chore: bump version to 0.9.2

* fix: resolve GitHub release asset API URL for private repo downloads

For private or SSO-protected GitHub repos, browser release download URLs
redirect to HTML/SSO instead of the ZIP asset. This commit resolves the
asset via the GitHub REST API and downloads with Accept: application/octet-stream,
falling back to the original URL if the API call fails.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

* fix: support direct GitHub REST release asset URLs in extension downloads

When a catalog download_url is already a GitHub REST release asset URL
(https://api.github.com/repos/<owner>/<repo>/releases/assets/<id>),
skip the release metadata lookup and download directly with
Accept: application/octet-stream. This complements the browser URL
resolution from the previous commit, covering catalogs that reference
the REST API directly.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

---------

Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>

.editorconfig

@@ -0,0 +1,28 @@
+root = true
+
+[*]
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+charset = utf-8
+indent_style = space
+indent_size = 4
+
+[*.{yml,yaml}]
+indent_size = 2
+
+[*.{json,jsonc}]
+indent_size = 2
+
+[*.md]
+indent_size = 2
+trim_trailing_whitespace = false
+
+[*.{sh,bash}]
+indent_size = 4
+
+[*.{ps1,psm1,psd1}]
+indent_size = 4
+
+[Makefile]
+indent_style = tab

CHANGELOG.md

@@ -2,6 +2,48 @@
 
 <!-- insert new changelog below this comment -->
 
+## [0.9.2] - 2026-06-02
+
+### Changed
+
+- Update agent parity governance preset catalog entry (#2777)
+- fix: resolve GitHub release asset API URL for private repo extension downloads (#2792)
+- fix: remove unsupported mode: frontmatter from Copilot skills mode (fixes #2799) (#2819)
+- refactor(integrations): co-locate integration commands in integrations/ domain dir (PR-5/8) (#2720)
+- Update Product Forge extension to v1.6.0 (#2820)
+- feat(workflows): add continue_on_error step field for non-halting failures (#2663)
+- chore: add .editorconfig for consistent code formatting (#2366)
+- fix(shared-infra): record skipped files in speckit.manifest.json (#2483)
+- chore: release 0.9.1, begin 0.9.2.dev0 development (#2818)
+
+## [0.9.1] - 2026-06-02
+
+### Changed
+
+- fix(cli): pin UTF-8 encoding on init-options and .extensionignore I/O (#2686)
+- docs: list Hermes in supported integrations table (#2768)
+- fix(copilot): resolve active spec template (#2765)
+- fix: add missing agent-context extension entries to Cline _expected_files (#2797)
+- Add spec-kit-linear extension to community catalog (#2795)
+- feat: add native Cline integration (#2508)
+- Update workflow-preset community catalog entry (#2756)
+- chore: release 0.9.0, begin 0.9.1.dev0 development (#2794)
+- Add RAG Azure Builder extension to community catalog (#2793)
+
+## [0.9.0] - 2026-06-01
+
+### Changed
+
+- chore: recompile workflow lock files (#2774)
+- Add Multi-Sites Spec Kit extension to community catalog (#2791)
+- Update Product Spec Extension to v0.8.3 (#2790)
+- Publish May 2026 Newsletter (#2787)
+- fix: move URL install confirmation prompt before spinner (#2783) (#2784)
+- Update Reqnroll BDD extension to v1.1.0 (#2775)
+- Extract agent context updates into bundled agent-context extension (#2546)
+- chore(deps): bump actions/setup-dotnet from 5.2.0 to 5.3.0 (#2755)
+- chore: release 0.8.18, begin 0.8.19.dev0 development (#2766)
+
 ## [0.8.18] - 2026-05-29
 
 ### Changed

docs/community/extensions.md

@@ -56,6 +56,7 @@ The following community-contributed extensions are available in [`catalog.commun
 | Iterate | Iterate on spec documents with a two-phase define-and-apply workflow — refine specs mid-implementation and go straight back to building | `docs` | Read+Write | [spec-kit-iterate](https://github.com/imviancagrace/spec-kit-iterate) |
 | Jira Integration | Create Jira Epics, Stories, and Issues from spec-kit specifications and task breakdowns with configurable hierarchy and custom field support | `integration` | Read+Write | [spec-kit-jira](https://github.com/mbachorik/spec-kit-jira) |
 | Learning Extension | Generate educational guides from implementations and enhance clarifications with mentoring context | `docs` | Read+Write | [spec-kit-learn](https://github.com/imviancagrace/spec-kit-learn) |
+| Linear Integration | Mirror spec-kit feature directories into Linear (filesystem → Linear, reconcile-based, unidirectional). | `integration` | Read+Write | [spec-kit-linear](https://github.com/ashbrener/spec-kit-linear) |
 | MAQA — Multi-Agent & Quality Assurance | Coordinator → feature → QA agent workflow with parallel worktree-based implementation. Language-agnostic. Auto-detects installed board plugins. Optional CI gate. | `process` | Read+Write | [spec-kit-maqa-ext](https://github.com/GenieRobot/spec-kit-maqa-ext) |
 | MAQA Azure DevOps Integration | Azure DevOps Boards integration for MAQA — syncs User Stories and Task children as features progress | `integration` | Read+Write | [spec-kit-maqa-azure-devops](https://github.com/GenieRobot/spec-kit-maqa-azure-devops) |
 | MAQA CI/CD Gate | Auto-detects GitHub Actions, CircleCI, GitLab CI, and Bitbucket Pipelines. Blocks QA handoff until pipeline is green. | `process` | Read+Write | [spec-kit-maqa-ci](https://github.com/GenieRobot/spec-kit-maqa-ci) |
@@ -78,11 +79,12 @@ The following community-contributed extensions are available in [`catalog.commun
 | Plan Review Gate | Require spec.md and plan.md to be merged via MR/PR before allowing task generation | `process` | Read-only | [spec-kit-plan-review-gate](https://github.com/luno/spec-kit-plan-review-gate) |
 | PR Bridge | Auto-generate pull request descriptions, checklists, and summaries from spec artifacts | `process` | Read-only | [spec-kit-pr-bridge-](https://github.com/Quratulain-bilal/spec-kit-pr-bridge-) |
 | Presetify | Create and validate presets and preset catalogs | `process` | Read+Write | [presetify](https://github.com/mnriem/spec-kit-extensions/tree/main/presetify) |
-| Product Forge | Full product lifecycle from research to release — portfolio, lite mode, monorepo, optional V-Model | `process` | Read+Write | [speckit-product-forge](https://github.com/VaiYav/speckit-product-forge) |
+| Product Forge | Full product lifecycle from research to release — express/lite/standard/v-model tracks, living spec + traceability, structured journeys → E2E, monorepo, and selectable doc-structure strategies | `process` | Read+Write | [speckit-product-forge](https://github.com/VaiYav/speckit-product-forge) |
 | Product Spec Extension | Generates PRFAQ, Lean PRD, stakeholder summaries, and technical designs from engineering specs | `docs` | Read+Write | [spec-kit-product](https://github.com/d0whc3r/spec-kit-product) |
 | Project Health Check | Diagnose a Spec Kit project and report health issues across structure, agents, features, scripts, extensions, and git | `visibility` | Read-only | [spec-kit-doctor](https://github.com/KhawarHabibKhan/spec-kit-doctor) |
 | Project Status | Show current SDD workflow progress — active feature, artifact status, task completion, workflow phase, and extensions summary | `visibility` | Read-only | [spec-kit-status](https://github.com/KhawarHabibKhan/spec-kit-status) |
 | QA Testing Extension | Systematic QA testing with browser-driven or CLI-based validation of acceptance criteria from spec | `code` | Read-only | [spec-kit-qa](https://github.com/arunt14/spec-kit-qa) |
+| RAG Azure Builder | Spec Kit extension for onboarding and operating an Azure RAG stack with guided workflows. | `process` | Read+Write | [spec-kit-extension-rag-azure-builder](https://github.com/Sertxito/spec-kit-extension-rag-azure-builder) |
 | Ralph Loop | Autonomous implementation loop using AI agent CLI | `code` | Read+Write | [spec-kit-ralph](https://github.com/Rubiss-Projects/spec-kit-ralph) |
 | Reconcile Extension | Reconcile implementation drift by surgically updating feature artifacts. | `docs` | Read+Write | [spec-kit-reconcile](https://github.com/stn1slv/spec-kit-reconcile) |
 | Red Team | Adversarial review of specs before /speckit.plan — parallel lens agents surface risks that clarify/analyze structurally can't (prompt injection, integrity gaps, cross-spec drift, silent failures). Produces a structured findings report; no auto-edits to specs. | `docs` | Read+Write | [spec-kit-red-team](https://github.com/ashbrener/spec-kit-red-team) |

docs/community/presets.md

@@ -8,7 +8,7 @@ The following community-contributed presets customize how Spec Kit behaves — o
 | Preset | Purpose | Provides | Requires | URL |
 |--------|---------|----------|----------|-----|
 | A11Y Governance | Adds WCAG 2.2 AA accessibility checks, bilingual DE/EN delivery, CEFR-B2 readability, CLI accessibility, and inclusive-content guidance | 9 templates, 3 commands | — | [spec-kit-preset-a11y-governance](https://github.com/hindermath/spec-kit-preset-a11y-governance) |
-| Agent Parity Governance | Keeps shared AI-agent instructions aligned across project-defined agent guidance surfaces and documents intentional deviations | 6 templates, 3 commands | — | [spec-kit-preset-agent-parity-governance](https://github.com/hindermath/spec-kit-preset-agent-parity-governance) |
+| Agent Parity Governance | Keeps shared AI-agent instructions aligned and adds agent-neutral Spec Kit model-routing guidance across project-defined agent guidance surfaces | 9 templates, 3 commands | — | [spec-kit-preset-agent-parity-governance](https://github.com/hindermath/spec-kit-preset-agent-parity-governance) |
 | AIDE In-Place Migration | Adapts the AIDE extension workflow for in-place technology migrations (X → Y pattern) — adds migration objectives, verification gates, knowledge documents, and behavioral equivalence criteria | 2 templates, 8 commands | AIDE extension | [spec-kit-presets](https://github.com/mnriem/spec-kit-presets) |
 | Architecture Governance | Adds secure architecture governance: trust boundaries, threat modeling, STRIDE/CAPEC, S-ADRs, Zero Trust applicability, and OWASP SAMM | 11 templates, 3 commands | — | [spec-kit-preset-architecture-governance](https://github.com/hindermath/spec-kit-preset-architecture-governance) |
 | Canon Core | Adapts original Spec Kit workflow to work together with Canon extension | 2 templates, 8 commands | — | [spec-kit-canon](https://github.com/maximiliamus/spec-kit-canon) |
@@ -27,6 +27,6 @@ The following community-contributed presets customize how Spec Kit behaves — o
 | 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) |
-| Workflow Preset | Behavior-first specification, design artifacts, and agent-native handoff orchestration — adds requirement-phase behavior drafts, formal BDD/UIF/behavior contracts, optional design artifacts, and scoped implementation handoffs with Core Agent, Vertical Planner Agent, and Worker Agent modes | 23 templates, 7 commands | — | [spec-kit-workflow-preset](https://github.com/bigsmartben/spec-kit-workflow-preset) |
+| Workflow Preset | Behavior-first specification, design artifacts, and agent-native handoff orchestration — adds requirement-phase behavior drafts, formal BDD/UIF/behavior contracts, optional design artifacts, and scoped implementation handoffs with Core Agent, Vertical Planner Agent, and Worker Agent modes | 22 templates, 8 commands | — | [spec-kit-workflow-preset](https://github.com/bigsmartben/spec-kit-workflow-preset) |
 
