTX_EXT_CONFIG
-    if not path.exists():
-        return defaults
-    try:
-        raw = yaml.safe_load(path.read_text(encoding="utf-8"))
-    except (OSError, UnicodeError, yaml.YAMLError):
-        return defaults
-    if not isinstance(raw, dict):
-        return defaults
-    return raw
-
-
-def _save_agent_context_config(
-    project_root: Path, config: dict[str, Any]
-) -> None:
-    """Persist *config* to the agent-context extension config file."""
-    path = project_root / _AGENT_CTX_EXT_CONFIG
-    path.parent.mkdir(parents=True, exist_ok=True)
-    path.write_text(yaml.safe_dump(config, default_flow_style=False, sort_keys=False), encoding="utf-8")
-
-
-def _update_agent_context_config_file(
-    project_root: Path,
-    context_file: str | None,
-    *,
-    preserve_markers: bool = True,
-    preserve_context_files: bool = True,
-) -> None:
-    """Update the agent-context extension config with *context_file*.
-
-    When *preserve_markers* is True (default), any existing
-    ``context_markers`` values are kept unchanged so user customisations
-    survive integration changes and reinit.  When False, the default
-    markers are written unconditionally.
-
-    When *preserve_context_files* is True (default), an existing
-    ``context_files`` list is kept unchanged, including an empty list.  This
-    lets projects opt into updating multiple agent context files while still
-    preserving the legacy singular ``context_file`` value for compatibility.
-    """
-    from .integrations.base import IntegrationBase
-
-    cfg = _load_agent_context_config(project_root)
-    cfg["context_file"] = context_file or ""
-    existing_context_files = cfg.get("context_files")
-    if preserve_context_files:
-        cfg["context_files"] = (
-            existing_context_files if isinstance(existing_context_files, list) else []
-        )
-    else:
-        cfg.pop("context_files", None)
-    if not preserve_markers or not isinstance(cfg.get("context_markers"), dict):
-        cfg["context_markers"] = {
-            "start": IntegrationBase.CONTEXT_MARKER_START,
-            "end": IntegrationBase.CONTEXT_MARKER_END,
-        }
-    _save_agent_context_config(project_root, cfg)
-
-
 def _get_skills_dir(project_path: Path, selected_ai: str) -> Path:
     """Resolve the agent-specific skills directory.
 
@@ -1128,9 +1052,10 @@ def workflow_add(
             raise typer.Exit(1)
 
         from specify_cli._github_http import resolve_github_release_asset_api_url as _resolve_gh_asset
+        from specify_cli.authentication.http import github_provider_hosts
 
         _wf_url_extra_headers = None
-        _resolved_wf_url = _resolve_gh_asset(source, _open_url, timeout=30)
+        _resolved_wf_url = _resolve_gh_asset(source, _open_url, timeout=30, github_hosts=github_provider_hosts())
         if _resolved_wf_url:
             source = _resolved_wf_url
             _wf_url_extra_headers = {"Accept": "application/octet-stream"}
@@ -1234,10 +1159,11 @@ def workflow_add(
 
     try:
         from specify_cli.authentication.http import open_url as _open_url
+        from specify_cli.authentication.http import github_provider_hosts
         from specify_cli._github_http import resolve_github_release_asset_api_url as _resolve_gh_asset
 
         _wf_cat_extra_headers = None
-        _resolved_workflow_url = _resolve_gh_asset(workflow_url, _open_url, timeout=30)
+        _resolved_workflow_url = _resolve_gh_asset(workflow_url, _open_url, timeout=30, github_hosts=github_provider_hosts())
         if _resolved_workflow_url:
             workflow_url = _resolved_workflow_url
             _wf_cat_extra_headers = {"Accept": "application/octet-stream"}

src/specify_cli/_console.py

@@ -34,6 +34,10 @@ TAGLINE = "GitHub Spec Kit - Spec-Driven Development Toolkit"
 
 console = Console(highlight=False)
 
+# Stderr-bound console for error/diagnostic output, so human-facing messages
+# never contaminate stdout (which carries machine-readable ``--json`` payloads).
+err_console = Console(stderr=True, highlight=False)
+
 class StepTracker:
     """Track and render hierarchical steps without emojis, similar to Claude Code tree output.
     Supports live auto-refresh via an attached refresh callback.

src/specify_cli/_github_http.py

@@ -10,6 +10,7 @@ through the config-driven helpers in :mod:`specify_cli.authentication.http`.
 
 import os
 import urllib.request
+from fnmatch import fnmatch
 from typing import Callable, Dict, Optional
 from urllib.parse import quote, unquote, urlparse
 
@@ -56,55 +57,79 @@ def build_github_request(url: str) -> urllib.request.Request:
     return urllib.request.Request(url, headers=headers)
 
 
+def _host_matches(hostname: str, patterns: tuple[str, ...]) -> bool:
+    """Return True when *hostname* matches a pattern (exact or ``*.suffix``)."""
+    hostname = hostname.lower()
+    return any(p == hostname or fnmatch(hostname, p) for p in patterns)
+
+
 def resolve_github_release_asset_api_url(
     download_url: str,
     open_url_fn: Callable,
     timeout: int = 60,
+    github_hosts: tuple[str, ...] = (),
 ) -> Optional[str]:
-    """Resolve a GitHub browser release URL to its REST API asset URL.
+    """Resolve a GitHub release browser-download URL to its REST API asset URL.
 
-    For private or SSO-protected repositories, browser release download
-    URLs (``https://github.com/<owner>/<repo>/releases/download/<tag>/<asset>``)
-    redirect to an HTML/SSO page instead of delivering the file.  This
-    helper resolves such a URL to the matching GitHub REST API asset URL
-    (``https://api.github.com/repos/…/releases/assets/<id>``), which can
-    then be downloaded with ``Accept: application/octet-stream`` and an
-    auth token to retrieve the actual file payload.
+    Works for public ``github.com`` and for GitHub Enterprise Server (GHES)
+    hosts. A host is treated as GHES when it matches one of *github_hosts*
+    (exact hostname or ``*.suffix``) — supply the hosts the user has trusted
+    under a ``github`` provider in ``auth.json``. This allowlist is the
+    security gate: unlisted hosts never receive GHES API treatment, so a
+    malicious catalog cannot induce an API request to an arbitrary host.
 
-    If *download_url* is already a REST API asset URL, it is returned
-    as-is.  Non-GitHub URLs and GitHub URLs that are not release-download
-    URLs return ``None``.  If the API lookup fails (e.g. network error or
-    asset not found), ``None`` is returned so callers can fall back to the
-    original URL.
+    For a public URL the API base is ``https://api.github.com``; for a GHES
+    host it is ``{scheme}://{host[:port]}/api/v3``. Returns the API asset URL
+    (downloadable with ``Accept: application/octet-stream`` + a token), the
+    input unchanged if it is already an API asset URL, or ``None`` when the
+    URL is not a resolvable GitHub release download or the lookup fails.
 
     Args:
         download_url: The URL to resolve.
         open_url_fn: A callable compatible with
-            ``specify_cli.authentication.http.open_url`` used to make the
-            authenticated API request.
+            ``specify_cli.authentication.http.open_url`` used for the
+            authenticated release-metadata lookup.
         timeout: Per-request timeout in seconds.
-
-    Returns:
-        The resolved REST API asset URL, or ``None`` if resolution is not
-        applicable or fails.
+        github_hosts: Host patterns to treat as GitHub Enterprise Server.
     """
     import json
     import urllib.error
 
     parsed = urlparse(download_url)
+    hostname = (parsed.hostname or "").lower()
     parts = [unquote(part) for part in parsed.path.strip("/").split("/")]
 
-    # Already a REST API asset URL — use it directly
-    if (
-        parsed.hostname == "api.github.com"
-        and len(parts) >= 6
-        and parts[:1] == ["repos"]
-        and parts[3:5] == ["releases", "assets"]
-    ):
+    is_ghes = (
+        bool(hostname)
+        and hostname not in GITHUB_HOSTS
+        and _host_matches(hostname, github_hosts)
+    )
+
+    def _is_asset_path(segments: list[str]) -> bool:
+        return (
+            len(segments) >= 6
+            and segments[:1] == ["repos"]
+            and segments[3:5] == ["releases", "assets"]
+        )
+
+    # Already a REST API asset URL — use it directly. Pure passthrough induces
+    # no new request: the caller fetches this same URL regardless, so it is
+    # gated on path shape alone rather than the GHES allowlist. The token stays
+    # independently gated by auth.json in the download helper, and only the
+    # resolving path below (which issues a tag-lookup request) needs the
+    # allowlist as its anti-SSRF gate.
+    if hostname == "api.github.com" and _is_asset_path(parts):
+        return download_url
+    if hostname and parts[:2] == ["api", "v3"] and _is_asset_path(parts[2:]):
         return download_url
 
-    # Only handle github.com browser release download URLs
-    if parsed.hostname != "github.com":
+    # Determine the REST API base for browser release-download URLs.
+    if hostname == "github.com":
+        api_base = "https://api.github.com"
+    elif is_ghes:
+        authority = hostname if parsed.port is None else f"{hostname}:{parsed.port}"
+        api_base = f"{parsed.scheme}://{authority}/api/v3"
+    else:
         return None
 
     # Expecting /<owner>/<repo>/releases/download/<tag>/<asset>
@@ -114,7 +139,7 @@ def resolve_github_release_asset_api_url(
     owner, repo, tag = parts[0], parts[1], parts[4]
     asset_name = "/".join(parts[5:])
     encoded_tag = quote(tag, safe="")
-    release_url = f"https://api.github.com/repos/{owner}/{repo}/releases/tags/{encoded_tag}"
+    release_url = f"{api_base}/repos/{owner}/{repo}/releases/tags/{encoded_tag}"
 
     try:
         with open_url_fn(release_url, timeout=timeout) as response:

src/specify_cli/agents.py

@@ -433,37 +433,6 @@ class CommandRegistrar:
 
         body = body.replace("{ARGS}", "$ARGUMENTS").replace("__AGENT__", agent_name)
 
-        # Resolve __CONTEXT_FILE__ from the agent-context extension config.
-        # When disabled, ignore stale context_files but keep the singular
-        # context_file value so generated commands still point at the agent
-        # context file managed before the extension was disabled.
-        from .integrations.base import IntegrationBase
-
-        # Local import: _load_agent_context_config lives in __init__.py which
-        # imports agents.py, so a top-level import would be circular.
-        from . import _load_agent_context_config
-
-        ac_cfg = _load_agent_context_config(project_root)
-        extension_enabled = IntegrationBase._agent_context_extension_enabled(
-            project_root
-        )
-        if extension_enabled:
-            context_files = IntegrationBase._resolve_context_file_values(
-                project_root,
-                ac_cfg,
-                legacy_context_file=init_opts.get("context_file"),
-            )
-        else:
-            context_files = IntegrationBase._resolve_context_file_values(
-                project_root,
-                ac_cfg,
-                legacy_context_file=init_opts.get("context_file"),
-                include_context_files=False,
-                validate=False,
-            )
-        context_file = IntegrationBase._format_context_file_values(context_files)
-        body = body.replace("__CONTEXT_FILE__", context_file)
-
         return CommandRegistrar.rewrite_project_relative_paths(body)
 
     def _convert_argument_placeholder(

src/specify_cli/authentication/http.py

@@ -118,6 +118,20 @@ def build_request(url: str, extra_headers: dict[str, str] | None = None) -> urll
     return urllib.request.Request(url, headers=headers)
 