 To build and publish your own preset, see the [Presets Publishing Guide](https://github.com/github/spec-kit/blob/main/presets/PUBLISHING.md).

docs/reference/integrations.md

@@ -10,6 +10,7 @@ The Specify CLI supports a wide range of AI coding agents. When you run `specify
 | [Antigravity (agy)](https://antigravity.google/)                                     | `agy`            | Skills-based integration; skills are installed automatically                                                                               |
 | [Auggie CLI](https://docs.augmentcode.com/cli/overview)                              | `auggie`         |                                                                                                                                           |
 | [Claude Code](https://www.anthropic.com/claude-code)                                 | `claude`         | Skills-based integration; installs skills in `.claude/skills`                                                                              |
+| [Cline](https://github.com/cline/cline)                                              | `cline`          | IDE-based agent                                                                                                                           |
 | [CodeBuddy CLI](https://www.codebuddy.ai/cli)                                        | `codebuddy`      |                                                                                                                                           |
 | [Codex CLI](https://github.com/openai/codex)                                         | `codex`          | Skills-based integration; installs skills into `.agents/skills` and invokes them as `$speckit-<command>` |
 | [Cursor](https://cursor.sh/)                                                         | `cursor-agent`   |                                                                                                                                           |
@@ -18,6 +19,7 @@ The Specify CLI supports a wide range of AI coding agents. When you run `specify
 | [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/`                                                                                              |
+| [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`          |                                                                                                                                           |
 | [Junie](https://junie.jetbrains.com/)                                                | `junie`          |                                                                                                                                           |

extensions/catalog.community.json

@@ -1,6 +1,6 @@
 {
   "schema_version": "1.0",
-  "updated_at": "2026-06-01T00:00:00Z",
+  "updated_at": "2026-06-02T00:00:00Z",
   "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/extensions/catalog.community.json",
   "extensions": {
     "aide": {
@@ -1246,6 +1246,39 @@
       "created_at": "2026-03-17T00:00:00Z",
       "updated_at": "2026-03-17T00:00:00Z"
     },
+    "linear": {
+      "name": "Linear Integration",
+      "id": "linear",
+      "description": "Mirror spec-kit feature directories into Linear (filesystem → Linear, reconcile-based, unidirectional).",
+      "author": "Ash Brener",
+      "version": "0.2.0",
+      "download_url": "https://github.com/ashbrener/spec-kit-linear/archive/refs/tags/v0.2.0.zip",
+      "repository": "https://github.com/ashbrener/spec-kit-linear",
+      "homepage": "https://github.com/ashbrener/spec-kit-linear",
+      "documentation": "https://github.com/ashbrener/spec-kit-linear/blob/main/README.md",
+      "changelog": "https://github.com/ashbrener/spec-kit-linear/releases",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.1.0"
+      },
+      "provides": {
+        "commands": 5,
+        "hooks": 6
+      },
+      "tags": [
+        "issue-tracking",
+        "linear",
+        "tasks-sync",
+        "lifecycle-mirror",
+        "memory",
+        "cross-repo"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-06-01T00:00:00Z",
+      "updated_at": "2026-06-01T00:00:00Z"
+    },
     "m365": {
       "name": "Microsoft 365 Integration",
       "id": "m365",
@@ -2022,10 +2055,10 @@
     "product-forge": {
       "name": "Product Forge",
       "id": "product-forge",
-      "description": "Full product lifecycle from research to release — portfolio, lite mode, monorepo, optional V-Model",
+      "description": "Full product lifecycle from research to release — express/lite/standard/v-model tracks, living spec + traceability, structured journeys → E2E, monorepo, and selectable doc-structure strategies",
       "author": "VaiYav",
-      "version": "1.5.1",
-      "download_url": "https://github.com/VaiYav/speckit-product-forge/archive/refs/tags/v1.5.1.zip",
+      "version": "1.6.0",
+      "download_url": "https://github.com/VaiYav/speckit-product-forge/archive/refs/tags/v1.6.0.zip",
       "repository": "https://github.com/VaiYav/speckit-product-forge",
       "homepage": "https://github.com/VaiYav/speckit-product-forge",
       "documentation": "https://github.com/VaiYav/speckit-product-forge/blob/main/README.md",
@@ -2035,7 +2068,7 @@
         "speckit_version": ">=0.1.0"
       },
       "provides": {
-        "commands": 29,
+        "commands": 31,
         "hooks": 0
       },
       "tags": [
@@ -2049,7 +2082,7 @@
       "downloads": 0,
       "stars": 0,
       "created_at": "2026-03-28T00:00:00Z",
-      "updated_at": "2026-04-24T15:52:00Z"
+      "updated_at": "2026-06-02T00:00:00Z"
     },
     "qa": {
       "name": "QA Testing Extension",
@@ -2081,6 +2114,38 @@
       "created_at": "2026-04-01T00:00:00Z",
       "updated_at": "2026-04-01T00:00:00Z"
     },
+    "rag-azure-builder": {
+      "name": "RAG Azure Builder",
+      "id": "rag-azure-builder",
+      "description": "Spec Kit extension for onboarding and operating an Azure RAG stack with guided workflows.",
+      "author": "Sertxito",
+      "version": "1.2.0",
+      "download_url": "https://github.com/Sertxito/spec-kit-extension-rag-azure-builder/archive/refs/tags/v1.2.0.zip",
+      "repository": "https://github.com/Sertxito/spec-kit-extension-rag-azure-builder",
+      "homepage": "https://github.com/Sertxito/spec-kit-extension-rag-azure-builder",
+      "documentation": "https://github.com/Sertxito/spec-kit-extension-rag-azure-builder#readme",
+      "changelog": "https://github.com/Sertxito/spec-kit-extension-rag-azure-builder/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.8.0"
+      },
+      "provides": {
+        "commands": 5,
+        "hooks": 0
+      },
+      "tags": [
+        "azure",
+        "rag",
+        "search",
+        "onboarding",
+        "cost-optimization"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-06-01T00:00:00Z",
+      "updated_at": "2026-06-01T00:00:00Z"
+    },
     "ralph": {
       "name": "Ralph Loop",
       "id": "ralph",

integrations/catalog.json

@@ -1,6 +1,6 @@
 {
   "schema_version": "1.0",
-  "updated_at": "2026-04-29T00:00:00Z",
+  "updated_at": "2026-05-13T00:00:00Z",
   "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/integrations/catalog.json",
   "integrations": {
     "claude": {
@@ -12,6 +12,15 @@
       "repository": "https://github.com/github/spec-kit",
       "tags": ["cli", "anthropic"]
     },
+    "cline": {
+      "id": "cline",
+      "name": "Cline",
+      "version": "1.0.0",
+      "description": "Cline IDE integration",
+      "author": "spec-kit-core",
+      "repository": "https://github.com/github/spec-kit",
+      "tags": ["ide"]
+    },
     "copilot": {
       "id": "copilot",
       "name": "GitHub Copilot",

presets/catalog.community.json

@@ -1,6 +1,6 @@
 {
   "schema_version": "1.0",
-  "updated_at": "2026-05-27T00:00:00Z",
+  "updated_at": "2026-05-31T00:00:00Z",
   "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/presets/catalog.community.json",
   "presets": {
     "a11y-governance": {
@@ -34,11 +34,11 @@
     "agent-parity-governance": {
       "name": "Agent Parity Governance",
       "id": "agent-parity-governance",
-      "version": "0.1.0",
-      "description": "Keeps shared AI-agent guidance aligned across a project-defined set of agent instruction surfaces.",
+      "version": "0.2.0",
+      "description": "Keeps shared AI-agent guidance aligned and adds agent-neutral Spec Kit model-routing guidance across declared agent instruction surfaces.",
       "author": "Thorsten Hindermann",
       "repository": "https://github.com/hindermath/spec-kit-preset-agent-parity-governance",
-      "download_url": "https://github.com/hindermath/spec-kit-preset-agent-parity-governance/archive/refs/tags/v0.1.0.zip",
+      "download_url": "https://github.com/hindermath/spec-kit-preset-agent-parity-governance/archive/refs/tags/v0.2.0.zip",
       "homepage": "https://github.com/hindermath/spec-kit-preset-agent-parity-governance",
       "documentation": "https://github.com/hindermath/spec-kit-preset-agent-parity-governance/blob/main/README.md",
       "license": "MIT",
@@ -46,18 +46,20 @@
         "speckit_version": ">=0.8.0"
       },
       "provides": {
-        "templates": 6,
+        "templates": 9,
         "commands": 3
       },
       "tags": [
         "agents",
         "governance",
         "parity",
+        "agent-md",
         "agent-guidance",
+        "model-routing",
         "multi-agent"
       ],
       "created_at": "2026-04-27T00:00:00Z",
-      "updated_at": "2026-04-27T00:00:00Z"
+      "updated_at": "2026-05-31T00:00:00Z"
     },
     "aide-in-place": {
       "name": "AIDE In-Place Migration",
@@ -593,11 +595,11 @@
     "workflow-preset": {
       "name": "Workflow Preset",
       "id": "workflow-preset",
-      "version": "1.2.0",
+      "version": "1.3.1",
       "description": "Behavior-first specification, design artifacts, and agent-native handoff orchestration.",
       "author": "bigsmartben",
       "repository": "https://github.com/bigsmartben/spec-kit-workflow-preset",
-      "download_url": "https://github.com/bigsmartben/spec-kit-workflow-preset/archive/refs/tags/v1.2.0.zip",
+      "download_url": "https://github.com/bigsmartben/spec-kit-workflow-preset/releases/download/v1.3.1/spec-kit-workflow-preset-v1.3.1.zip",
       "homepage": "https://github.com/bigsmartben/spec-kit-workflow-preset",
       "documentation": "https://github.com/bigsmartben/spec-kit-workflow-preset/blob/main/README.md",
       "license": "MIT",
@@ -605,8 +607,8 @@
         "speckit_version": ">=0.8.10.dev0"
       },
       "provides": {
-        "templates": 23,
-        "commands": 7
+        "templates": 22,
+        "commands": 8
       },
       "tags": [
         "behavior",
@@ -616,7 +618,7 @@
         "handoff"
       ],
       "created_at": "2026-05-27T00:00:00Z",
-      "updated_at": "2026-05-27T00:00:00Z"
+      "updated_at": "2026-05-28T00:00:00Z"
     }
   }
 }