 
+def github_provider_hosts() -> tuple[str, ...]:
+    """Return host patterns from every ``github`` provider entry in ``auth.json``.
+
+    Used to classify which hosts are GitHub Enterprise Server instances when
+    resolving release-asset download URLs. Returns an empty tuple when no
+    ``auth.json`` exists or it contains no ``github`` entries.
+    """
+    hosts: list[str] = []
+    for entry in _load_config():
+        if entry.provider == "github":
+            hosts.extend(entry.hosts)
+    return tuple(hosts)
+
+
 def open_url(
     url: str,
     timeout: int = 10,

src/specify_cli/catalogs.py

@@ -78,7 +78,10 @@ class CatalogStackBase:
                 f"Catalog URL must use HTTPS (got {parsed.scheme}://). "
                 "HTTP is only allowed for localhost."
             )
-        if not parsed.netloc:
+        # Check hostname, not netloc: netloc is truthy for host-less URLs like
+        # "https://:8080" or "https://user@", so the host guarantee this error
+        # promises would not actually hold. hostname is None in those cases.
+        if not parsed.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

@@ -13,7 +13,7 @@ from pathlib import Path
 
 import typer
 
-from ..._console import console
+from ..._console import console, err_console
 from ...bundler import BundlerError
 from ...bundler.lib.project import (
     active_integration,
@@ -41,7 +41,9 @@ bundle_app.add_typer(bundle_catalog_app, name="catalog")
 
 def _fail(message: str) -> None:
     """Print an actionable error to stderr and exit non-zero."""
-    console.print(f"[red]Error:[/red] {message}", style=None)
+    # Use the stderr console so the error never lands on stdout, which under
+    # ``--json`` carries the machine-readable payload and must stay parseable.
+    err_console.print(f"[red]Error:[/red] {message}", style=None)
     raise typer.Exit(code=1)
 
 

src/specify_cli/commands/init.py

@@ -18,7 +18,6 @@ from .._agent_config import (
     SCRIPT_TYPE_CHOICES,
 )
 from .._assets import (
-    _locate_bundled_extension,
     _locate_bundled_preset,
     _locate_bundled_workflow,
     get_speckit_version,
@@ -171,7 +170,6 @@ def register(app: typer.Typer) -> None:
         from .. import (
             _install_shared_infra_or_exit,
             _print_cli_warning,
-            _update_agent_context_config_file,
             ensure_executable_scripts,
             save_init_options,
         )
@@ -376,7 +374,6 @@ def register(app: typer.Typer) -> None:
             ("chmod", "Ensure scripts executable"),
             ("constitution", "Constitution setup"),
             ("workflow", "Install bundled workflow"),
-            ("agent-context", "Install agent-context extension"),
             ("final", "Finalize"),
         ]:
             tracker.add(key, label)
@@ -507,47 +504,6 @@ def register(app: typer.Typer) -> None:
                     init_opts["ai_skills"] = True
                 save_init_options(project_path, init_opts)
 
-                # --- agent-context extension (bundled, auto-installed) ---
-                # Installed after init-options.json is written so that skill
-                # registration can read ai_skills + integration key.
-                try:
-                    from ..extensions import ExtensionManager as _ExtMgr
-
-                    bundled_ac = _locate_bundled_extension("agent-context")
-                    if bundled_ac:
-                        ac_mgr = _ExtMgr(project_path)
-                        if ac_mgr.registry.is_installed("agent-context"):
-                            tracker.complete("agent-context", "already installed")
-                        else:
-                            ac_mgr.install_from_directory(
-                                bundled_ac, get_speckit_version()
-                            )
-                            tracker.complete("agent-context", "extension installed")
-                    else:
-                        from ..extensions import REINSTALL_COMMAND as _ac_reinstall
-
-                        tracker.error(
-                            "agent-context",
-                            f"bundled extension not found — installation may be "
-                            f"incomplete. Run: {_ac_reinstall}",
-                        )
-                except Exception as ac_err:
-                    sanitized_ac = str(ac_err).replace("\n", " ").strip()
-                    tracker.error(
-                        "agent-context",
-                        f"extension install failed: {sanitized_ac[:120]}",
-                    )
-
-                # Write context_file to the agent-context extension config
-                # AFTER the extension install (which copies the template config
-                # with an empty context_file).
-                if resolved_integration.context_file:
-                    _update_agent_context_config_file(
-                        project_path,
-                        resolved_integration.context_file,
-                        preserve_markers=True,
-                    )
-
                 ensure_executable_scripts(project_path, tracker=tracker)
 
                 if preset:

src/specify_cli/extensions/__init__.py

@@ -2057,12 +2057,18 @@ class ExtensionCatalog(CatalogStackBase):
     ) -> Optional[str]:
         """Resolve a GitHub release asset URL to its API asset URL.
 
-        Delegates to the shared helper in :mod:`specify_cli._github_http`.
+        Delegates to the shared helper in :mod:`specify_cli._github_http`,
+        passing the ``github`` provider hosts from ``auth.json`` so GitHub
+        Enterprise Server release assets resolve via ``/api/v3``.
         """
         from specify_cli._github_http import resolve_github_release_asset_api_url
+        from specify_cli.authentication.http import github_provider_hosts
 
         return resolve_github_release_asset_api_url(
-            download_url, self._open_url, timeout=timeout
+            download_url,
+            self._open_url,
+            timeout=timeout,
+            github_hosts=github_provider_hosts(),
         )
 
     def _validate_catalog_payload(self, catalog_data: Any, url: str) -> None:

src/specify_cli/extensions/_commands.py

@@ -482,6 +482,7 @@ def extension_add(
 
             elif from_url:
                 # Install from URL (ZIP file)
+                import io
                 import urllib.error
 
                 console.print(f"Downloading from {safe_url}...")
@@ -498,10 +499,33 @@ def extension_add(
                     zip_path = Path(download_file.name)
 
                 try:
-                    from specify_cli.authentication.http import open_url as _open_url
+                    # Use the catalog's authenticated fetch so configured
+                    # credentials (incl. GitHub Enterprise Server) are applied
+                    # and GHES release-asset URLs resolve via /api/v3 — keeping
+                    # --from consistent with catalog-based installs.
+                    dl_catalog = ExtensionCatalog(project_root)
+                    download_url = from_url
+                    extra_headers = None
+                    resolved_url = dl_catalog._resolve_github_release_asset_api_url(download_url)
+                    if resolved_url:
+                        download_url = resolved_url
+                        extra_headers = {"Accept": "application/octet-stream"}
 
-                    with _open_url(from_url, timeout=60) as response:
+                    with dl_catalog._open_url(
+                        download_url, timeout=60, extra_headers=extra_headers
+                    ) as response:
                         zip_data = response.read()
+
+                    if not zipfile.is_zipfile(io.BytesIO(zip_data)):
+                        console.print(
+                            f"[red]Error:[/red] {safe_url} did not return a ZIP archive "
+                            f"(got {len(zip_data)} bytes). This usually means the request "
+                            f"was not authenticated and a login/HTML page was returned. "
+                            f"Verify the URL is correct and that credentials for its host "
+                            f"are configured in ~/.specify/auth.json."
+                        )
+                        raise typer.Exit(1)
+
                     zip_path.write_bytes(zip_data)
 
                     # Install from downloaded ZIP

src/specify_cli/integration_scaffold.py

@@ -117,11 +117,6 @@ class {class_name}({template.base_class}):
         "args": "{template.args}",
         "extension": "{template.extension}",
     }}
-    context_file = "AGENTS.md"
-    # Default to False so the generated boilerplate passes the registry
-    # contract out of the box: multi-install-safe integrations must each have a
-    # distinct context_file, and the placeholder above ("AGENTS.md") collides
-    # with the existing codex integration. Opt in once you pick a unique one.
     multi_install_safe = False
 '''
 
@@ -155,7 +150,6 @@ def test_metadata():
     assert integration.registrar_config["format"] == "{template.registrar_format}"
     assert integration.registrar_config["args"] == "{template.args}"
     assert integration.registrar_config["extension"] == "{template.extension}"
-    assert integration.context_file == "AGENTS.md"
     assert integration.multi_install_safe is False
 '''
 
@@ -274,7 +268,7 @@ def scaffold_integration(
 
     next_steps = (
         f"Register {class_name} in src/specify_cli/integrations/__init__.py.",
-        "Review config metadata, install_url, requires_cli, context_file, and multi_install_safe.",
+        "Review config metadata, install_url, requires_cli, and multi_install_safe.",
         f"Run pytest tests/integrations/test_integration_{package_name}.py -v.",
     )
     return IntegrationScaffoldResult(

src/specify_cli/integrations/_helpers.py

@@ -103,38 +103,17 @@ def _refresh_init_options_speckit_version(project_root: Path) -> None:
 
 
 def _clear_init_options_for_integration(project_root: Path, integration_key: str) -> None:
-    """Clear active integration keys from init-options.json when they match.
-
-    Also clears ``context_file`` from the agent-context extension config so
-    no stale path is left behind when the integration is uninstalled.
-    """
+    """Clear active integration keys from init-options.json when they match."""
     from .. import (
-        _AGENT_CTX_EXT_CONFIG,
-        _update_agent_context_config_file,
         load_init_options,
         save_init_options,
     )
     opts = load_init_options(project_root)
-    has_legacy_context_keys = ("context_file" in opts) or ("context_markers" in opts)
-    # Remove legacy fields that older versions may have written.
-    opts.pop("context_file", None)
-    opts.pop("context_markers", None)
-
     if opts.get("integration") == integration_key or opts.get("ai") == integration_key:
         opts.pop("integration", None)
         opts.pop("ai", None)
         opts.pop("ai_skills", None)
         save_init_options(project_root, opts)
-        # Clear context_file in the extension config if it already exists.
-        # Avoid creating the config (and parent dirs) in projects where the
-        # agent-context extension was never installed.
-        ext_cfg_path = project_root / _AGENT_CTX_EXT_CONFIG
-        if ext_cfg_path.exists():
-            _update_agent_context_config_file(
-                project_root, "", preserve_markers=True, preserve_context_files=False
-            )
-    elif has_legacy_context_keys:
-        save_init_options(project_root, opts)
 
 
 def _remove_integration_json(project_root: Path) -> None:
@@ -274,21 +253,13 @@ def _update_init_options_for_integration(
     integration: Any,
     script_type: str | None = None,
 ) -> None:
-    """Update init-options.json and the agent-context extension config to
-    reflect *integration* as the active one.
+    """Update init-options.json to reflect *integration* as the active one.
 