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "specify-cli"
-version = "0.8.19.dev0"
+version = "0.9.2"
 description = "Specify CLI, part of GitHub Spec Kit. A tool to bootstrap your projects for Spec-Driven Development (SDD)."
 requires-python = ">=3.11"
 dependencies = [

src/specify_cli/agents.py

@@ -67,6 +67,33 @@ class CommandRegistrar:
             except ImportError:
                 pass  # Circular import during module init; retry on next access
 
+    @staticmethod
+    def _hyphenate_frontmatter_refs(val: Any) -> Any:
+        """Recursively find any dotted references starting with speckit. and hyphenate them."""
+        if isinstance(val, dict):
+            return {
+                k: CommandRegistrar._hyphenate_frontmatter_refs(v)
+                for k, v in val.items()
+            }
+        elif isinstance(val, list):
+            return [CommandRegistrar._hyphenate_frontmatter_refs(x) for x in val]
+        elif isinstance(val, str):
+            return re.sub(
+                r"\bspeckit\.[A-Za-z0-9-_]+(?:\.[A-Za-z0-9-_]+)*\b",
+                lambda m: m.group(0).replace(".", "-"),
+                val,
+            )
+        return val
+
+    @staticmethod
+    def _hyphenate_body_refs(body: str) -> str:
+        """Hyphenate dotted speckit references in command body text."""
+        return re.sub(
+            r"\bspeckit\.[A-Za-z0-9-_]+(?:\.[A-Za-z0-9-_]+)*\b",
+            lambda m: m.group(0).replace(".", "-"),
+            body,
+        )
+
     @staticmethod
     def parse_frontmatter(content: str) -> tuple[dict, str]:
         """Parse YAML frontmatter from Markdown content.
@@ -408,6 +435,9 @@ class CommandRegistrar:
     ) -> str:
         """Compute the on-disk command or skill name for an agent."""
         if agent_config["extension"] != "/SKILL.md":
+            format_name = agent_config.get("format_name")
+            if format_name:
+                return format_name(cmd_name)
             return cmd_name
 
         short_name = cmd_name
@@ -437,6 +467,13 @@ class CommandRegistrar:
         if not normalized.is_relative_to(base_normalized):
             raise ValueError(f"Output path {candidate!r} escapes directory {base!r}")
 
+    @staticmethod
+    def _is_safe_command_name(name: str) -> bool:
+        """Reject names that could escape the commands directory via path traversal."""
+        if os.path.sep in name or "/" in name or "\\" in name:
+            return False
+        return os.path.normpath(name) == name
+
     def register_commands(
         self,
         agent_name: str,
@@ -482,9 +519,11 @@ class CommandRegistrar:
         commands_dir.mkdir(parents=True, exist_ok=True)
 
         registered = []
+        is_cline_ext = agent_name == "cline" and source_id != "core"
 
         for cmd_info in commands:
             cmd_name = cmd_info["name"]
+            aliases = cmd_info.get("aliases", [])
             cmd_file = cmd_info["file"]
 
             source_file = source_dir / cmd_file
@@ -516,6 +555,10 @@ class CommandRegistrar:
                 format_name = agent_config.get("format_name")
                 frontmatter["name"] = format_name(cmd_name) if format_name else cmd_name
 
+            if is_cline_ext:
+                frontmatter = self._hyphenate_frontmatter_refs(frontmatter)
+                body = self._hyphenate_body_refs(body)
+
             body = self._convert_argument_placeholder(
                 body, "$ARGUMENTS", agent_config["args"]
             )
@@ -585,7 +628,7 @@ class CommandRegistrar:
 
             registered.append(cmd_name)
 
-            for alias in cmd_info.get("aliases", []):
+            for alias in aliases:
                 alias_output_name = self._compute_output_name(
                     agent_name, alias, agent_config
                 )
@@ -909,22 +952,32 @@ class CommandRegistrar:
                 output_name = self._compute_output_name(
                     agent_name, cmd_name, agent_config
                 )
+
+                names_to_clean = [output_name]
+                if output_name != cmd_name and self._is_safe_command_name(cmd_name):
+                    names_to_clean.append(cmd_name)
+
                 for target_dir in dirs_to_clean:
-                    cmd_file = (
-                        target_dir / f"{output_name}{agent_config['extension']}"
-                    )
-                    if cmd_file.exists() or cmd_file.is_symlink():
-                        cmd_file.unlink()
-                        # For SKILL.md agents each command lives in its own
-                        # subdirectory (e.g. .agents/skills/speckit-ext-cmd/
-                        # SKILL.md).  Remove the parent dir when it becomes
-                        # empty to avoid orphaned directories.
-                        parent = cmd_file.parent
-                        if parent != target_dir and parent.exists():
-                            try:
-                                parent.rmdir()
-                            except OSError:
-                                pass
+                    for name in names_to_clean:
+                        cmd_file = (
+                            target_dir / f"{name}{agent_config['extension']}"
+                        )
+                        try:
+                            self._ensure_inside(cmd_file, target_dir)
+                        except ValueError:
+                            continue
+                        if cmd_file.exists() or cmd_file.is_symlink():
+                            cmd_file.unlink()
+                            # For SKILL.md agents each command lives in its own
+                            # subdirectory (e.g. .agents/skills/speckit-ext-cmd/
+                            # SKILL.md).  Remove the parent dir when it becomes
+                            # empty to avoid orphaned directories.
+                            parent = cmd_file.parent
+                            if parent != target_dir and parent.exists():
+                                try:
+                                    parent.rmdir()
+                                except OSError:
+                                    pass
 
                 if agent_name == "copilot":
                     prompt_file = (

src/specify_cli/commands/extension.py

@@ -1,2 +0,0 @@
-"""specify extension * commands — placeholder for future extraction."""
-from __future__ import annotations

src/specify_cli/commands/init.py

@@ -151,13 +151,15 @@ def register(app: typer.Typer) -> None:
         # Lazy imports to avoid circular dependency — __init__.py imports this module
         from .. import (
             _install_shared_infra_or_exit,
-            _parse_integration_options,
             _print_cli_warning,
             _update_agent_context_config_file,
-            _write_integration_json,
             ensure_executable_scripts,
             save_init_options,
         )
+        from ..integrations._commands import (
+            _parse_integration_options,
+            _write_integration_json,
+        )
         from ..integration_runtime import with_integration_setting as _with_integration_setting
 
         show_banner()
@@ -726,6 +728,7 @@ def register(app: typer.Typer) -> None:
         cursor_agent_skill_mode = selected_ai == "cursor-agent" and (ai_skills or _is_skills_integration)
         copilot_skill_mode = selected_ai == "copilot" and _is_skills_integration
         devin_skill_mode = selected_ai == "devin"
+        cline_skill_mode = selected_ai == "cline"
         native_skill_mode = codex_skill_mode or claude_skill_mode or kimi_skill_mode or agy_skill_mode or trae_skill_mode or cursor_agent_skill_mode or copilot_skill_mode or devin_skill_mode
 
         if codex_skill_mode and not ai_skills:
@@ -749,7 +752,7 @@ def register(app: typer.Typer) -> None:
                 return f"/speckit-{name}"
             if kimi_skill_mode:
                 return f"/skill:speckit-{name}"
-            if cursor_agent_skill_mode or copilot_skill_mode or devin_skill_mode:
+            if cursor_agent_skill_mode or copilot_skill_mode or devin_skill_mode or cline_skill_mode:
                 return f"/speckit-{name}"
             return f"/speckit.{name}"
 

src/specify_cli/commands/integration.py

@@ -1,2 +0,0 @@
-"""specify integration * commands — placeholder for future extraction."""
-from __future__ import annotations

src/specify_cli/commands/preset.py

@@ -1,2 +0,0 @@
-"""specify preset * commands — placeholder for future extraction."""
-from __future__ import annotations

src/specify_cli/commands/workflow.py

@@ -1,2 +0,0 @@
-"""specify workflow * commands — placeholder for future extraction."""
-from __future__ import annotations

src/specify_cli/extensions.py

@@ -761,7 +761,28 @@ class ExtensionManager:
         if not ignore_file.exists():
             return None
 
-        lines: List[str] = ignore_file.read_text().splitlines()
+        # Pin UTF-8 explicitly: ``Path.read_text`` defaults to the system
+        # locale codec on Windows (cp1252 / gb2312 / cp932), which silently
+        # corrupts multibyte patterns when the file is shared across
+        # machines with different locales. The next line already
+        # normalises backslashes "so Windows-authored files work" — the
+        # codebase already expects Windows authors to write this file.
+        #
+        # A file that is not valid UTF-8 is a user-authoring mistake, so
+        # surface it as ``ValidationError`` with a pointer to the offending
+        # byte — the same pattern ``ExtensionManifest._load_yaml`` uses
+        # for ``extension.yml`` (see ``UnicodeDecodeError`` handler in
+        # this module). Without the wrap, the raw ``UnicodeDecodeError``
+        # would abort installation with a Python traceback instead of a
+        # clear message naming the file.
+        try:
+            raw = ignore_file.read_text(encoding="utf-8")
+        except UnicodeDecodeError as e:
+            raise ValidationError(
+                f".extensionignore is not valid UTF-8: {ignore_file} "
+                f"({e.reason} at byte {e.start})"
+            )
+        lines: List[str] = raw.splitlines()
 
         # Normalise backslashes in patterns so Windows-authored files work
         normalised: List[str] = []
@@ -1728,13 +1749,59 @@ class ExtensionCatalog(CatalogStackBase):
         from specify_cli.authentication.http import build_request
         return build_request(url)
 
-    def _open_url(self, url: str, timeout: int = 10):
+    def _open_url(
+        self,
+        url: str,
+        timeout: int = 10,
+        extra_headers: Optional[Dict[str, str]] = None,
+    ):
         """Open a URL with provider-based auth, trying each configured provider.
 
         Delegates to :func:`specify_cli.authentication.http.open_url`.
         """
         from specify_cli.authentication.http import open_url
-        return open_url(url, timeout)
+        return open_url(url, timeout, extra_headers=extra_headers)
+
+    def _resolve_github_release_asset_api_url(
+        self,
+        download_url: str,
+        timeout: int = 60,
+    ) -> Optional[str]:
+        """Resolve a GitHub release asset URL to its API asset URL."""
+        import urllib.error
+        from urllib.parse import unquote, urlparse
+
+        parsed = urlparse(download_url)
+        parts = [unquote(part) for part in parsed.path.strip("/").split("/")]
+        if (
+            parsed.hostname == "api.github.com"
+            and len(parts) >= 6
+            and parts[:1] == ["repos"]
+            and parts[3:5] == ["releases", "assets"]
+        ):
+            return download_url
+
+        if parsed.hostname != "github.com":
+            return None
+
+        if len(parts) < 6 or parts[2:4] != ["releases", "download"]:
+            return None
+
+        owner, repo, tag = parts[0], parts[1], parts[4]
+        asset_name = "/".join(parts[5:])
+        release_url = f"https://api.github.com/repos/{owner}/{repo}/releases/tags/{tag}"
+
+        try:
+            with self._open_url(release_url, timeout=timeout) as response:
+                release_data = json.loads(response.read())
+        except (urllib.error.URLError, json.JSONDecodeError):
+            return None
+
+        for asset in release_data.get("assets", []):
+            if asset.get("name") == asset_name and asset.get("url"):
+                return str(asset["url"])
+
+        return None
 
     def get_active_catalogs(self) -> List[CatalogEntry]:
         """Get the ordered list of active catalogs.
@@ -2134,9 +2201,15 @@ class ExtensionCatalog(CatalogStackBase):
         zip_filename = f"{extension_id}-{version}.zip"
         zip_path = target_dir / zip_filename
 
+        extra_headers = None
+        resolved_download_url = self._resolve_github_release_asset_api_url(download_url)
+        if resolved_download_url:
+            download_url = resolved_download_url
+            extra_headers = {"Accept": "application/octet-stream"}
+
         # Download the ZIP file
         try:
-            with self._open_url(download_url, timeout=60) as response:
+            with self._open_url(download_url, timeout=60, extra_headers=extra_headers) as response:
                 zip_data = response.read()
 
             zip_path.write_bytes(zip_data)
@@ -2413,6 +2486,7 @@ class HookExecutor:
         claude_skill_mode = selected_ai == "claude" and bool(init_options.get("ai_skills"))
         kimi_skill_mode = selected_ai == "kimi"
         cursor_skill_mode = selected_ai == "cursor-agent" and bool(init_options.get("ai_skills"))
+        cline_mode = selected_ai == "cline"
 
         skill_name = self._skill_name_from_command(command_id)
         if codex_skill_mode and skill_name:
@@ -2423,6 +2497,10 @@ class HookExecutor:
             return f"/skill:{skill_name}"
         if cursor_skill_mode and skill_name:
             return f"/{skill_name}"
+        if cline_mode:
+            from .integrations.cline import format_cline_command_name
+
+            return f"/{format_cline_command_name(command_id)}"
 
         return f"/{command_id}"
 

src/specify_cli/integrations/__init__.py

@@ -52,6 +52,7 @@ def _register_builtins() -> None:
     from .auggie import AuggieIntegration
     from .bob import BobIntegration
     from .claude import ClaudeIntegration
+    from .cline import ClineIntegration
     from .codebuddy import CodebuddyIntegration
     from .codex import CodexIntegration
     from .copilot import CopilotIntegration
@@ -85,6 +86,7 @@ def _register_builtins() -> None:
     _register(AuggieIntegration())
     _register(BobIntegration())
     _register(ClaudeIntegration())
+    _register(ClineIntegration())
     _register(CodebuddyIntegration())
     _register(CodexIntegration())
     _register(CopilotIntegration())

src/specify_cli/integrations/_commands.py

@@ -0,0 +1,34 @@
+"""specify integration * commands — app objects and register() entry point."""
+from __future__ import annotations
+
+import typer
+
+from .._assets import get_speckit_version  # noqa: F401 — re-exported for monkeypatching in tests
+
+# Re-export helpers used by commands/init.py and tests
+from ._helpers import (  # noqa: F401
+    _cli_error_detail,
+    _cli_phase_label,
+    _parse_integration_options,
+    _write_integration_json,
+)
+
+integration_app = typer.Typer(
+    name="integration",
+    help="Manage coding agent integrations",
+    add_completion=False,
+)
+
+integration_catalog_app = typer.Typer(
+    name="catalog",
+    help="Manage integration catalog sources",
+    add_completion=False,
+)
+integration_app.add_typer(integration_catalog_app, name="catalog")
+
+
+def register(app: typer.Typer) -> None:
+    from . import _install_commands  # noqa: F401 — registers handlers via decorators
+    from . import _migrate_commands  # noqa: F401
+    from . import _query_commands    # noqa: F401
+    app.add_typer(integration_app, name="integration")