-    ``context_file``, ``context_files``, and ``context_markers`` are stored in the agent-context
-    extension config (``.specify/extensions/agent-context/agent-context-config.yml``),
-    not in ``init-options.json``.  Existing user-customised markers are
-    always preserved when the config already exists. Existing ``context_files``
-    lists are also preserved so projects can keep multi-agent context anchors
-    during integration switches. Invalid marker values are
-    silently ignored at runtime by ``_resolve_context_markers()`` which falls
-    back to the class-level defaults.
+    Agent context/instruction files are owned entirely by the opt-in
+    agent-context extension, so this function never touches the extension
+    or its config.
     """
     from .. import (
-        _AGENT_CTX_EXT_CONFIG,
-        _update_agent_context_config_file,
         load_init_options,
         save_init_options,
     )
@@ -296,9 +267,6 @@ def _update_init_options_for_integration(
     opts = load_init_options(project_root)
     opts["integration"] = integration.key
     opts["ai"] = integration.key
-    # Remove legacy fields if they were written by an older version.
-    opts.pop("context_file", None)
-    opts.pop("context_markers", None)
     opts["speckit_version"] = _get_speckit_version()
     if script_type:
         opts["script"] = script_type
@@ -307,24 +275,6 @@ def _update_init_options_for_integration(
     else:
         opts.pop("ai_skills", None)
 
-    # Update the agent-context extension config BEFORE init-options.json
-    # so a failure here doesn't leave init-options partially updated.
-    ext_cfg_path = project_root / _AGENT_CTX_EXT_CONFIG
-    if ext_cfg_path.exists():
-        _update_agent_context_config_file(
-            project_root,
-            integration.context_file,
-            preserve_markers=True,
-        )
-    elif integration.context_file:
-        # Extension config doesn't exist yet (extension not installed).
-        # Write defaults so scripts have something to read.
-        _update_agent_context_config_file(
-            project_root,
-            integration.context_file,
-            preserve_markers=False,
-        )
-
     save_init_options(project_root, opts)
 
 

src/specify_cli/integrations/agy/__init__.py

@@ -42,7 +42,6 @@ class AgyIntegration(SkillsIntegration):
         "args": "$ARGUMENTS",
         "extension": "/SKILL.md",
     }
-    context_file = "AGENTS.md"
 
     @staticmethod
     def _inject_hook_command_note(content: str) -> str:

src/specify_cli/integrations/amp/__init__.py

@@ -18,4 +18,3 @@ class AmpIntegration(MarkdownIntegration):
         "args": "$ARGUMENTS",
         "extension": ".md",
     }
-    context_file = "AGENTS.md"

src/specify_cli/integrations/auggie/__init__.py

@@ -18,5 +18,4 @@ class AuggieIntegration(MarkdownIntegration):
         "args": "$ARGUMENTS",
         "extension": ".md",
     }
-    context_file = ".augment/rules/specify-rules.md"
     multi_install_safe = True

src/specify_cli/integrations/base.py

@@ -13,14 +13,13 @@ Provides:
 
 from __future__ import annotations
 
-import json
 import os
 import re
 import shlex
 import shutil
 from abc import ABC
 from dataclasses import dataclass
-from pathlib import Path, PureWindowsPath
+from pathlib import Path
 from typing import TYPE_CHECKING, Any
 
 import yaml
@@ -91,13 +90,9 @@ class IntegrationBase(ABC):
 
     And may optionally set:
 
-    * ``context_file``     — path (relative to project root) of the agent
-                             context/instructions file (e.g. ``"CLAUDE.md"``)
-
-    Projects may additionally opt into managing multiple context files by
-    setting ``context_files`` in the agent-context extension config. The
-    integration class still declares one default ``context_file`` for backwards
-    compatibility and command-template rendering.
+    * ``invoke_separator`` — slash-command separator (defaults to ``"."``)
+    * ``multi_install_safe`` — declare the integration safe to install
+      alongside others (defaults to ``False``)
     """
 
     # -- Must be set by every subclass ------------------------------------
@@ -113,9 +108,6 @@ class IntegrationBase(ABC):
 
     # -- Optional ---------------------------------------------------------
 
-    context_file: str | None = None
-    """Relative path to the agent context file (e.g. ``CLAUDE.md``)."""
-
     invoke_separator: str = "."
     """Separator used in slash-command invocations (``"."`` → ``/speckit.plan``)."""
 
@@ -125,16 +117,11 @@ class IntegrationBase(ABC):
     multi_install_safe: bool = False
     """Whether this integration is declared safe to install alongside others.
 
-    Safe integrations must use a static, unique agent root, command directory,
-    and context file. Registry tests enforce those invariants for every
+    Safe integrations must use a static, unique agent root and command
+    directory. Registry tests enforce those invariants for every
     integration that sets this flag.
     """
 
-    # -- Markers for managed context section ------------------------------
-
-    CONTEXT_MARKER_START = "<!-- SPECKIT START -->"
-    CONTEXT_MARKER_END = "<!-- SPECKIT END -->"
-
     # -- Public API -------------------------------------------------------
 
     @classmethod
@@ -533,498 +520,6 @@ class IntegrationBase(ABC):
 