src/specify_cli/integrations/_helpers.py

@@ -0,0 +1,402 @@
+"""specify integration helpers — internal utilities shared across command modules."""
+from __future__ import annotations
+
+import os
+from pathlib import Path
+from typing import Any
+
+import typer
+
+from .._agent_config import SCRIPT_TYPE_CHOICES
+from .._console import console
+from ..integration_runtime import (
+    invoke_separator_for_integration as _invoke_separator_for_integration,
+    resolve_integration_options as _resolve_integration_options_impl,
+    with_integration_setting as _with_integration_setting,
+)
+from ..integration_state import (
+    INTEGRATION_JSON,
+    INTEGRATION_STATE_SCHEMA,
+    integration_setting as _integration_setting,
+    try_read_integration_json as _try_read_integration_json,
+    write_integration_json as _write_integration_json_file,
+)
+
+
+def _get_speckit_version() -> str:
+    """Return the current Spec Kit version.
+
+    Resolved lazily through ``_commands.get_speckit_version`` so that tests
+    that monkeypatch ``specify_cli.integrations._commands.get_speckit_version``
+    still affect helpers called from the command handlers.
+    """
+    from . import _commands  # noqa: PLC0415 — intentional late import to avoid circular + enable patching
+    return _commands.get_speckit_version()
+
+
+# ---------------------------------------------------------------------------
+# JSON read / write helpers
+# ---------------------------------------------------------------------------
+
+def _read_integration_json(project_root: Path) -> dict[str, Any]:
+    """Load ``.specify/integration.json``. Returns normalized state when present.
+
+    Delegates the parse / schema-guard logic to the shared
+    :func:`_try_read_integration_json` helper so the CLI and workflow engine
+    cannot drift on validation rules. Each error variant is translated into
+    the existing loud-fail UX (console message + ``typer.Exit(1)``).
+    """
+    path = project_root / INTEGRATION_JSON
+    state, error = _try_read_integration_json(project_root)
+    if error is None:
+        return state or {}
+    if error.kind == "decode":
+        console.print(f"[red]Error:[/red] {path} contains invalid JSON or is not valid UTF-8.")
+        console.print(f"Please fix or delete {INTEGRATION_JSON} and retry.")
+        console.print(f"[dim]Details:[/dim] {error.detail}")
+    elif error.kind == "os":
+        console.print(f"[red]Error:[/red] Could not read {path}.")
+        console.print(f"Please fix file permissions or delete {INTEGRATION_JSON} and retry.")
+        console.print(f"[dim]Details:[/dim] {error.detail}")
+    elif error.kind == "not_object":
+        console.print(
+            f"[red]Error:[/red] {path} must contain a JSON object, got {error.detail}."
+        )
+        console.print(f"Please fix or delete {INTEGRATION_JSON} and retry.")
+    elif error.kind == "schema_too_new":
+        console.print(
+            f"[red]Error:[/red] {path} uses integration state schema {error.schema}, "
+            f"but this CLI only supports schema {INTEGRATION_STATE_SCHEMA}."
+        )
+        console.print("Please upgrade Spec Kit before modifying integrations.")
+    raise typer.Exit(1)
+
+
+def _write_integration_json(
+    project_root: Path,
+    integration_key: str | None,
+    installed_integrations: list[str] | None = None,
+    integration_settings: dict[str, dict[str, Any]] | None = None,
+) -> None:
+    """Write ``.specify/integration.json`` with legacy-compatible state."""
+    _write_integration_json_file(
+        project_root,
+        version=_get_speckit_version(),
+        integration_key=integration_key,
+        installed_integrations=installed_integrations,
+        settings=integration_settings,
+    )
+
+
+# ---------------------------------------------------------------------------
+# init-options.json helpers
+# ---------------------------------------------------------------------------
+
+def _refresh_init_options_speckit_version(project_root: Path) -> None:
+    """Refresh only the Spec Kit version recorded in init-options.json."""
+    from .. import load_init_options, save_init_options
+    opts = load_init_options(project_root)
+    if not isinstance(opts, dict) or not opts:
+        return
+    opts["speckit_version"] = _get_speckit_version()
+    save_init_options(project_root, opts)
+
+
+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.
+    """
+    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
+            )
+    elif has_legacy_context_keys:
+        save_init_options(project_root, opts)
+
+
+def _remove_integration_json(project_root: Path) -> None:
+    """Remove ``.specify/integration.json`` if it exists."""
+    path = project_root / INTEGRATION_JSON
+    if path.exists():
+        path.unlink()
+
+
+# ---------------------------------------------------------------------------
+# Error sentinels
+# ---------------------------------------------------------------------------
+
+_MANIFEST_READ_ERRORS = (ValueError, FileNotFoundError, OSError, UnicodeDecodeError)
+
+
+class _SharedTemplateRefreshError(RuntimeError):
+    """Raised when default integration metadata should not be persisted."""
+
+
+# ---------------------------------------------------------------------------
+# Script type resolution
+# ---------------------------------------------------------------------------
+
+def _normalize_script_type(script_type: str, source: str) -> str:
+    """Normalize and validate a script type from CLI/config sources."""
+    normalized = script_type.strip().lower()
+    if normalized in SCRIPT_TYPE_CHOICES:
+        return normalized
+    console.print(
+        f"[red]Error:[/red] Invalid script type {script_type!r} from {source}. "
+        f"Expected one of: {', '.join(sorted(SCRIPT_TYPE_CHOICES.keys()))}."
+    )
+    raise typer.Exit(1)
+
+
+def _resolve_script_type(project_root: Path, script_type: str | None) -> str:
+    """Resolve the script type from the CLI flag or init-options.json."""
+    from .. import load_init_options
+    if script_type:
+        return _normalize_script_type(script_type, "--script")
+    opts = load_init_options(project_root)
+    saved = opts.get("script")
+    if isinstance(saved, str) and saved.strip():
+        return _normalize_script_type(saved, ".specify/init-options.json")
+    return "ps" if os.name == "nt" else "sh"
+
+
+def _resolve_integration_script_type(
+    project_root: Path,
+    state: dict[str, Any],
+    key: str,
+    script_type: str | None = None,
+) -> str:
+    """Resolve script type for an integration, preferring stored settings."""
+    if script_type:
+        return _normalize_script_type(script_type, "--script")
+
+    stored = _integration_setting(state, key).get("script")
+    if isinstance(stored, str) and stored.strip():
+        return _normalize_script_type(stored, f"{INTEGRATION_JSON} integration_settings.{key}.script")
+
+    return _resolve_script_type(project_root, None)
+
+
+# ---------------------------------------------------------------------------
+# Integration options
+# ---------------------------------------------------------------------------
+
+def _parse_integration_options(integration: Any, raw_options: str) -> dict[str, Any] | None:
+    """Parse --integration-options string into a dict matching the integration's declared options.
+
+    Returns ``None`` when no options are provided.
+    """
+    import shlex
+    parsed: dict[str, Any] = {}
+    tokens = shlex.split(raw_options)
+    declared_options = list(integration.options())
+    declared = {opt.name.lstrip("-"): opt for opt in declared_options}
+    allowed = ", ".join(sorted(opt.name for opt in declared_options))
+    i = 0
+    while i < len(tokens):
+        token = tokens[i]
+        if not token.startswith("-"):
+            console.print(f"[red]Error:[/red] Unexpected integration option value '{token}'.")
+            if allowed:
+                console.print(f"Allowed options: {allowed}")
+            raise typer.Exit(1)
+        name = token.lstrip("-")
+        value: str | None = None
+        # Handle --name=value syntax
+        if "=" in name:
+            name, value = name.split("=", 1)
+        opt = declared.get(name)
+        if not opt:
+            console.print(f"[red]Error:[/red] Unknown integration option '{token}'.")
+            if allowed:
+                console.print(f"Allowed options: {allowed}")
+            raise typer.Exit(1)
+        key = name.replace("-", "_")
+        if opt.is_flag:
+            if value is not None:
+                console.print(f"[red]Error:[/red] Option '{opt.name}' is a flag and does not accept a value.")
+                raise typer.Exit(1)
+            parsed[key] = True
+            i += 1
+        elif value is not None:
+            parsed[key] = value
+            i += 1
+        elif i + 1 < len(tokens) and not tokens[i + 1].startswith("-"):
+            parsed[key] = tokens[i + 1]
+            i += 2
+        else:
+            console.print(f"[red]Error:[/red] Option '{opt.name}' requires a value.")
+            raise typer.Exit(1)
+    return parsed or None
+
+
+def _resolve_integration_options(
+    integration: Any,
+    state: dict[str, Any],
+    key: str,
+    raw_options: str | None,
+) -> tuple[str | None, dict[str, Any] | None]:
+    """Resolve raw and parsed options for an integration operation."""
+    return _resolve_integration_options_impl(
+        integration,
+        state,
+        key,
+        raw_options,
+        parse_options=_parse_integration_options,
+    )
+
+
+def _update_init_options_for_integration(
+    project_root: Path,
+    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.
+
+    ``context_file`` 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; invalid marker values
+    are silently ignored at runtime by ``_resolve_context_markers()`` which
+    falls back to the class-level defaults.
+    """
+    from .. import (
+        _AGENT_CTX_EXT_CONFIG,
+        _update_agent_context_config_file,
+        load_init_options,
+        save_init_options,
+    )
+    from .base import SkillsIntegration
+    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
+    if isinstance(integration, SkillsIntegration) or getattr(integration, "_skills_mode", False):
+        opts["ai_skills"] = True
+    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)
+
+
+# ---------------------------------------------------------------------------
+# Default integration persistence
+# ---------------------------------------------------------------------------
+
+def _set_default_integration(
+    project_root: Path,
+    state: dict[str, Any],
+    key: str,
+    integration: Any,
+    installed_keys: list[str],
+    *,
+    script_type: str | None = None,
+    raw_options: str | None = None,
+    parsed_options: dict[str, Any] | None = None,
+    refresh_templates: bool = True,
+    refresh_templates_force: bool = False,
+    refresh_hint: str | None = None,
+) -> None:
+    """Persist *key* as default and align active runtime metadata."""
+    from .. import _install_shared_infra
+    resolved_script = _resolve_integration_script_type(project_root, state, key, script_type)
+    settings = _with_integration_setting(
+        state,
+        key,
+        integration,
+        script_type=resolved_script,
+        raw_options=raw_options,
+        parsed_options=parsed_options,
+    )
+
+    if refresh_templates:
+        try:
+            _install_shared_infra(
+                project_root,
+                resolved_script,
+                invoke_separator=_invoke_separator_for_integration(
+                    integration, {"integration_settings": settings}, key, parsed_options
+                ),
+                force=refresh_templates_force,
+                refresh_managed=True,
+                refresh_hint=refresh_hint,
+            )
+        except (ValueError, OSError) as exc:
+            raise _SharedTemplateRefreshError(
+                f"Failed to refresh shared infrastructure for '{key}': {exc}"
+            ) from exc
+
+    _write_integration_json(project_root, key, installed_keys, settings)
+    _update_init_options_for_integration(project_root, integration, script_type=resolved_script)
+
+
+def _set_default_integration_or_exit(*args: Any, **kwargs: Any) -> None:
+    try:
+        _set_default_integration(*args, **kwargs)
+    except _SharedTemplateRefreshError as exc:
+        console.print(f"[red]Error:[/red] {exc}")
+        raise typer.Exit(1)
+
+
+# ---------------------------------------------------------------------------
+# CLI formatting helpers (re-exported from _commands.py)
+# ---------------------------------------------------------------------------
+
+def _cli_error_detail(exc: BaseException) -> str:
+    """Return a compact one-line exception detail for CLI output."""
+    return str(exc).replace("\n", " ").strip() or exc.__class__.__name__
+
+
+def _cli_phase_label(phase: str, target_kind: str, target: str | None = None) -> str:
+    """Format a stable operation label for user-visible diagnostics."""
+    label = f"{phase} {target_kind}".strip()
+    if target:
+        label = f"{label} '{target}'"
+    return label