         return created
 
-    # -- Agent context file management ------------------------------------
-
-    @staticmethod
-    def _ensure_mdc_frontmatter(content: str) -> str:
-        """Ensure ``.mdc`` content has YAML frontmatter with ``alwaysApply: true``.
-
-        If frontmatter is missing, prepend it.  If frontmatter exists but
-        ``alwaysApply`` is absent or not ``true``, inject/fix it.
-
-        Uses string/regex manipulation to preserve comments and formatting
-        in existing frontmatter.
-        """
-        import re as _re
-
-        leading_ws = len(content) - len(content.lstrip())
-        leading = content[:leading_ws]
-        stripped = content[leading_ws:]
-
-        if not stripped.startswith("---"):
-            return "---\nalwaysApply: true\n---\n\n" + content
-
-        # Match frontmatter block: ---\n...\n---
-        match = _re.match(
-            r"^(---[ \t]*\r?\n)(.*?)(\r?\n---[ \t]*)(\r?\n|$)(.*)",
-            stripped,
-            _re.DOTALL,
-        )
-        if not match:
-            return "---\nalwaysApply: true\n---\n\n" + content
-
-        opening, fm_text, closing, sep, rest = match.groups()
-        newline = "\r\n" if "\r\n" in opening else "\n"
-
-        # Already correct?
-        if _re.search(
-            r"(?m)^[ \t]*alwaysApply[ \t]*:[ \t]*true[ \t]*(?:#.*)?$", fm_text
-        ):
-            return content
-
-        # alwaysApply exists but wrong value — fix in place while preserving
-        # indentation and any trailing inline comment.
-        if _re.search(r"(?m)^[ \t]*alwaysApply[ \t]*:", fm_text):
-            fm_text = _re.sub(
-                r"(?m)^([ \t]*)alwaysApply[ \t]*:.*?([ \t]*(?:#.*)?)$",
-                r"\1alwaysApply: true\2",
-                fm_text,
-                count=1,
-            )
-        elif fm_text.strip():
-            fm_text = fm_text + newline + "alwaysApply: true"
-        else:
-            fm_text = "alwaysApply: true"
-
-        return f"{leading}{opening}{fm_text}{closing}{sep}{rest}"
-
-    @staticmethod
-    def _build_context_section(plan_path: str = "") -> str:
-        """Build the content for the managed section between markers.
-
-        *plan_path* is the project-relative path to the current plan
-        (e.g. ``"specs/<feature>/plan.md"``).  When empty, the section
-        contains only the generic directive without a concrete path.
-        """
-        lines = [
-            "For additional context about technologies to be used, project structure,",
-            "shell commands, and other important information, read the current plan",
-        ]
-        if plan_path:
-            lines.append(f"at {plan_path}")
-        return "\n".join(lines)
-
-    @staticmethod
-    def _agent_context_extension_enabled(project_root: Path) -> bool:
-        """Return whether the bundled ``agent-context`` extension is enabled.
-
-        The extension is the single source of truth for managing coding
-        agent context/instruction files (e.g. ``CLAUDE.md``,
-        ``.github/copilot-instructions.md``).
-
-        Returns ``True`` (enabled) when:
-        - the extension registry does not exist (legacy project, backwards
-          compatibility), or
-        - the registry has no ``agent-context`` entry (older project layout
-          predating the extension), or
-        - the entry is present and not explicitly disabled.
-
-        Returns ``False`` only when an entry exists with ``enabled: false``.
-        """
-        registry_path = (
-            project_root / ".specify" / "extensions" / ".registry"
-        )
-        if not registry_path.exists():
-            return True
-        try:
-            data = json.loads(registry_path.read_text(encoding="utf-8"))
-        except (OSError, ValueError, UnicodeError):
-            return True
-        if not isinstance(data, dict):
-            return True
-        extensions = data.get("extensions")
-        if not isinstance(extensions, dict):
-            return True
-        entry = extensions.get("agent-context")
-        if not isinstance(entry, dict):
-            return True
-        return entry.get("enabled", True) is not False
-
-    @staticmethod
-    def _context_file_dedupe_key(path: str) -> str:
-        """Return the comparison key for context file de-duplication."""
-        return path.casefold() if os.name == "nt" else path
-
-    def _resolve_context_markers(self, project_root: Path) -> tuple[str, str]:
-        """Return the (start, end) context markers to use for *project_root*.
-
-        Reads ``context_markers.start`` / ``context_markers.end`` from the
-        agent-context extension config
-        (``.specify/extensions/agent-context/agent-context-config.yml``)
-        when present.  Falls back to the class-level constants
-        ``CONTEXT_MARKER_START`` / ``CONTEXT_MARKER_END`` when the file is
-        missing, the section is absent, or the values are not non-empty
-        strings.
-        """
-        from .._console import console  # local import to avoid cycles
-
-        start = self.CONTEXT_MARKER_START
-        end = self.CONTEXT_MARKER_END
-        config_path = (
-            project_root
-            / ".specify"
-            / "extensions"
-            / "agent-context"
-            / "agent-context-config.yml"
-        )
-        try:
-            raw = config_path.read_text(encoding="utf-8")
-            cfg = yaml.safe_load(raw)
-        except (OSError, UnicodeError, ValueError, yaml.YAMLError):
-            return start, end
-        markers = cfg.get("context_markers") if isinstance(cfg, dict) else None
-        if isinstance(markers, dict):
-            cm_start = markers.get("start")
-            cm_end = markers.get("end")
-            s_valid = isinstance(cm_start, str) and cm_start
-            e_valid = isinstance(cm_end, str) and cm_end
-            if not s_valid and cm_start is not None:
-                console.print(
-                    f"[yellow]agent-context: ignoring invalid context_markers.start "
-                    f"({cm_start!r}), using default[/yellow]"
-                )
-            if not e_valid and cm_end is not None:
-                console.print(
-                    f"[yellow]agent-context: ignoring invalid context_markers.end "
-                    f"({cm_end!r}), using default[/yellow]"
-                )
-            if s_valid:
-                start = cm_start  # type: ignore[assignment]
-            if e_valid:
-                end = cm_end  # type: ignore[assignment]
-        return start, end
-
-    @staticmethod
-    def _validate_context_file_path(project_root: Path, context_file: str) -> str:
-        """Return a safe project-relative context file path.
-
-        The agent-context scripts reject paths that can escape the project
-        root; the Python integration path must apply the same guard before
-        setup or teardown touches context files.
-        """
-        candidate = context_file.strip()
-        if not candidate:
-            raise ValueError("agent-context: context file path must not be empty")
-
-        win_path = PureWindowsPath(candidate)
-        if Path(candidate).is_absolute() or win_path.drive or win_path.root:
-            raise ValueError(
-                "agent-context: context files must be project-relative paths; "
-                f"got {candidate!r}"
-            )
-        if "\\" in candidate:
-            raise ValueError(
-                "agent-context: context files must not contain backslash "
-                f"separators; got {candidate!r}"
-            )
-
-        parts = [part for part in re.split(r"[\\/]+", candidate) if part]
-        if ".." in parts:
-            raise ValueError(
-                "agent-context: context files must not contain '..' path "
-                f"segments; got {candidate!r}"
-            )
-
-        root = project_root.resolve()
-        target = (root / candidate).resolve(strict=False)
-        try:
-            target.relative_to(root)
-        except ValueError as exc:
-            raise ValueError(
-                "agent-context: context file path resolves outside the project "
-                f"root; got {candidate!r}"
-            ) from exc
-
-        return candidate
-
-    @classmethod
-    def _resolve_context_file_values(
-        cls,
-        project_root: Path,
-        cfg: dict[str, Any] | None,
-        *,
-        fallback_context_file: Any = None,
-        legacy_context_file: Any = None,
-        include_context_files: bool = True,
-        validate: bool = True,
-    ) -> list[str]:
-        """Resolve context file config with shared precedence and de-duplication."""
-        files: list[str] = []
-        seen: set[str] = set()
-
-        def add_context_file(value: Any) -> None:
-            if not isinstance(value, str):
-                return
-            candidate = value.strip()
-            if not candidate:
-                return
-            if validate:
-                candidate = cls._validate_context_file_path(project_root, candidate)
-            key = cls._context_file_dedupe_key(candidate)
-            if key in seen:
-                return
-            files.append(candidate)
-            seen.add(key)
-
-        if isinstance(cfg, dict) and include_context_files:
-            configured = cfg.get("context_files")
-            if isinstance(configured, list):
-                for value in configured:
-                    add_context_file(value)
-                if files:
-                    return files
-
-        if isinstance(cfg, dict):
-            add_context_file(cfg.get("context_file"))
-            if files:
-                return files
-
-        add_context_file(fallback_context_file)
-        if files:
-            return files
-
-        add_context_file(legacy_context_file)
-        return files
-
-    @staticmethod
-    def _format_context_file_values(context_files: list[str]) -> str:
-        """Return context file targets as the template display string."""
-        return ", ".join(context_files)
-
-    def _resolve_context_files(self, project_root: Path) -> list[str]:
-        """Return project-relative context files managed for *project_root*.
-
-        ``context_files`` in the agent-context extension config, when present
-        and non-empty, takes precedence over the config's singular
-        ``context_file``. The integration class default is used only when the
-        extension config has no context file target.
-        Raises ``ValueError`` when a configured path can escape the project
-        root.
-        """
-        config_path = (
-            project_root
-            / ".specify"
-            / "extensions"
-            / "agent-context"
-            / "agent-context-config.yml"
-        )
-        try:
-            raw = config_path.read_text(encoding="utf-8")
-            cfg = yaml.safe_load(raw)
-        except (OSError, UnicodeError, ValueError, yaml.YAMLError):
-            cfg = None
-        return self._resolve_context_file_values(
-            project_root,
-            cfg,
-            fallback_context_file=self.context_file,
-        )
-
-    def _context_file_display(self, project_root: Path) -> str:
-        """Return human-readable context file target(s) for templates."""
-        if not self._agent_context_extension_enabled(project_root):
-            from .. import _load_agent_context_config
-
-            context_files = self._resolve_context_file_values(
-                project_root,
-                _load_agent_context_config(project_root),
-                fallback_context_file=self.context_file,
-                include_context_files=False,
-                validate=False,
-            )
-            return context_files[0] if context_files else ""
-        return self._format_context_file_values(
-            self._resolve_context_files(project_root)
-        )
-
-    @staticmethod
-    def _upsert_context_file(
-        ctx_path: Path,
-        section: str,
-        marker_start: str,
-        marker_end: str,
-    ) -> None:
-        """Create or update one managed context section."""
-        if ctx_path.exists():
-            content = ctx_path.read_text(encoding="utf-8-sig")
-            start_idx = content.find(marker_start)
-            end_idx = content.find(
-                marker_end,
-                start_idx if start_idx != -1 else 0,
-            )
-
-            if start_idx != -1 and end_idx != -1 and end_idx > start_idx:
-                # Replace existing section (include the end marker + newline)
-                end_of_marker = end_idx + len(marker_end)
-                # Consume trailing line ending (CRLF or LF)
-                if end_of_marker < len(content) and content[end_of_marker] == "\r":
-                    end_of_marker += 1
-                if end_of_marker < len(content) and content[end_of_marker] == "\n":
-                    end_of_marker += 1
-                new_content = content[:start_idx] + section + content[end_of_marker:]
-            elif start_idx != -1:
-                # Corrupted: start marker without end — replace from start through EOF
-                new_content = content[:start_idx] + section
-            elif end_idx != -1:
-                # Corrupted: end marker without start — replace BOF through end marker
-                end_of_marker = end_idx + len(marker_end)
-                if end_of_marker < len(content) and content[end_of_marker] == "\r":
-                    end_of_marker += 1
-                if end_of_marker < len(content) and content[end_of_marker] == "\n":
-                    end_of_marker += 1
-                new_content = section + content[end_of_marker:]
-            else:
-                # No markers found — append
-                if content:
-                    if not content.endswith("\n"):
-                        content += "\n"
-                    new_content = content + "\n" + section
-                else:
-                    new_content = section
-
-            # Ensure .mdc files have required YAML frontmatter
-            if ctx_path.suffix == ".mdc":
-                new_content = IntegrationBase._ensure_mdc_frontmatter(new_content)
-        else:
-            ctx_path.parent.mkdir(parents=True, exist_ok=True)
-            # Cursor .mdc files require YAML frontmatter to be loaded
-            if ctx_path.suffix == ".mdc":
-                new_content = IntegrationBase._ensure_mdc_frontmatter(section)
-            else:
-                new_content = section
-
-        normalized = new_content.replace("\r\n", "\n").replace("\r", "\n")
-        ctx_path.write_bytes(normalized.encode("utf-8"))
-
-    def upsert_context_section(
-        self,
-        project_root: Path,
-        plan_path: str = "",
-    ) -> Path | None:
-        """Create or update the managed section in the agent context file.
-
-        If the context file does not exist it is created with just the
-        managed section.  If it exists, the content between the configured
-        start/end markers (default ``<!-- SPECKIT START -->`` /
-        ``<!-- SPECKIT END -->``) is replaced, or appended when no markers
-        are found. Markers are read from the agent-context extension config
-        (``.specify/extensions/agent-context/agent-context-config.yml``)
-        when present, falling back to the class-level constants.
-
-        Returns the path to the first context file, or ``None`` when no context
-        files are configured or the ``agent-context`` extension is
-        disabled.
-        """
-        if not self._agent_context_extension_enabled(project_root):
-            return None
-
-        context_files = self._resolve_context_files(project_root)
-        if not context_files:
-            return None
-
-        from .._console import console  # local import to avoid cycles
-
-        console.print(
-            "[yellow]Deprecation:[/yellow] Inline agent-context updates during "
-            "integration setup will be disabled in v0.12.0. Context file "
-            "management has moved to the bundled [bold]agent-context[/bold] "
-            "extension. Run [cyan]specify extension disable agent-context[/cyan] "
-            "to opt out early.",
-            highlight=False,
-        )
-
-        marker_start, marker_end = self._resolve_context_markers(project_root)
-
-        section = (
-            f"{marker_start}\n"
-            f"{self._build_context_section(plan_path)}\n"
-            f"{marker_end}\n"
-        )
-
-        first_path: Path | None = None
-        for context_file in context_files:
-            ctx_path = project_root / context_file
-            self._upsert_context_file(ctx_path, section, marker_start, marker_end)
-            if first_path is None:
-                first_path = ctx_path
-        return first_path
-
-    def remove_context_section(self, project_root: Path) -> bool:
-        """Remove the managed section from the agent context file.
-
-        Returns ``True`` if the section was found and removed.  If the
-        file becomes empty (or whitespace-only) after removal it is deleted.
-        Markers are read from the agent-context extension config
-        (``.specify/extensions/agent-context/agent-context-config.yml``)
-        when present, falling back to the class-level constants.
-        """
-        if not self._agent_context_extension_enabled(project_root):
-            return False
-
-        context_files = self._resolve_context_files(project_root)
-        if not context_files:
-            return False
-
-        marker_start, marker_end = self._resolve_context_markers(project_root)
-        removed_any = False
-
-        for context_file in context_files:
-            ctx_path = project_root / context_file
-            if not ctx_path.exists():
-                continue
-
-            content = ctx_path.read_text(encoding="utf-8-sig")
-            start_idx = content.find(marker_start)
-            end_idx = content.find(
-                marker_end,
-                start_idx if start_idx != -1 else 0,
-            )
-
-            # Only remove a complete, well-ordered managed section. If either
-            # marker is missing, leave the file unchanged to avoid deleting
-            # unrelated user-authored content.
-            if start_idx == -1 or end_idx == -1 or end_idx <= start_idx:
-                continue
-
-            removal_start = start_idx
-            removal_end = end_idx + len(marker_end)
-
-            # Consume trailing line ending (CRLF or LF)
-            if removal_end < len(content) and content[removal_end] == "\r":
-                removal_end += 1
-            if removal_end < len(content) and content[removal_end] == "\n":
-                removal_end += 1
-
-            # Also strip a blank line before the section if present
-            if removal_start > 0 and content[removal_start - 1] == "\n":
-                if removal_start > 1 and content[removal_start - 2] == "\n":
-                    removal_start -= 1
-
-            new_content = content[:removal_start] + content[removal_end:]
-
-            # Normalize line endings before comparisons
-            normalized = new_content.replace("\r\n", "\n").replace("\r", "\n")
-
-            # For .mdc files, treat Speckit-generated frontmatter-only content as empty
-            if ctx_path.suffix == ".mdc":
-                import re
-
-                # Delete the file if only YAML frontmatter remains (no body content)
-                frontmatter_only = re.match(
-                    r"^---\n.*?\n---\s*$", normalized, re.DOTALL
-                )
-                if not normalized.strip() or frontmatter_only:
-                    ctx_path.unlink()
-                    removed_any = True
-                    continue
-
-            if not normalized.strip():
-                ctx_path.unlink()
-            else:
-                ctx_path.write_bytes(normalized.encode("utf-8"))
-            removed_any = True
-
-        return removed_any
-
     @staticmethod
     def resolve_command_refs(content: str, separator: str = ".") -> str:
         """Replace ``__SPECKIT_COMMAND_<NAME>__`` placeholders with invocations.
@@ -1049,7 +544,6 @@ class IntegrationBase(ABC):
         agent_name: str,
         script_type: str,
         arg_placeholder: str = "$ARGUMENTS",
-        context_file: str = "",
         invoke_separator: str = ".",
     ) -> str:
         """Process a raw command template into agent-ready content.
@@ -1060,9 +554,8 @@ class IntegrationBase(ABC):
         3. Strip ``scripts:`` section from frontmatter
         4. Replace ``{ARGS}`` and ``$ARGUMENTS`` with *arg_placeholder*
         5. Replace ``__AGENT__`` with *agent_name*
-        6. Replace ``__CONTEXT_FILE__`` with *context_file*
-        7. Rewrite paths: ``scripts/`` → ``.specify/scripts/`` etc.
-        8. Replace ``__SPECKIT_COMMAND_<NAME>__`` with invocation strings
+        6. Rewrite paths: ``scripts/`` → ``.specify/scripts/`` etc.
+        7. Replace ``__SPECKIT_COMMAND_<NAME>__`` with invocation strings
         """
         # 1. Extract script command from frontmatter
         script_command = ""
@@ -1122,10 +615,7 @@ class IntegrationBase(ABC):
         # 5. Replace __AGENT__
         content = content.replace("__AGENT__", agent_name)
 
-        # 6. Replace __CONTEXT_FILE__
-        content = content.replace("__CONTEXT_FILE__", context_file)
-
-        # 7. Rewrite paths — delegate to the shared implementation in
+        # 6. Rewrite paths — delegate to the shared implementation in
         #    CommandRegistrar so extension-local paths are preserved and
         #    boundary rules stay consistent across the codebase.
         from specify_cli.agents import CommandRegistrar
@@ -1180,8 +670,6 @@ class IntegrationBase(ABC):
             self.record_file_in_manifest(dst_file, project_root, manifest)
             created.append(dst_file)
 
-        # Upsert managed context section into the agent context file
-        self.upsert_context_section(project_root)
 
         return created
 
@@ -1196,11 +684,9 @@ class IntegrationBase(ABC):
 
         Delegates to ``manifest.uninstall()`` which only removes files
         whose hash still matches the recorded value (unless *force*).
-        Also removes the managed context section from the agent file.
 
         Returns ``(removed, skipped)`` file lists.
         """
-        self.remove_context_section(project_root)
         return manifest.uninstall(project_root, force=force)
 
     # -- Convenience helpers for subclasses -------------------------------
@@ -1234,12 +720,11 @@ class IntegrationBase(ABC):
 class MarkdownIntegration(IntegrationBase):
     """Concrete base for integrations that use standard Markdown commands.
 
-    Subclasses only need to set ``key``, ``config``, ``registrar_config``
-    (and optionally ``context_file``).  Everything else is inherited.
+    Subclasses only need to set ``key``, ``config``, ``registrar_config``.
+    Everything else is inherited.
 