src/specify_cli/integrations/_install_commands.py

@@ -0,0 +1,309 @@
+"""specify integration install / uninstall command handlers."""
+from __future__ import annotations
+
+import os
+
+import typer
+
+from .._console import console
+from .._utils import _display_project_path
+from ..integration_runtime import (
+    invoke_separator_for_integration as _invoke_separator_for_integration,
+    with_integration_setting as _with_integration_setting,
+)
+from ..integration_state import (
+    dedupe_integration_keys as _dedupe_integration_keys,
+    default_integration_key as _default_integration_key,
+    installed_integration_keys as _installed_integration_keys,
+    integration_settings as _integration_settings,
+)
+from ._commands import integration_app
+from ._helpers import (
+    _MANIFEST_READ_ERRORS,
+    _clear_init_options_for_integration,
+    _cli_error_detail,
+    _cli_phase_label,
+    _get_speckit_version,
+    _read_integration_json,
+    _refresh_init_options_speckit_version,
+    _remove_integration_json,
+    _resolve_integration_options,
+    _resolve_script_type,
+    _set_default_integration_or_exit,
+    _update_init_options_for_integration,
+    _write_integration_json,
+)
+
+
+@integration_app.command("install")
+def integration_install(
+    key: str = typer.Argument(help="Integration key to install (e.g. claude, copilot)"),
+    script: str | None = typer.Option(None, "--script", help="Script type: sh or ps (default: from init-options.json or platform default)"),
+    force: bool = typer.Option(False, "--force", help="Allow multi-install when integrations are not declared safe"),
+    integration_options: str | None = typer.Option(None, "--integration-options", help='Options for the integration (e.g. --integration-options="--commands-dir .myagent/cmds")'),
+):
+    """Install an integration into an existing project."""
+    from . import INTEGRATION_REGISTRY, get_integration
+    from .manifest import IntegrationManifest
+    from .. import _require_specify_project, _install_shared_infra_or_exit
+
+    project_root = _require_specify_project()
+    integration = get_integration(key)
+    if integration is None:
+        console.print(f"[red]Error:[/red] Unknown integration '{key}'")
+        available = ", ".join(sorted(INTEGRATION_REGISTRY.keys()))
+        console.print(f"Available integrations: {available}")
+        raise typer.Exit(1)
+
+    current = _read_integration_json(project_root)
+    default_key = _default_integration_key(current)
+    installed_keys = _installed_integration_keys(current)
+
+    if key in installed_keys:
+        console.print(f"[yellow]Integration '{key}' is already installed.[/yellow]")
+        if default_key == key:
+            console.print("It is already the default integration.")
+        else:
+            console.print(
+                f"To make it the default integration, run "
+                f"[cyan]specify integration use {key}[/cyan]."
+            )
+        console.print(
+            f"To refresh its managed files or options, run "
+            f"[cyan]specify integration upgrade {key}[/cyan]."
+        )
+        console.print("No files were changed.")
+        raise typer.Exit(0)
+
+    if installed_keys and not force:
+        unsafe_keys = []
+        for installed_key in installed_keys:
+            installed_integration = get_integration(installed_key)
+            if not installed_integration or not getattr(installed_integration, "multi_install_safe", False):
+                unsafe_keys.append(installed_key)
+        if unsafe_keys or not getattr(integration, "multi_install_safe", False):
+            console.print(
+                f"[red]Error:[/red] Installed integrations: {', '.join(installed_keys)}."
+            )
+            if default_key:
+                console.print(f"Default integration: [cyan]{default_key}[/cyan].")
+            console.print(
+                "Installing multiple integrations is only automatic when all involved "
+                "integrations are declared multi-install safe."
+            )
+            console.print(
+                f"To replace the default integration, run "
+                f"[cyan]specify integration switch {key}[/cyan]."
+            )
+            console.print(
+                f"To install '{key}' alongside the existing integrations anyway, "
+                "retry the same install command with [cyan]--force[/cyan]."
+            )
+            raise typer.Exit(1)
+
+    selected_script = _resolve_script_type(project_root, script)
+
+    # Build parsed options from --integration-options so the integration
+    # can determine its effective invoke separator before shared infra
+    # is installed.
+    raw_options, parsed_options = _resolve_integration_options(
+        integration, current, key, integration_options
+    )
+
+    # Ensure shared infrastructure is present (safe to run unconditionally;
+    # _install_shared_infra merges missing files without overwriting).
+    infra_integration = integration
+    infra_key = key
+    infra_parsed = parsed_options
+    if default_key:
+        default_integration = get_integration(default_key)
+        if default_integration is not None:
+            infra_integration = default_integration
+            infra_key = default_key
+            _, infra_parsed = _resolve_integration_options(
+                default_integration, current, default_key, None
+            )
+    _install_shared_infra_or_exit(
+        project_root,
+        selected_script,
+        invoke_separator=_invoke_separator_for_integration(
+            infra_integration, current, infra_key, infra_parsed
+        ),
+    )
+    if os.name != "nt":
+        from .. import ensure_executable_scripts
+        ensure_executable_scripts(project_root)
+
+    manifest = IntegrationManifest(
+        integration.key, project_root, version=_get_speckit_version()
+    )
+
+    try:
+        integration.setup(
+            project_root, manifest,
+            parsed_options=parsed_options,
+            script_type=selected_script,
+            raw_options=raw_options,
+        )
+        manifest.save()
+        new_installed = _dedupe_integration_keys([*installed_keys, integration.key])
+        new_default = default_key or integration.key
+        settings = _with_integration_setting(
+            current,
+            integration.key,
+            integration,
+            script_type=selected_script,
+            raw_options=raw_options,
+            parsed_options=parsed_options,
+        )
+        _write_integration_json(project_root, new_default, new_installed, settings)
+        if new_default == integration.key:
+            _update_init_options_for_integration(project_root, integration, script_type=selected_script)
+        else:
+            _refresh_init_options_speckit_version(project_root)
+
+    except Exception as exc:
+        # Attempt rollback of any files written by setup
+        try:
+            integration.teardown(project_root, manifest, force=True)
+        except Exception as rollback_err:
+            # Suppress so the original setup error remains the primary failure
+            from .. import _print_cli_warning
+            _print_cli_warning(
+                "rollback",
+                "integration",
+                key,
+                rollback_err,
+                continuing="The original install failure is still the primary error.",
+            )
+        if installed_keys:
+            _write_integration_json(
+                project_root, default_key, installed_keys, _integration_settings(current)
+            )
+        else:
+            _remove_integration_json(project_root)
+        console.print(
+            f"[red]Error:[/red] Failed to {_cli_phase_label('install', 'integration', key)}: "
+            f"{_cli_error_detail(exc)}"
+        )
+        raise typer.Exit(1)
+
+    name = (integration.config or {}).get("name", key)
+    console.print(f"\n[green]✓[/green] Integration '{name}' installed successfully")
+    if default_key:
+        console.print(f"[dim]Default integration remains:[/dim] [cyan]{default_key}[/cyan]")
+
+
+@integration_app.command("uninstall")
+def integration_uninstall(
+    key: str = typer.Argument(None, help="Integration key to uninstall (default: current integration)"),
+    force: bool = typer.Option(False, "--force", help="Remove files even if modified"),
+):
+    """Uninstall an integration, safely preserving modified files."""
+    from . import get_integration
+    from .manifest import IntegrationManifest
+    from .. import _require_specify_project
+
+    project_root = _require_specify_project()
+    current = _read_integration_json(project_root)
+    default_key = _default_integration_key(current)
+    installed_keys = _installed_integration_keys(current)
+
+    if key is None:
+        if not default_key:
+            console.print("[yellow]No integration is currently installed.[/yellow]")
+            raise typer.Exit(0)
+        key = default_key
+
+    if key not in installed_keys:
+        console.print(f"[red]Error:[/red] Integration '{key}' is not installed.")
+        raise typer.Exit(1)
+
+    integration = get_integration(key)
+
+    manifest_path = project_root / ".specify" / "integrations" / f"{key}.manifest.json"
+    if not manifest_path.exists():
+        console.print(f"[yellow]No manifest found for integration '{key}'. Nothing to uninstall.[/yellow]")
+        remaining = [installed for installed in installed_keys if installed != key]
+        new_default = default_key if default_key != key else (remaining[0] if remaining else None)
+        if remaining:
+            if default_key == key and new_default and (new_integration := get_integration(new_default)):
+                raw_options, parsed_options = _resolve_integration_options(
+                    new_integration, current, new_default, None
+                )
+                _set_default_integration_or_exit(
+                    project_root,
+                    current,
+                    new_default,
+                    new_integration,
+                    remaining,
+                    raw_options=raw_options,
+                    parsed_options=parsed_options,
+                )
+            else:
+                _write_integration_json(
+                    project_root, new_default, remaining, _integration_settings(current)
+                )
+        else:
+            _remove_integration_json(project_root)
+        if default_key == key:
+            _clear_init_options_for_integration(project_root, key)
+        raise typer.Exit(0)
+
+    try:
+        manifest = IntegrationManifest.load(key, project_root)
+    except _MANIFEST_READ_ERRORS as exc:
+        console.print(f"[red]Error:[/red] Integration manifest for '{key}' is unreadable.")
+        console.print(f"Manifest: {manifest_path}")
+        console.print(
+            f"To recover, delete the unreadable manifest, run "
+            f"[cyan]specify integration uninstall {key}[/cyan] to clear stale metadata, "
+            f"then run [cyan]specify integration install {key}[/cyan] to regenerate."
+        )
+        console.print(f"[dim]Details:[/dim] {exc}")
+        raise typer.Exit(1)
+
+    if not integration:
+        console.print(
+            f"[yellow]Warning:[/yellow] Integration '{key}' not found "
+            "in registry. Falling back to manifest-based cleanup."
+        )
+        removed, skipped = manifest.uninstall(project_root, force=force)
+    else:
+        removed, skipped = integration.teardown(project_root, manifest, force=force)
+
+    remaining = [installed for installed in installed_keys if installed != key]
+    new_default = default_key if default_key != key else (remaining[0] if remaining else None)
+    if remaining:
+        if default_key == key and new_default and (new_integration := get_integration(new_default)):
+            raw_options, parsed_options = _resolve_integration_options(
+                new_integration, current, new_default, None
+            )
+            _set_default_integration_or_exit(
+                project_root,
+                current,
+                new_default,
+                new_integration,
+                remaining,
+                raw_options=raw_options,
+                parsed_options=parsed_options,
+            )
+        else:
+            _write_integration_json(
+                project_root, new_default, remaining, _integration_settings(current)
+            )
+    else:
+        _remove_integration_json(project_root)
+
+    if default_key == key:
+        _clear_init_options_for_integration(project_root, key)
+
+    name = (integration.config or {}).get("name", key) if integration else key
+    console.print(f"\n[green]✓[/green] Integration '{name}' uninstalled")
+    if removed:
+        console.print(f"  Removed {len(removed)} file(s)")
+    if skipped:
+        console.print(f"\n[yellow]⚠[/yellow]  {len(skipped)} modified file(s) were preserved:")
+        for path in skipped:
+            rel = _display_project_path(project_root, path)
+            console.print(f"    {rel}")