     ``setup()`` processes command templates (replacing ``{SCRIPT}``,
-    ``{ARGS}``, ``__AGENT__``, rewriting paths) and upserts the
-    managed context section into the agent context file.
+    ``{ARGS}``, ``__AGENT__``, rewriting paths).
     """
 
     def build_exec_args(
@@ -1294,13 +779,11 @@ class MarkdownIntegration(IntegrationBase):
             else "$ARGUMENTS"
         )
         created: list[Path] = []
-        context_file_display = self._context_file_display(project_root)
 
         for src_file in templates:
             raw = src_file.read_text(encoding="utf-8")
             processed = self.process_template(
                 raw, self.key, script_type, arg_placeholder,
-                context_file=context_file_display,
             )
             dst_name = self.command_filename(src_file.stem)
             dst_file = self.write_file_and_record(
@@ -1308,8 +791,6 @@ class MarkdownIntegration(IntegrationBase):
             )
             created.append(dst_file)
 
-        # Upsert managed context section into the agent context file
-        self.upsert_context_section(project_root)
 
         return created
 
@@ -1323,8 +804,7 @@ class TomlIntegration(IntegrationBase):
     """Concrete base for integrations that use TOML command format.
 
     Mirrors ``MarkdownIntegration`` closely: subclasses only need to set
-    ``key``, ``config``, ``registrar_config`` (and optionally
-    ``context_file``).  Everything else is inherited.
+    ``key``, ``config``, ``registrar_config``.  Everything else is inherited.
 
     ``setup()`` processes command templates through the same placeholder
     pipeline as ``MarkdownIntegration``, then converts the result to
@@ -1500,14 +980,12 @@ class TomlIntegration(IntegrationBase):
             else "{{args}}"
         )
         created: list[Path] = []
-        context_file_display = self._context_file_display(project_root)
 
         for src_file in templates:
             raw = src_file.read_text(encoding="utf-8")
             description = self._extract_description(raw)
             processed = self.process_template(
                 raw, self.key, script_type, arg_placeholder,
-                context_file=context_file_display,
             )
             _, body = self._split_frontmatter(processed)
             toml_content = self._render_toml(description, body)
@@ -1517,8 +995,6 @@ class TomlIntegration(IntegrationBase):
             )
             created.append(dst_file)
 
-        # Upsert managed context section into the agent context file
-        self.upsert_context_section(project_root)
 
         return created
 
@@ -1532,8 +1008,7 @@ class YamlIntegration(IntegrationBase):
     """Concrete base for integrations that use YAML recipe format.
 
     Mirrors ``TomlIntegration`` closely: subclasses only need to set
-    ``key``, ``config``, ``registrar_config`` (and optionally
-    ``context_file``).  Everything else is inherited.
+    ``key``, ``config``, ``registrar_config``.  Everything else is inherited.
 
     ``setup()`` processes command templates through the same placeholder
     pipeline as ``MarkdownIntegration``, then converts the result to
@@ -1696,7 +1171,6 @@ class YamlIntegration(IntegrationBase):
             else "{{args}}"
         )
         created: list[Path] = []
-        context_file_display = self._context_file_display(project_root)
 
         for src_file in templates:
             raw = src_file.read_text(encoding="utf-8")
@@ -1712,7 +1186,6 @@ class YamlIntegration(IntegrationBase):
 
             processed = self.process_template(
                 raw, self.key, script_type, arg_placeholder,
-                context_file=context_file_display,
             )
             _, body = self._split_frontmatter(processed)
             yaml_content = self._render_yaml(
@@ -1724,8 +1197,6 @@ class YamlIntegration(IntegrationBase):
             )
             created.append(dst_file)
 
-        # Upsert managed context section into the agent context file
-        self.upsert_context_section(project_root)
 
         return created
 
@@ -1741,8 +1212,8 @@ class SkillsIntegration(IntegrationBase):
     Skills use the ``speckit-<name>/SKILL.md`` directory layout following
     the `agentskills.io <https://agentskills.io/specification>`_ spec.
 
-    Subclasses set ``key``, ``config``, ``registrar_config`` (and
-    optionally ``context_file``) like any integration.  They may also
+    Subclasses set ``key``, ``config``, ``registrar_config`` like any
+    integration.  They may also
     override ``options()`` to declare additional CLI flags (e.g.
     ``--skills``, ``--migrate-legacy``).
 
@@ -1887,7 +1358,6 @@ class SkillsIntegration(IntegrationBase):
             else "$ARGUMENTS"
         )
         created: list[Path] = []
-        context_file_display = self._context_file_display(project_root)
 
         for src_file in templates:
             raw = src_file.read_text(encoding="utf-8")
@@ -1911,7 +1381,6 @@ class SkillsIntegration(IntegrationBase):
             # Process body through the standard template pipeline
             processed_body = self.process_template(
                 raw, self.key, script_type, arg_placeholder,
-                context_file=context_file_display,
                 invoke_separator=self.invoke_separator,
             )
             # Strip the processed frontmatter — we rebuild it for skills.
@@ -1958,7 +1427,5 @@ class SkillsIntegration(IntegrationBase):
             )
             created.append(dst)
 
-        # Upsert managed context section into the agent context file
-        self.upsert_context_section(project_root)
 
         return created

src/specify_cli/integrations/bob/__init__.py

@@ -18,4 +18,3 @@ class BobIntegration(MarkdownIntegration):
         "args": "$ARGUMENTS",
         "extension": ".md",
     }
-    context_file = "AGENTS.md"

src/specify_cli/integrations/claude/__init__.py

@@ -22,13 +22,17 @@ ARGUMENT_HINTS: dict[str, str] = {
 }
 
 # Per-command frontmatter overrides for skills that should run in a forked
-# subagent context. Read-only analysis commands are good candidates: the
-# heavy reads (spec/plan/tasks artefacts) collapse to a short summary,
-# so isolating them keeps the main conversation context clean.
-# See https://code.claude.com/docs/en/skills#run-skills-in-a-subagent
-FORK_CONTEXT_COMMANDS: dict[str, dict[str, str]] = {
-    "analyze": {"context": "fork", "agent": "general-purpose"},
-}
+# subagent context. See https://code.claude.com/docs/en/skills#run-skills-in-a-subagent
+#
+# This is intentionally empty. ``analyze`` was previously forked (added in
+# #2511) on the assumption that its heavy reads collapse to a short summary,
+# but in practice ``/speckit-analyze`` returns a 300-500 line report that is
+# injected back into the main conversation. In long sessions each subsequent
+# fork inherits that growing context, compounding overhead until the chat
+# freezes (#3185). Until a command genuinely returns a compact result, no
+# command opts into ``context: fork``. The injection mechanism below stays in
+# place so a future command can be added here when that holds true.
+FORK_CONTEXT_COMMANDS: dict[str, dict[str, str]] = {}
 
 
 class ClaudeIntegration(SkillsIntegration):
@@ -48,7 +52,6 @@ class ClaudeIntegration(SkillsIntegration):
         "args": "$ARGUMENTS",
         "extension": "/SKILL.md",
     }
-    context_file = "CLAUDE.md"
     multi_install_safe = True
 
     @staticmethod

src/specify_cli/integrations/cline/__init__.py

@@ -70,7 +70,6 @@ class ClineIntegration(MarkdownIntegration):
         "format_name": format_cline_command_name,
         "invoke_separator": "-",
     }
-    context_file = ".clinerules/specify-rules.md"
     invoke_separator = "-"
     multi_install_safe = True
 

src/specify_cli/integrations/codebuddy/__init__.py

@@ -9,7 +9,7 @@ class CodebuddyIntegration(MarkdownIntegration):
         "name": "CodeBuddy",
         "folder": ".codebuddy/",
         "commands_subdir": "commands",
-        "install_url": "https://www.codebuddy.ai/cli",
+        "install_url": "https://www.codebuddy.cn/docs/cli/installation",
         "requires_cli": True,
     }
     registrar_config = {
@@ -18,5 +18,4 @@ class CodebuddyIntegration(MarkdownIntegration):
         "args": "$ARGUMENTS",
         "extension": ".md",
     }
-    context_file = "CODEBUDDY.md"
     multi_install_safe = True

src/specify_cli/integrations/codex/__init__.py

@@ -26,7 +26,6 @@ class CodexIntegration(SkillsIntegration):
         "args": "$ARGUMENTS",
         "extension": "/SKILL.md",
     }
-    context_file = "AGENTS.md"
     dev_no_symlink = True
     multi_install_safe = True
 

src/specify_cli/integrations/copilot/__init__.py

@@ -4,7 +4,6 @@ Copilot has several unique behaviors compared to standard markdown agents:
 - Commands use ``.agent.md`` extension (not ``.md``)
 - Each command gets a companion ``.prompt.md`` file in ``.github/prompts/``
 - Installs ``.vscode/settings.json`` with prompt file recommendations
-- Context file lives at ``.github/copilot-instructions.md``
 
 When ``--skills`` is passed via ``--integration-options``, Copilot scaffolds
 commands as ``speckit-<name>/SKILL.md`` directories under ``.github/skills/``
@@ -79,7 +78,6 @@ class _CopilotSkillsHelper(SkillsIntegration):
         "args": "$ARGUMENTS",
         "extension": "/SKILL.md",
     }
-    context_file = ".github/copilot-instructions.md"
 
 
 class CopilotIntegration(IntegrationBase):
@@ -108,7 +106,6 @@ class CopilotIntegration(IntegrationBase):
         "args": "$ARGUMENTS",
         "extension": ".agent.md",
     }
-    context_file = ".github/copilot-instructions.md"
 
     # Mutable flag set by setup() — indicates the active scaffolding mode.
     _skills_mode: bool = False
@@ -354,14 +351,12 @@ class CopilotIntegration(IntegrationBase):
 
         script_type = opts.get("script_type", "sh")
         arg_placeholder = self.registrar_config.get("args", "$ARGUMENTS")
-        context_file_display = self._context_file_display(project_root)
 
         # 1. Process and write command files as .agent.md
         for src_file in templates:
             raw = src_file.read_text(encoding="utf-8")
             processed = self.process_template(
                 raw, self.key, script_type, arg_placeholder,
-                context_file=context_file_display,
             )
             dst_name = self.command_filename(src_file.stem)
             dst_file = self.write_file_and_record(
@@ -396,8 +391,6 @@ class CopilotIntegration(IntegrationBase):
                 self.record_file_in_manifest(dst_settings, project_root, manifest)
                 created.append(dst_settings)
 
-        # 4. Upsert managed context section into the agent context file
-        self.upsert_context_section(project_root)
 
         return created
 

src/specify_cli/integrations/cursor_agent/__init__.py

@@ -36,7 +36,6 @@ class CursorAgentIntegration(SkillsIntegration):
         "extension": "/SKILL.md",
     }
 
-    context_file = ".cursor/rules/specify-rules.mdc"
     multi_install_safe = True
 
     def build_exec_args(

src/specify_cli/integrations/devin/__init__.py

@@ -30,7 +30,6 @@ class DevinIntegration(SkillsIntegration):
         "args": "$ARGUMENTS",
         "extension": "/SKILL.md",
     }
-    context_file = "AGENTS.md"
 
     def build_exec_args(
         self,

src/specify_cli/integrations/firebender/__init__.py

@@ -3,8 +3,8 @@
 Firebender (https://firebender.com/) is an AI coding agent for Android Studio
 and IntelliJ. It reads project-local custom slash commands from
 ``.firebender/commands/*.mdc`` and project rules from ``.firebender/rules/*.mdc``,
-so Spec Kit installs its command templates as ``.mdc`` command files and writes
-the managed context section into a ``.firebender/rules/`` rule file.
+so Spec Kit installs its command templates as ``.mdc`` command files. The managed
+context section (when used) is owned by the ``agent-context`` extension.
 """
 
 from ..base import MarkdownIntegration
@@ -25,7 +25,6 @@ class FirebenderIntegration(MarkdownIntegration):
         "args": "$ARGUMENTS",
         "extension": ".mdc",
     }
-    context_file = ".firebender/rules/specify-rules.mdc"
     multi_install_safe = True
 
     def command_filename(self, template_name: str) -> str:

src/specify_cli/integrations/forge/__init__.py

@@ -89,7 +89,6 @@ class ForgeIntegration(MarkdownIntegration):
         "format_name": format_forge_command_name,  # Custom name formatter
         "invoke_separator": "-",
     }
-    context_file = "AGENTS.md"
     invoke_separator = "-"
 
     def setup(
@@ -128,14 +127,12 @@ class ForgeIntegration(MarkdownIntegration):
         script_type = opts.get("script_type", "sh")
         arg_placeholder = self.registrar_config.get("args", "{{parameters}}")
         created: list[Path] = []
-        context_file_display = self._context_file_display(project_root)
 
         for src_file in templates:
             raw = src_file.read_text(encoding="utf-8")
             # Process template with standard MarkdownIntegration logic
             processed = self.process_template(
                 raw, self.key, script_type, arg_placeholder,
-                context_file=context_file_display,
                 invoke_separator=self.invoke_separator,
             )
 
@@ -152,8 +149,6 @@ class ForgeIntegration(MarkdownIntegration):
             )
             created.append(dst_file)
 
-        # Upsert managed context section into the agent context file
-        self.upsert_context_section(project_root)
 
         return created
 

src/specify_cli/integrations/gemini/__init__.py

@@ -18,5 +18,4 @@ class GeminiIntegration(TomlIntegration):
         "args": "{{args}}",
         "extension": ".toml",
     }
-    context_file = "GEMINI.md"
     multi_install_safe = True

src/specify_cli/integrations/generic/__init__.py

@@ -31,7 +31,6 @@ class GenericIntegration(MarkdownIntegration):
         "args": "$ARGUMENTS",
         "extension": ".md",
     }
-    context_file = "AGENTS.md"
 
     @classmethod
     def options(cls) -> list[IntegrationOption]:
@@ -119,13 +118,11 @@ class GenericIntegration(MarkdownIntegration):
         script_type = opts.get("script_type", "sh")
         arg_placeholder = "$ARGUMENTS"
         created: list[Path] = []
-        context_file_display = self._context_file_display(project_root)
 
         for src_file in templates:
             raw = src_file.read_text(encoding="utf-8")
             processed = self.process_template(
                 raw, self.key, script_type, arg_placeholder,
-                context_file=context_file_display,
             )
             dst_name = self.command_filename(src_file.stem)
             dst_file = self.write_file_and_record(
@@ -133,7 +130,5 @@ class GenericIntegration(MarkdownIntegration):
             )
             created.append(dst_file)
 
-        # Upsert managed context section into the agent context file
-        self.upsert_context_section(project_root)
 
         return created

src/specify_cli/integrations/goose/__init__.py

@@ -1,4 +1,4 @@
-"""Goose integration — Block's open source AI agent."""
+"""Goose integration — open source AI agent (Agentic AI Foundation)."""
 
 from ..base import YamlIntegration
 
@@ -9,7 +9,7 @@ class GooseIntegration(YamlIntegration):
         "name": "Goose",
         "folder": ".goose/",
         "commands_subdir": "recipes",
-        "install_url": "https://block.github.io/goose/docs/getting-started/installation",
+        "install_url": "https://goose-docs.ai/docs/getting-started/installation",
         "requires_cli": True,
     }
     registrar_config = {
@@ -18,4 +18,3 @@ class GooseIntegration(YamlIntegration):
         "args": "{{args}}",
         "extension": ".yaml",
     }
-    context_file = "AGENTS.md"

src/specify_cli/integrations/hermes/__init__.py

@@ -50,7 +50,6 @@ class HermesIntegration(SkillsIntegration):
         "args": "$ARGUMENTS",
         "extension": "/SKILL.md",
     }
-    context_file = "AGENTS.md"
 
     # -- Helpers -----------------------------------------------------------
 
@@ -114,7 +113,6 @@ class HermesIntegration(SkillsIntegration):
         global_skills_dir.mkdir(parents=True, exist_ok=True)
 
         created: list[Path] = []
-        context_file_display = self._context_file_display(project_root)
 
         for src_file in templates:
             raw = src_file.read_text(encoding="utf-8")
@@ -141,7 +139,6 @@ class HermesIntegration(SkillsIntegration):
                 self.key,
                 script_type,
                 arg_placeholder,
-                context_file=context_file_display,
                 invoke_separator=self.invoke_separator,
             )
             # Strip the processed frontmatter — we rebuild it for skills.
@@ -183,8 +180,6 @@ class HermesIntegration(SkillsIntegration):
             skill_file.write_bytes(normalized.encode("utf-8"))
             created.append(skill_file)
 
-        # Upsert managed context section into the agent context file
-        self.upsert_context_section(project_root)
 
         # Create project-local marker directory so extension commands
         # (e.g. git) can detect Hermes as an active integration.
@@ -204,8 +199,7 @@ class HermesIntegration(SkillsIntegration):
     ) -> tuple[list[Path], list[Path]]:
         """Uninstall integration files including global Hermes skills.
 
-        Removes the managed context section from AGENTS.md, removes the
-        project-local marker directory (if empty), delegates to
+        Removes the project-local marker directory (if empty), delegates to
         ``manifest.uninstall()`` for project-local tracked files, and
         removes all ``speckit-*`` skills under ``~/.hermes/skills/``.
 
@@ -213,8 +207,6 @@ class HermesIntegration(SkillsIntegration):
         standard integration behaviour where all files created by the
         integration are removed on ``specify integration uninstall``.
         """
-        # Remove managed context section from AGENTS.md
-        self.remove_context_section(project_root)
 
         # Delegate to manifest for project-local tracked files (scripts,
         # templates, context entries tracked in the manifest).

src/specify_cli/integrations/iflow/__init__.py

@@ -18,5 +18,4 @@ class IflowIntegration(MarkdownIntegration):
         "args": "$ARGUMENTS",
         "extension": ".md",
     }
-    context_file = "IFLOW.md"
     multi_install_safe = True

src/specify_cli/integrations/junie/__init__.py

@@ -18,5 +18,4 @@ class JunieIntegration(MarkdownIntegration):
         "args": "$ARGUMENTS",
         "extension": ".md",
     }
-    context_file = ".junie/AGENTS.md"
     multi_install_safe = True

src/specify_cli/integrations/kilocode/__init__.py

@@ -18,5 +18,4 @@ class KilocodeIntegration(MarkdownIntegration):
         "args": "$ARGUMENTS",
         "extension": ".md",
     }
-    context_file = ".kilocode/rules/specify-rules.md"
     multi_install_safe = True

src/specify_cli/integrations/kimi/__init__.py

@@ -5,8 +5,7 @@ Kimi uses the ``.kimi-code/skills/speckit-<name>/SKILL.md`` layout with
 
 Legacy migration covers projects created before Kimi Code CLI moved to
 this layout and handles two distinct changes: the directory move from
-``.kimi/`` to ``.kimi-code/`` (including the ``KIMI.md`` → ``AGENTS.md``
-context file), and the dotted-to-hyphenated skill naming
+``.kimi/`` to ``.kimi-code/``, and the dotted-to-hyphenated skill naming
 (``speckit.xxx`` → ``speckit-xxx``).
 """
 
@@ -16,7 +15,7 @@ import shutil
 from pathlib import Path
 from typing import Any
 
-from ..base import IntegrationBase, IntegrationOption, SkillsIntegration
+from ..base import IntegrationOption, SkillsIntegration
 from ..manifest import IntegrationManifest
 
 
@@ -37,7 +36,6 @@ class KimiIntegration(SkillsIntegration):
         "args": "$ARGUMENTS",
         "extension": "/SKILL.md",
     }
-    context_file = "AGENTS.md"
     multi_install_safe = False
 
     def build_command_invocation(self, command_name: str, args: str = "") -> str:
@@ -79,9 +77,7 @@ class KimiIntegration(SkillsIntegration):
                 default=False,
                 help=(
                     "Migrate legacy Kimi installations: "
-                    ".kimi/skills/ → .kimi-code/skills/, speckit.xxx → speckit-xxx, "
-                    "and (when the agent-context extension is enabled) "
-                    "KIMI.md user content → AGENTS.md"
+                    ".kimi/skills/ → .kimi-code/skills/ and speckit.xxx → speckit-xxx"
                 ),
             ),
         ]
@@ -128,14 +124,6 @@ class KimiIntegration(SkillsIntegration):
                 _is_safe_legacy_dir(new_skills_dir, project_root)
             ):
                 _migrate_legacy_kimi_skills_dir(old_skills_dir, new_skills_dir)
-            # Mirror upsert/remove_context_section: a disabled agent-context
-            # extension is a full opt-out, so skip the KIMI.md → AGENTS.md
-            # migration entirely and leave both files untouched.
-            if self._agent_context_extension_enabled(project_root):
-                marker_start, marker_end = self._resolve_context_markers(project_root)
-                _migrate_legacy_kimi_context_file(
-                    project_root, marker_start=marker_start, marker_end=marker_end
-                )
 
         return created
 
@@ -363,112 +351,6 @@ def _is_speckit_generated_skill(skill_dir: Path) -> bool:
     )
 
 
-def _migrate_legacy_kimi_context_file(
-    project_root: Path,
-    *,
-    marker_start: str = IntegrationBase.CONTEXT_MARKER_START,
-    marker_end: str = IntegrationBase.CONTEXT_MARKER_END,
-) -> bool:
-    """Migrate user content from legacy ``KIMI.md`` to ``AGENTS.md``.
-
-    The Speckit managed section is stripped from ``KIMI.md`` before the
-    remaining content is appended to ``AGENTS.md``. The legacy file is
-    deleted if it becomes empty. Returns ``True`` if ``KIMI.md`` was
-    migrated, ``False`` when the migration is skipped.
-
-    The migration is skipped (leaving ``KIMI.md`` untouched) in any of these
-    cases, so a best-effort legacy cleanup never aborts ``setup()`` or
-    corrupts ``AGENTS.md``:
-
-    - ``KIMI.md`` is a symlink, missing, or unreadable (its target could be
-      read from outside the project, or it may not be valid UTF-8).
-    - ``AGENTS.md`` is a symlink (it could redirect the write to a file
-      outside the project root), exists as a non-file (e.g. a directory),
-      or is unreadable/unwritable.
-    - ``KIMI.md`` has a corrupted managed section — only one marker is
-      present, or the end marker precedes the start. Stripping is only done
-      when both markers are present and well-ordered, so a partial managed
-      block is never copied into ``AGENTS.md``; the user repairs it manually.
-    """
-    legacy_path = project_root / "KIMI.md"
-    if legacy_path.is_symlink() or not legacy_path.is_file():
-        return False
-
-    target_path = project_root / "AGENTS.md"
-    # Never follow a symlinked target, and never treat an existing non-file
-    # (e.g. a directory) as a writable context file.
-    if target_path.is_symlink() or (target_path.exists() and not target_path.is_file()):
-        return False
-
-    try:
-        content = legacy_path.read_text(encoding="utf-8-sig")
-    except (OSError, UnicodeDecodeError):
-        return False
-
-    marker_pairs = [(marker_start, marker_end)]
-    default_pair = (
-        IntegrationBase.CONTEXT_MARKER_START,
-        IntegrationBase.CONTEXT_MARKER_END,
-    )
-    if default_pair not in marker_pairs:
-        marker_pairs.append(default_pair)
-
-    start_idx = -1
-    end_idx = -1
-    has_start = False
-    has_end = False
-    for s, e in marker_pairs:
-        s_idx = content.find(s)
-        e_idx = content.find(e, s_idx if s_idx != -1 else 0)
-        has_s = s_idx != -1
-        has_e = e_idx != -1
-        if not has_s and not has_e:
-            continue
-        # Refuse to migrate a corrupted managed section: exactly one marker, or
-        # an end marker that does not follow the start.
-        if has_s != has_e or e_idx <= s_idx:
-            return False
-        marker_start, marker_end = s, e
-        start_idx, end_idx = s_idx, e_idx
-        has_start = True
-        has_end = True
-        break
-    if has_start and has_end:
-        removal_start = start_idx
-        removal_end = end_idx + len(marker_end)
-        if removal_end < len(content) and content[removal_end] == "\r":
-            removal_end += 1
-        if removal_end < len(content) and content[removal_end] == "\n":
-            removal_end += 1
-        if removal_start > 0 and content[removal_start - 1] == "\n":
-            if removal_start > 1 and content[removal_start - 2] == "\n":
-                removal_start -= 1
-        content = content[:removal_start] + content[removal_end:]
-
-    user_content = content.replace("\r\n", "\n").replace("\r", "\n").strip()
-    if not user_content:
-        legacy_path.unlink()
-        return True
-
-    try:
-        if target_path.is_file():
-            existing = target_path.read_text(encoding="utf-8-sig")
-            existing = existing.replace("\r\n", "\n").replace("\r", "\n")
-            if not existing.endswith("\n"):
-                existing += "\n"
-            new_content = existing + "\n" + user_content + "\n"
-        else:
-            new_content = user_content + "\n"
-
-        target_path.parent.mkdir(parents=True, exist_ok=True)
-        target_path.write_bytes(new_content.encode("utf-8"))
-    except (OSError, UnicodeDecodeError):
-        return False
-
-    legacy_path.unlink()
-    return True
-
-
 def _migrate_legacy_kimi_dotted_skills(skills_dir: Path) -> tuple[int, int]:
     """Compatibility shim — migrate legacy dotted skill dirs in place.
 