src/specify_cli/integrations/_migrate_commands.py

@@ -0,0 +1,490 @@
+"""specify integration switch / upgrade command handlers."""
+from __future__ import annotations
+
+import os
+
+import typer
+
+from .._console import console
+from ..integration_runtime import (
+    invoke_separator_for_integration as _invoke_separator_for_integration,
+    with_integration_setting as _with_integration_setting,
+)
+from ..integration_state import (
+    dedupe_integration_keys as _dedupe_integration_keys,
+    default_integration_key as _default_integration_key,
+    installed_integration_keys as _installed_integration_keys,
+    integration_settings as _integration_settings,
+)
+from ._commands import integration_app
+from ._helpers import (
+    _MANIFEST_READ_ERRORS,
+    _SharedTemplateRefreshError,
+    _clear_init_options_for_integration,
+    _cli_error_detail,
+    _cli_phase_label,
+    _get_speckit_version,
+    _read_integration_json,
+    _refresh_init_options_speckit_version,
+    _remove_integration_json,
+    _resolve_integration_options,
+    _resolve_integration_script_type,
+    _resolve_script_type,
+    _set_default_integration,
+    _set_default_integration_or_exit,
+    _update_init_options_for_integration,
+    _write_integration_json,
+)
+
+
+@integration_app.command("switch")
+def integration_switch(
+    target: str = typer.Argument(help="Integration key to switch to"),
+    script: str | None = typer.Option(None, "--script", help="Script type: sh or ps (default: from init-options.json or platform default)"),
+    force: bool = typer.Option(False, "--force", help="Force removal of modified files during uninstall of the previous integration"),
+    refresh_shared_infra: bool = typer.Option(False, "--refresh-shared-infra", help="Also overwrite shared infrastructure files even if you customized them (otherwise customizations are preserved)"),
+    integration_options: str | None = typer.Option(None, "--integration-options", help='Options for the target integration'),
+):
+    """Switch from the current integration to a different one."""
+    from . import INTEGRATION_REGISTRY, get_integration
+    from .manifest import IntegrationManifest
+    from .. import _print_cli_warning, _require_specify_project, _install_shared_infra_or_exit
+
+    project_root = _require_specify_project()
+    target_integration = get_integration(target)
+    if target_integration is None:
+        console.print(f"[red]Error:[/red] Unknown integration '{target}'")
+        available = ", ".join(sorted(INTEGRATION_REGISTRY.keys()))
+        console.print(f"Available integrations: {available}")
+        raise typer.Exit(1)
+
+    current = _read_integration_json(project_root)
+    installed_keys = _installed_integration_keys(current)
+    installed_key = _default_integration_key(current)
+
+    if installed_key == target:
+        if integration_options is not None:
+            console.print(
+                "[red]Error:[/red] --integration-options cannot be used when switching "
+                "to an already installed integration."
+            )
+            console.print(
+                f"Run [cyan]specify integration upgrade {target} --integration-options ...[/cyan] "
+                "to update managed files/options."
+            )
+            raise typer.Exit(1)
+        if force:
+            raw_options, parsed_options = _resolve_integration_options(
+                target_integration, current, target, None
+            )
+            _set_default_integration_or_exit(
+                project_root,
+                current,
+                target,
+                target_integration,
+                installed_keys,
+                raw_options=raw_options,
+                parsed_options=parsed_options,
+                refresh_templates_force=True,
+            )
+            console.print(
+                f"\n[green]✓[/green] Default integration remains [bold]{target}[/bold]; "
+                "shared infrastructure refreshed."
+            )
+            raise typer.Exit(0)
+        console.print(f"[yellow]Integration '{target}' is already the default integration. Nothing to switch.[/yellow]")
+        raise typer.Exit(0)
+
+    if target in installed_keys:
+        if integration_options is not None:
+            console.print(
+                "[red]Error:[/red] --integration-options cannot be used when switching "
+                "to an already installed integration."
+            )
+            console.print(
+                f"Run [cyan]specify integration upgrade {target} --integration-options ...[/cyan] "
+                f"to update managed files/options, then [cyan]specify integration use {target}[/cyan]."
+            )
+            raise typer.Exit(1)
+        raw_options, parsed_options = _resolve_integration_options(
+            target_integration, current, target, None
+        )
+        _set_default_integration_or_exit(
+            project_root,
+            current,
+            target,
+            target_integration,
+            installed_keys,
+            raw_options=raw_options,
+            parsed_options=parsed_options,
+            refresh_templates_force=force,
+        )
+        console.print(f"\n[green]✓[/green] Default integration set to [bold]{target}[/bold].")
+        raise typer.Exit(0)
+
+    selected_script = _resolve_script_type(project_root, script)
+
+    # Phase 1: Uninstall current integration (if any)
+    if installed_key:
+        current_integration = get_integration(installed_key)
+        manifest_path = project_root / ".specify" / "integrations" / f"{installed_key}.manifest.json"
+
+        if current_integration and manifest_path.exists():
+            console.print(f"Uninstalling current integration: [cyan]{installed_key}[/cyan]")
+            try:
+                old_manifest = IntegrationManifest.load(installed_key, project_root)
+            except _MANIFEST_READ_ERRORS as exc:
+                console.print(f"[red]Error:[/red] Could not read integration manifest for '{installed_key}': {manifest_path}")
+                console.print(f"[dim]{exc}[/dim]")
+                console.print(
+                    f"To recover, delete the unreadable manifest at {manifest_path}, "
+                    f"run [cyan]specify integration uninstall {installed_key}[/cyan], then retry."
+                )
+                raise typer.Exit(1)
+            removed, skipped = current_integration.teardown(
+                project_root, old_manifest, force=force,
+            )
+            if removed:
+                console.print(f"  Removed {len(removed)} file(s)")
+            if skipped:
+                console.print(f"  [yellow]⚠[/yellow]  {len(skipped)} modified file(s) preserved")
+        elif not current_integration and manifest_path.exists():
+            # Integration removed from registry but manifest exists — use manifest-only uninstall
+            console.print(f"Uninstalling unknown integration '{installed_key}' via manifest")
+            try:
+                old_manifest = IntegrationManifest.load(installed_key, project_root)
+                removed, skipped = old_manifest.uninstall(project_root, force=force)
+                if removed:
+                    console.print(f"  Removed {len(removed)} file(s)")
+                if skipped:
+                    console.print(f"  [yellow]⚠[/yellow]  {len(skipped)} modified file(s) preserved")
+            except _MANIFEST_READ_ERRORS as exc:
+                console.print(f"[yellow]Warning:[/yellow] Could not read manifest for '{installed_key}': {exc}")
+        else:
+            console.print(f"[red]Error:[/red] Integration '{installed_key}' is installed but has no manifest.")
+            console.print(
+                f"Run [cyan]specify integration uninstall {installed_key}[/cyan] to clear metadata, "
+                f"then retry [cyan]specify integration switch {target}[/cyan]."
+            )
+            raise typer.Exit(1)
+
+        # Unregister extension commands for the old agent so they don't
+        # remain as orphans in the old agent's directory.
+        try:
+            from ..extensions import ExtensionManager
+
+            ext_mgr = ExtensionManager(project_root)
+            ext_mgr.unregister_agent_artifacts(installed_key)
+        except Exception as ext_err:
+            _print_cli_warning(
+                "clean up extension artifacts for",
+                "integration",
+                installed_key,
+                ext_err,
+                continuing="Continuing with integration switch; old extension artifacts may need manual cleanup.",
+            )
+
+        # Clear metadata so a failed Phase 2 doesn't leave stale references
+        installed_keys = [installed for installed in installed_keys if installed != installed_key]
+        _clear_init_options_for_integration(project_root, installed_key)
+        if installed_keys:
+            fallback_key = installed_keys[0]
+            fallback_integration = get_integration(fallback_key)
+            if fallback_integration is not None:
+                raw_options, parsed_options = _resolve_integration_options(
+                    fallback_integration, current, fallback_key, None
+                )
+                _set_default_integration_or_exit(
+                    project_root,
+                    current,
+                    fallback_key,
+                    fallback_integration,
+                    installed_keys,
+                    raw_options=raw_options,
+                    parsed_options=parsed_options,
+                )
+            else:
+                _write_integration_json(
+                    project_root, fallback_key, installed_keys, _integration_settings(current)
+                )
+        else:
+            _remove_integration_json(project_root)
+        current = _read_integration_json(project_root)
+
+    # Build parsed options from --integration-options so the integration
+    # can determine its effective invoke separator before shared infra
+    # is installed.
+    raw_options, parsed_options = _resolve_integration_options(
+        target_integration, current, target, integration_options
+    )
+
+    # Refresh shared infrastructure to the current CLI version. Switching
+    # integrations is exactly when stale vendored shared scripts (e.g.
+    # update-agent-context.sh that pre-dates the target integration's
+    # supported-agent list) would silently break the new integration.
+    #
+    # Use refresh_managed=True so only files that match their previously
+    # recorded hash are overwritten — user customizations are detected via
+    # hash divergence and preserved with a warning. Pass
+    # --refresh-shared-infra to overwrite customizations as well. See #2293.
+    _install_shared_infra_or_exit(
+        project_root,
+        selected_script,
+        force=refresh_shared_infra,
+        refresh_managed=True,
+        invoke_separator=_invoke_separator_for_integration(
+            target_integration, current, target, parsed_options
+        ),
+        refresh_hint=(
+            "To overwrite customizations, re-run with "
+            "[cyan]specify integration switch ... --refresh-shared-infra[/cyan]."
+        ),
+    )
+    if os.name != "nt":
+        from .. import ensure_executable_scripts
+        ensure_executable_scripts(project_root)
+
+    # Phase 2: Install target integration
+    console.print(f"Installing integration: [cyan]{target}[/cyan]")
+    manifest = IntegrationManifest(
+        target_integration.key, project_root, version=_get_speckit_version()
+    )
+
+    try:
+        target_integration.setup(
+            project_root, manifest,
+            parsed_options=parsed_options,
+            script_type=selected_script,
+            raw_options=raw_options,
+        )
+        manifest.save()
+        _set_default_integration(
+            project_root,
+            current,
+            target_integration.key,
+            target_integration,
+            _dedupe_integration_keys([*installed_keys, target_integration.key]),
+            script_type=selected_script,
+            raw_options=raw_options,
+            parsed_options=parsed_options,
+        )
+
+        # Re-register extension commands for the new agent so that
+        # previously-installed extensions are available in the new integration.
+        try:
+            from ..extensions import ExtensionManager
+
+            ext_mgr = ExtensionManager(project_root)
+            ext_mgr.register_enabled_extensions_for_agent(target)
+        except Exception as ext_err:
+            _print_cli_warning(
+                "register extension artifacts for",
+                "integration",
+                target,
+                ext_err,
+                continuing="The integration switch succeeded, but installed extensions may need re-registration.",
+            )
+
+    except Exception as exc:
+        # Attempt rollback of any files written by setup
+        try:
+            target_integration.teardown(project_root, manifest, force=True)
+        except Exception as rollback_err:
+            # Suppress so the original setup error remains the primary failure
+            _print_cli_warning(
+                "rollback",
+                "integration",
+                target,
+                rollback_err,
+                continuing="The original switch failure is still the primary error.",
+            )
+        if installed_keys:
+            fallback_key = installed_keys[0]
+            fallback_integration = get_integration(fallback_key)
+            if fallback_integration is not None:
+                raw_options, parsed_options = _resolve_integration_options(
+                    fallback_integration, current, fallback_key, None
+                )
+                try:
+                    _set_default_integration(
+                        project_root,
+                        current,
+                        fallback_key,
+                        fallback_integration,
+                        installed_keys,
+                        raw_options=raw_options,
+                        parsed_options=parsed_options,
+                    )
+                except _SharedTemplateRefreshError as restore_err:
+                    console.print(
+                        f"[yellow]Warning:[/yellow] Failed to restore default "
+                        f"integration '{fallback_key}': {restore_err}"
+                    )
+            else:
+                _write_integration_json(
+                    project_root, fallback_key, installed_keys, _integration_settings(current)
+                )
+        else:
+            _remove_integration_json(project_root)
+        console.print(
+            f"[red]Error:[/red] Failed to {_cli_phase_label('install', 'integration', target)} "
+            f"during switch: {_cli_error_detail(exc)}"
+        )
+        raise typer.Exit(1)
+
+    name = (target_integration.config or {}).get("name", target)
+    console.print(f"\n[green]✓[/green] Switched to integration '{name}'")
+
+
+@integration_app.command("upgrade")
+def integration_upgrade(
+    key: str | None = typer.Argument(None, help="Integration key to upgrade (default: current integration)"),
+    force: bool = typer.Option(False, "--force", help="Force upgrade even if files are modified"),
+    script: str | None = typer.Option(None, "--script", help="Script type: sh or ps (default: from init-options.json or platform default)"),
+    integration_options: str | None = typer.Option(None, "--integration-options", help="Options for the integration"),
+):
+    """Upgrade an integration by reinstalling with diff-aware file handling.
+
+    Compares manifest hashes to detect locally modified files and
+    blocks the upgrade unless --force is used.
+    """
+    from . import get_integration
+    from .manifest import IntegrationManifest
+    from .. import _require_specify_project, _install_shared_infra_or_exit, _install_shared_infra
+
+    project_root = _require_specify_project()
+    current = _read_integration_json(project_root)
+    installed_key = _default_integration_key(current)
+    installed_keys = _installed_integration_keys(current)
+
+    if key is None:
+        if not installed_key:
+            console.print("[yellow]No integration is currently installed.[/yellow]")
+            raise typer.Exit(0)
+        key = installed_key
+
+    if key not in installed_keys:
+        console.print(f"[red]Error:[/red] Integration '{key}' is not installed.")
+        raise typer.Exit(1)
+
+    integration = get_integration(key)
+    if integration is None:
+        console.print(f"[red]Error:[/red] Unknown integration '{key}'")
+        raise typer.Exit(1)
+
+    manifest_path = project_root / ".specify" / "integrations" / f"{key}.manifest.json"
+    if not manifest_path.exists():
+        console.print(f"[yellow]No manifest found for integration '{key}'. Nothing to upgrade.[/yellow]")
+        console.print(f"Run [cyan]specify integration install {key}[/cyan] to perform a fresh install.")
+        raise typer.Exit(0)
+
+    try:
+        old_manifest = IntegrationManifest.load(key, project_root)
+    except _MANIFEST_READ_ERRORS as exc:
+        console.print(f"[red]Error:[/red] Integration manifest for '{key}' is unreadable: {exc}")
+        raise typer.Exit(1)
+
+    # Detect modified files via manifest hashes
+    modified = old_manifest.check_modified()
+    if modified and not force:
+        console.print(f"[yellow]⚠[/yellow]  {len(modified)} file(s) have been modified since installation:")
+        for rel in modified:
+            console.print(f"    {rel}")
+        console.print("\nUse [cyan]--force[/cyan] to overwrite modified files, or resolve manually.")
+        raise typer.Exit(1)
+
+    selected_script = _resolve_integration_script_type(project_root, current, key, script)
+
+    # Build parsed options from --integration-options so the integration
+    # can determine its effective invoke separator before shared infra
+    # is installed.
+    raw_options, parsed_options = _resolve_integration_options(
+        integration, current, key, integration_options
+    )
+
+    # Ensure shared infrastructure is up to date; --force overwrites existing files.
+    infra_integration = integration
+    infra_key = key
+    infra_parsed = parsed_options
+    if installed_key and installed_key != key:
+        default_integration = get_integration(installed_key)
+        if default_integration is not None:
+            infra_integration = default_integration
+            infra_key = installed_key
+            _, infra_parsed = _resolve_integration_options(
+                default_integration, current, installed_key, None
+            )
+    _install_shared_infra_or_exit(
+        project_root,
+        selected_script,
+        force=force,
+        invoke_separator=_invoke_separator_for_integration(
+            infra_integration, current, infra_key, infra_parsed
+        ),
+    )
+    if os.name != "nt":
+        from .. import ensure_executable_scripts
+        ensure_executable_scripts(project_root)
+
+    # Phase 1: Install new files (overwrites existing; old-only files remain)
+    console.print(f"Upgrading integration: [cyan]{key}[/cyan]")
+    new_manifest = IntegrationManifest(key, project_root, version=_get_speckit_version())
+
+    try:
+        integration.setup(
+            project_root,
+            new_manifest,
+            parsed_options=parsed_options,
+            script_type=selected_script,
+            raw_options=raw_options,
+        )
+        settings = _with_integration_setting(
+            current,
+            key,
+            integration,
+            script_type=selected_script,
+            raw_options=raw_options,
+            parsed_options=parsed_options,
+        )
+        if installed_key == key:
+            try:
+                _install_shared_infra(
+                    project_root,
+                    selected_script,
+                    invoke_separator=_invoke_separator_for_integration(
+                        integration, {"integration_settings": settings}, key, parsed_options
+                    ),
+                    force=force,
+                    refresh_managed=True,
+                )
+            except (ValueError, OSError) as exc:
+                raise _SharedTemplateRefreshError(
+                    f"Failed to refresh shared infrastructure for '{key}': {exc}"
+                ) from exc
+        new_manifest.save()
+        _write_integration_json(project_root, installed_key, installed_keys, settings)
+        if installed_key == key:
+            _update_init_options_for_integration(project_root, integration, script_type=selected_script)
+        else:
+            _refresh_init_options_speckit_version(project_root)
+    except Exception as exc:
+        # Don't teardown — setup overwrites in-place, so teardown would
+        # delete files that were working before the upgrade.  Just report.
+        console.print(f"[red]Error:[/red] Failed to {_cli_phase_label('upgrade', 'integration', key)}.")
+        console.print(f"[dim]Details:[/dim] {_cli_error_detail(exc)}")
+        console.print("[yellow]The previous integration files may still be in place.[/yellow]")
+        raise typer.Exit(1)
+
+    # Phase 2: Remove stale files from old manifest that are not in the new one
+    old_files = old_manifest.files
+    new_files = new_manifest.files
+    stale_keys = set(old_files) - set(new_files)
+    if stale_keys:
+        stale_manifest = IntegrationManifest(key, project_root, version="stale-cleanup")
+        stale_manifest._files = {k: old_files[k] for k in stale_keys}
+        stale_removed, _ = stale_manifest.uninstall(project_root, force=True)
+        if stale_removed:
+            console.print(f"  Removed {len(stale_removed)} stale file(s) from previous install")
+
+    name = (integration.config or {}).get("name", key)
+    console.print(f"\n[green]✓[/green] Integration '{name}' upgraded successfully")