src/specify_cli/integrations/kiro_cli/__init__.py

@@ -26,4 +26,3 @@ class KiroCliIntegration(MarkdownIntegration):
         "args": _KIRO_ARG_FALLBACK,
         "extension": ".md",
     }
-    context_file = "AGENTS.md"

src/specify_cli/integrations/lingma/__init__.py

@@ -27,7 +27,6 @@ class LingmaIntegration(SkillsIntegration):
         "args": "$ARGUMENTS",
         "extension": "/SKILL.md",
     }
-    context_file = ".lingma/rules/specify-rules.md"
 
     @classmethod
     def options(cls) -> list[IntegrationOption]:

src/specify_cli/integrations/omp/__init__.py

@@ -20,7 +20,6 @@ class OmpIntegration(MarkdownIntegration):
         "args": "$ARGUMENTS",
         "extension": ".md",
     }
-    context_file = "AGENTS.md"
 
     def build_exec_args(
         self,

src/specify_cli/integrations/opencode/__init__.py

@@ -19,7 +19,6 @@ class OpencodeIntegration(MarkdownIntegration):
         "args": "$ARGUMENTS",
         "extension": ".md",
     }
-    context_file = "AGENTS.md"
 
     def build_exec_args(
         self,

src/specify_cli/integrations/pi/__init__.py

@@ -9,7 +9,7 @@ class PiIntegration(MarkdownIntegration):
         "name": "Pi Coding Agent",
         "folder": ".pi/",
         "commands_subdir": "prompts",
-        "install_url": "https://www.npmjs.com/package/@mariozechner/pi-coding-agent",
+        "install_url": "https://www.npmjs.com/package/@earendil-works/pi-coding-agent",
         "requires_cli": True,
     }
     registrar_config = {
@@ -18,4 +18,3 @@ class PiIntegration(MarkdownIntegration):
         "args": "$ARGUMENTS",
         "extension": ".md",
     }
-    context_file = "AGENTS.md"

src/specify_cli/integrations/qodercli/__init__.py

@@ -18,5 +18,4 @@ class QodercliIntegration(MarkdownIntegration):
         "args": "$ARGUMENTS",
         "extension": ".md",
     }
-    context_file = "QODER.md"
     multi_install_safe = True

src/specify_cli/integrations/qwen/__init__.py

@@ -18,5 +18,4 @@ class QwenIntegration(MarkdownIntegration):
         "args": "$ARGUMENTS",
         "extension": ".md",
     }
-    context_file = "QWEN.md"
     multi_install_safe = True

src/specify_cli/integrations/roo/__init__.py

@@ -18,5 +18,4 @@ class RooIntegration(MarkdownIntegration):
         "args": "$ARGUMENTS",
         "extension": ".md",
     }
-    context_file = ".roo/rules/specify-rules.md"
     multi_install_safe = True

src/specify_cli/integrations/rovodev/__init__.py

@@ -39,7 +39,6 @@ class RovodevIntegration(SkillsIntegration):
         "args": "$ARGUMENTS",
         "extension": "/SKILL.md",
     }
-    context_file = "AGENTS.md"
 
     # -- CLI dispatch ------------------------------------------------------
 
@@ -228,8 +227,7 @@ class RovodevIntegration(SkillsIntegration):
     ) -> list[Path]:
         """Install RovoDev skills, then generate prompt wrappers and manifest.
 
-        1. ``SkillsIntegration.setup()`` generates skill files and
-           upserts the context section.
+        1. ``SkillsIntegration.setup()`` generates the skill files.
         2. Generates prompt wrappers and ``prompts.yml`` for each skill
            created in step 1.
         """

src/specify_cli/integrations/shai/__init__.py

@@ -18,5 +18,4 @@ class ShaiIntegration(MarkdownIntegration):
         "args": "$ARGUMENTS",
         "extension": ".md",
     }
-    context_file = "SHAI.md"
     multi_install_safe = True

src/specify_cli/integrations/tabnine/__init__.py

@@ -18,5 +18,4 @@ class TabnineIntegration(TomlIntegration):
         "args": "{{args}}",
         "extension": ".toml",
     }
-    context_file = "TABNINE.md"
     multi_install_safe = True

src/specify_cli/integrations/trae/__init__.py

@@ -26,7 +26,6 @@ class TraeIntegration(SkillsIntegration):
         "args": "$ARGUMENTS",
         "extension": "/SKILL.md",
     }
-    context_file = ".trae/rules/project_rules.md"
     multi_install_safe = True
 
     @classmethod

src/specify_cli/integrations/vibe/__init__.py

@@ -28,7 +28,6 @@ class VibeIntegration(SkillsIntegration):
         "args": "$ARGUMENTS",
         "extension": "/SKILL.md",
     }
-    context_file = "AGENTS.md"
 
     @classmethod
     def options(cls) -> list[IntegrationOption]:

src/specify_cli/integrations/windsurf/__init__.py

@@ -18,5 +18,4 @@ class WindsurfIntegration(MarkdownIntegration):
         "args": "$ARGUMENTS",
         "extension": ".md",
     }
-    context_file = ".windsurf/rules/specify-rules.md"
     multi_install_safe = True

src/specify_cli/integrations/zcode/__init__.py

@@ -28,7 +28,6 @@ class ZcodeIntegration(SkillsIntegration):
         "args": "$ARGUMENTS",
         "extension": "/SKILL.md",
     }
-    context_file = "ZCODE.md"
     multi_install_safe = True
 
     @classmethod

src/specify_cli/integrations/zed/__init__.py

@@ -27,7 +27,6 @@ class ZedIntegration(SkillsIntegration):
         "args": "$ARGUMENTS",
         "extension": "/SKILL.md",
     }
-    context_file = "AGENTS.md"
 
     @classmethod
     def options(cls) -> list[IntegrationOption]:

src/specify_cli/presets/__init__.py

@@ -1861,7 +1861,10 @@ class PresetCatalog:
                 f"Catalog URL must use HTTPS (got {parsed.scheme}://). "
                 "HTTP is only allowed for localhost."
             )
-        if not parsed.netloc:
+        # Check hostname, not netloc: netloc is truthy for host-less URLs like
+        # "https://:8080" or "https://user@", so the host guarantee this error
+        # promises would not actually hold. hostname is None in those cases.
+        if not parsed.hostname:
             raise PresetValidationError(
                 "Catalog URL must be a valid URL with a host."
             )
@@ -1892,10 +1895,19 @@ class PresetCatalog:
         download_url: str,
         timeout: int = 60,
     ) -> Optional[str]:
-        """Resolve a GitHub release asset URL to its REST API asset URL."""
+        """Resolve a GitHub release asset URL to its REST API asset URL.
+
+        Passes the ``github`` provider hosts from ``auth.json`` so GitHub
+        Enterprise Server release assets resolve via ``/api/v3``.
+        """
         from specify_cli._github_http import resolve_github_release_asset_api_url
+        from specify_cli.authentication.http import github_provider_hosts
+
         return resolve_github_release_asset_api_url(
-            download_url, self._open_url, timeout=timeout
+            download_url,
+            self._open_url,
+            timeout=timeout,
+            github_hosts=github_provider_hosts(),
         )
 
     def _validate_catalog_payload(self, catalog_data: Any, url: str) -> None:

src/specify_cli/presets/_commands.py

@@ -144,10 +144,13 @@ def preset_add(
                 zip_path = Path(tmpdir) / "preset.zip"
                 try:
                     from specify_cli.authentication.http import open_url as _open_url
+                    from specify_cli.authentication.http import github_provider_hosts
                     from specify_cli._github_http import resolve_github_release_asset_api_url
 
                     _preset_extra_headers = None
-                    _resolved_from_url = resolve_github_release_asset_api_url(from_url, _open_url)
+                    _resolved_from_url = resolve_github_release_asset_api_url(
+                        from_url, _open_url, github_hosts=github_provider_hosts()
+                    )
                     if _resolved_from_url:
                         from_url = _resolved_from_url
                         _preset_extra_headers = {"Accept": "application/octet-stream"}

src/specify_cli/workflows/engine.py

@@ -296,6 +296,40 @@ def _validate_steps(
                     f"boolean, got {type(coe).__name__}."
                 )
 
+        # Fan-in: every wait_for id must reference a step declared at or before
+        # this point. An id not yet seen is either a typo (unknown step) or a
+        # forward reference (the target runs after this fan-in, so its results
+        # cannot exist yet) — both are wiring errors that previously surfaced as
+        # a silent empty result + COMPLETED. A step that is declared but only
+        # conditionally executed (e.g. inside an if/switch branch) is still
+        # "seen" here, so a legitimately-empty result at runtime stays valid.
+        if step_type == "fan-in":
+            wait_for = step_config.get("wait_for")
+            if isinstance(wait_for, list):
+                for wid in wait_for:
+                    if not isinstance(wid, str):
+                        # A non-string entry (e.g. YAML `wait_for: [123]`) can
+                        # never match a real step id, so the join is silently
+                        # empty at runtime — surface it as a wiring error.
+                        errors.append(
+                            f"Fan-in step {step_id!r}: 'wait_for' entries must "
+                            f"be step-id strings, got {type(wid).__name__} "
+                            f"({wid!r})."
+                        )
+                    elif wid == step_id:
+                        # The fan-in's own id is already in seen_ids by now, so
+                        # a self-reference would pass the membership check below
+                        # while still producing an empty join at runtime.
+                        errors.append(
+                            f"Fan-in step {step_id!r}: 'wait_for' references "
+                            f"itself; a fan-in cannot wait for its own results."
+                        )
+                    elif wid not in seen_ids:
+                        errors.append(
+                            f"Fan-in step {step_id!r}: 'wait_for' references "
+                            f"unknown or not-yet-declared step id {wid!r}."
+                        )
+
         # Recursively validate nested steps
         for nested_key in ("then", "else", "steps"):
             nested = step_config.get(nested_key)
@@ -1010,7 +1044,12 @@ class WorkflowEngine:
                 value = float(value)
                 if value == int(value):
                     value = int(value)
-            except (ValueError, TypeError):
+            except (ValueError, TypeError, OverflowError):
+                # OverflowError: `int(value)` raises it for an infinite float
+                # (e.g. a `default: .inf` authoring mistake), which would
+                # otherwise escape validate_workflow's `except ValueError` and
+                # break its "return errors, never raise" contract. Surface it as
+                # the same clean "expected a number" error as NaN does.
                 msg = f"Input {name!r} expected a number, got {value!r}."
                 raise ValueError(msg) from None
         elif input_type == "boolean":

src/specify_cli/workflows/expressions.py

@@ -180,6 +180,35 @@ def _split_top_level_commas(text: str) -> list[str]:
     return parts
 
 
+def _find_top_level(text: str, token: str) -> int:
+    """Return the index of the first occurrence of *token* in *text* that lies
+    outside any quoted string or nested bracket, or ``-1`` if there is none.
+
+    Used so operator/keyword splitting (``and``/``or``/``in``/comparisons) does
+    not match a separator that appears *inside* a quoted operand -- e.g. the
+    ``and`` in ``mode == 'read and write'`` or the ``or`` in ``'approve or reject'``.
+    """
+    quote: str | None = None
+    depth = 0
+    i = 0
+    n = len(text)
+    while i < n:
+        ch = text[i]
+        if quote is not None:
+            if ch == quote:
+                quote = None
+        elif ch in ("'", '"'):
+            quote = ch
+        elif ch in "([{":
+            depth += 1
+        elif ch in ")]}":
+            depth = max(0, depth - 1)
+        elif depth == 0 and text.startswith(token, i):
+            return i
+        i += 1
+    return -1
+
+
 def _evaluate_simple_expression(expr: str, namespace: dict[str, Any]) -> Any:
     """Evaluate a simple expression against the namespace.
 
@@ -193,18 +222,21 @@ def _evaluate_simple_expression(expr: str, namespace: dict[str, Any]) -> Any:
     """
     expr = expr.strip()
 
-    # String literal — check before pipes and operators so quoted strings
-    # containing | or operator keywords are not mis-parsed.
-    if (expr.startswith("'") and expr.endswith("'")) or (
-        expr.startswith('"') and expr.endswith('"')
-    ):
+    # String literal — only when the WHOLE expression is one quoted string,
+    # i.e. the opening quote's matching close is the final character. Checking
+    # startswith/endswith alone would also grab `'a' == 'b'` and strip it to the
+    # garbage `a' == 'b`; a genuine single literal short-circuits here so quoted
+    # strings containing `|` or operator keywords are not mis-parsed downstream.
+    if expr[:1] in ("'", '"') and expr.find(expr[0], 1) == len(expr) - 1:
         return expr[1:-1]
 
-    # Handle pipe filters
-    if "|" in expr:
-        parts = expr.split("|", 1)
-        value = _evaluate_simple_expression(parts[0].strip(), namespace)
-        filter_expr = parts[1].strip()
+    # Handle pipe filters. Detect the pipe at the top level only, so a literal
+    # '|' inside a quoted operand (e.g. `inputs.x == 'a|b'`) or nested brackets is
+    # not mistaken for a filter separator — mirroring the operator parsing below.
+    pipe_idx = _find_top_level(expr, "|")
+    if pipe_idx != -1:
+        value = _evaluate_simple_expression(expr[:pipe_idx].strip(), namespace)
+        filter_expr = expr[pipe_idx + 1:].strip()
 
         # `from_json` is strict: it takes no arguments and tolerates no
         # trailing tokens. Match on the leading filter name and require the
@@ -262,29 +294,33 @@ def _evaluate_simple_expression(expr: str, namespace: dict[str, Any]) -> Any:
         )
 
     # Boolean operators — parse 'or' first (lower precedence) so that
-    # 'a or b and c' is evaluated as 'a or (b and c)'.
-    if " or " in expr:
-        parts = expr.split(" or ", 1)
-        left = _evaluate_simple_expression(parts[0].strip(), namespace)
-        right = _evaluate_simple_expression(parts[1].strip(), namespace)
+    # 'a or b and c' is evaluated as 'a or (b and c)'. Splits are quote/bracket
+    # aware so a keyword inside a quoted operand (e.g. the 'and' in
+    # 'read and write') is not mistaken for an operator.
+    or_idx = _find_top_level(expr, " or ")
+    if or_idx != -1:
+        left = _evaluate_simple_expression(expr[:or_idx].strip(), namespace)
+        right = _evaluate_simple_expression(expr[or_idx + 4:].strip(), namespace)
         return bool(left) or bool(right)
 
-    if " and " in expr:
-        parts = expr.split(" and ", 1)
-        left = _evaluate_simple_expression(parts[0].strip(), namespace)
-        right = _evaluate_simple_expression(parts[1].strip(), namespace)
+    and_idx = _find_top_level(expr, " and ")
+    if and_idx != -1:
+        left = _evaluate_simple_expression(expr[:and_idx].strip(), namespace)
+        right = _evaluate_simple_expression(expr[and_idx + 5:].strip(), namespace)
         return bool(left) and bool(right)
 
     if expr.startswith("not "):
         inner = _evaluate_simple_expression(expr[4:].strip(), namespace)
         return not bool(inner)
 
-    # Comparison operators (order matters — check multi-char ops first)
+    # Comparison operators (order matters — check multi-char ops first). Split at
+    # the first top-level occurrence so an operator inside a quoted operand is
+    # ignored.
     for op in ("!=", "==", ">=", "<=", ">", "<", " not in ", " in "):
-        if op in expr:
-            parts = expr.split(op, 1)
-            left = _evaluate_simple_expression(parts[0].strip(), namespace)
-            right = _evaluate_simple_expression(parts[1].strip(), namespace)
+        op_idx = _find_top_level(expr, op)
+        if op_idx != -1:
+            left = _evaluate_simple_expression(expr[:op_idx].strip(), namespace)
+            right = _evaluate_simple_expression(expr[op_idx + len(op):].strip(), namespace)
             if op == "==":
                 return left == right
             if op == "!=":

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

@@ -194,7 +194,14 @@ class GateStep(StepBase):
                 f"Gate step {config.get('id', '?')!r}: 'on_reject' must be "
                 f"'abort', 'skip', or 'retry'."
             )
-        if on_reject in ("abort", "retry") and isinstance(options, list):
+        # Only inspect option text when every option is a string; otherwise the
+        # `o.lower()` below would raise AttributeError on a non-string option
+        # (already reported above) and break validate_workflow's never-raise contract.
+        if (
+            on_reject in ("abort", "retry")
+            and isinstance(options, list)
+            and all(isinstance(o, str) for o in options)
+        ):
             reject_choices = {"reject", "abort"}
             if not any(o.lower() in reject_choices for o in options):
                 errors.append(

templates/commands/analyze.md

@@ -45,6 +45,7 @@ You **MUST** consider the user input before proceeding (if not empty).
 
     Wait for the result of the hook command before proceeding to the Goal.
     ```
+    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.
 - If no hooks are registered or `.specify/extensions.yml` does not exist, skip silently
 
 ## Goal
@@ -228,6 +229,7 @@ After reporting, check if `.specify/extensions.yml` exists in the project root.
     Executing: `/{command}`
     EXECUTE_COMMAND: {command}
     ```
+    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.
 - If no hooks are registered or `.specify/extensions.yml` does not exist, skip silently
 
 ## Operating Principles

templates/commands/checklist.md

@@ -66,6 +66,7 @@ You **MUST** consider the user input before proceeding (if not empty).
 
     Wait for the result of the hook command before proceeding to the Execution Steps.
     ```
+    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.
 - If no hooks are registered or `.specify/extensions.yml` does not exist, skip silently
 
 ## Execution Steps
@@ -363,4 +364,5 @@ Check if `.specify/extensions.yml` exists in the project root.
     Executing: `/{command}`
     EXECUTE_COMMAND: {command}
     ```
+    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.
 - If no hooks are registered or `.specify/extensions.yml` does not exist, skip silently

templates/commands/clarify.md

@@ -49,6 +49,7 @@ You **MUST** consider the user input before proceeding (if not empty).
 
     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.
 - If no hooks are registered or `.specify/extensions.yml` does not exist, skip silently
 
 ## Outline
@@ -251,6 +252,7 @@ Check if `.specify/extensions.yml` exists in the project root.
     Executing: `/{command}`
     EXECUTE_COMMAND: {command}
     ```
+    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.
   - **Optional hook** (`optional: true`):
     ```
     ## Extension Hooks

templates/commands/constitution.md

@@ -46,6 +46,7 @@ You **MUST** consider the user input before proceeding (if not empty).
 
     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.
 - If no hooks are registered or `.specify/extensions.yml` does not exist, skip silently
 
 ## Outline
@@ -147,4 +148,5 @@ Check if `.specify/extensions.yml` exists in the project root.
     Executing: `/{command}`
     EXECUTE_COMMAND: {command}
     ```
+    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.
 - If no hooks are registered or `.specify/extensions.yml` does not exist, skip silently

templates/commands/converge.md

@@ -49,6 +49,7 @@ You **MUST** consider the user input before proceeding (if not empty).
 
     Wait for the result of the hook command before proceeding to the Goal.
     ```
+    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.
 
 - If no hooks are registered or `.specify/extensions.yml` does not exist, skip silently
 
@@ -266,5 +267,6 @@ After producing the result, check if `.specify/extensions.yml` exists in the pro
     Executing: `/{command}`
     EXECUTE_COMMAND: {command}
     ```
+    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.
 
 - If no hooks are registered or `.specify/extensions.yml` does not exist, skip silently

templates/commands/implement.md

@@ -45,6 +45,7 @@ You **MUST** consider the user input before proceeding (if not empty).
     
     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.
 - If no hooks are registered or `.specify/extensions.yml` does not exist, skip silently
 
 ## Outline
@@ -192,6 +193,7 @@ Check if `.specify/extensions.yml` exists in the project root.
     Executing: `/{command}`
     EXECUTE_COMMAND: {command}
     ```
+    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.
   - **Optional hook** (`optional: true`):
     ```
     ## Extension Hooks

templates/commands/plan.md

@@ -53,6 +53,7 @@ You **MUST** consider the user input before proceeding (if not empty).
 
     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.
 - If no hooks are registered or `.specify/extensions.yml` does not exist, skip silently
 
 ## Outline
@@ -91,6 +92,7 @@ Check if `.specify/extensions.yml` exists in the project root.
     Executing: `/{command}`
     EXECUTE_COMMAND: {command}
     ```
+    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.
   - **Optional hook** (`optional: true`):
     ```
     ## Extension Hooks
@@ -154,14 +156,11 @@ Command ends after Phase 2 planning. Report branch, IMPL_PLAN path, and generate
    - Do not include full implementation code, model/service/controller bodies, migrations, or complete test suites
    - Keep this artifact as a validation/run guide; implementation details belong in `tasks.md` and the implementation phase
 
-4. **Agent context update**:
-   - Update the plan reference between the `<!-- SPECKIT START -->` and `<!-- SPECKIT END -->` markers in `__CONTEXT_FILE__` to point to the plan file created in step 1 (the IMPL_PLAN path)
-
-**Output**: data-model.md, /contracts/*, quickstart.md, updated agent context file
+**Output**: data-model.md, /contracts/*, quickstart.md
 
 ## Key rules
 
-- Use absolute paths for filesystem operations; use project-relative paths for references in documentation and agent context files
+- Use absolute paths for filesystem operations; use project-relative paths for references in documentation
 - ERROR on gate failures or unresolved clarifications
 
 ## Done When

templates/commands/specify.md

@@ -50,6 +50,7 @@ You **MUST** consider the user input before proceeding (if not empty).
 
     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.
 - If no hooks are registered or `.specify/extensions.yml` does not exist, skip silently
 
 ## Outline
@@ -253,6 +254,7 @@ Check if `.specify/extensions.yml` exists in the project root.
     Executing: `/{command}`
     EXECUTE_COMMAND: {command}
     ```
+    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.
   - **Optional hook** (`optional: true`):
     ```
     ## Extension Hooks