src/specify_cli/integrations/_query_commands.py

@@ -0,0 +1,464 @@
+"""specify integration list/use/search/info + catalog list/add/remove command handlers."""
+from __future__ import annotations
+
+import os
+from typing import Optional
+
+import typer
+from rich.table import Table
+
+from .._console import console
+from ..integration_state import (
+    default_integration_key as _default_integration_key,
+    installed_integration_keys as _installed_integration_keys,
+)
+from ._commands import integration_app, integration_catalog_app
+from ._helpers import (
+    _read_integration_json,
+    _resolve_integration_options,
+    _set_default_integration_or_exit,
+)
+
+
+@integration_app.command("list")
+def integration_list(
+    catalog: bool = typer.Option(False, "--catalog", help="Browse full catalog (built-in + community)"),
+):
+    """List available integrations and installed status."""
+    from . import INTEGRATION_REGISTRY
+    from .. import _require_specify_project
+
+    project_root = _require_specify_project()
+    current = _read_integration_json(project_root)
+    default_key = _default_integration_key(current)
+    installed_keys = set(_installed_integration_keys(current))
+
+    if catalog:
+        from .catalog import IntegrationCatalog, IntegrationCatalogError
+
+        ic = IntegrationCatalog(project_root)
+        try:
+            entries = ic.search()
+        except IntegrationCatalogError as exc:
+            console.print(f"[red]Error:[/red] {exc}")
+            raise typer.Exit(1)
+
+        if not entries:
+            console.print("[yellow]No integrations found in catalog.[/yellow]")
+            return
+
+        table = Table(title="Integration Catalog")
+        table.add_column("ID", style="cyan")
+        table.add_column("Name")
+        table.add_column("Version")
+        table.add_column("Source")
+        table.add_column("Status")
+        table.add_column("Multi-install Safe")
+
+        for entry in sorted(entries, key=lambda e: e["id"]):
+            eid = entry["id"]
+            cat_name = entry.get("_catalog_name", "")
+            install_allowed = entry.get("_install_allowed", True)
+            if eid == default_key:
+                status = "[green]installed (default)[/green]"
+            elif eid in installed_keys:
+                status = "[green]installed[/green]"
+            elif eid in INTEGRATION_REGISTRY:
+                status = "built-in"
+            elif install_allowed is False:
+                status = "discovery-only"
+            else:
+                status = ""
+            safe = ""
+            if eid in INTEGRATION_REGISTRY:
+                reg_integ = INTEGRATION_REGISTRY[eid]
+                safe = "yes" if getattr(reg_integ, "multi_install_safe", False) else "no"
+            table.add_row(
+                eid,
+                entry.get("name", eid),
+                entry.get("version", ""),
+                cat_name,
+                status,
+                safe,
+            )
+        console.print(table)
+        return
+
+    if not INTEGRATION_REGISTRY:
+        console.print("[yellow]No integrations available.[/yellow]")
+        return
+
+    table = Table(title="Coding Agent Integrations")
+    table.add_column("Key", style="cyan")
+    table.add_column("Name")
+    table.add_column("Status")
+    table.add_column("CLI Required")
+    table.add_column("Multi-install Safe")
+
+    for key in sorted(INTEGRATION_REGISTRY.keys()):
+        integration = INTEGRATION_REGISTRY[key]
+        cfg = integration.config or {}
+        name = cfg.get("name", key)
+        requires_cli = cfg.get("requires_cli", False)
+        if key == default_key:
+            status = "[green]installed (default)[/green]"
+        elif key in installed_keys:
+            status = "[green]installed[/green]"
+        else:
+            status = ""
+        cli_req = "yes" if requires_cli else "no (IDE)"
+        safe = "yes" if getattr(integration, "multi_install_safe", False) else "no"
+        table.add_row(key, name, status, cli_req, safe)
+
+    console.print(table)
+
+    if installed_keys:
+        console.print(f"\n[dim]Default integration:[/dim] [cyan]{default_key or 'none'}[/cyan]")
+        console.print(f"[dim]Installed integrations:[/dim] [cyan]{', '.join(sorted(installed_keys))}[/cyan]")
+    else:
+        console.print("\n[yellow]No integration currently installed.[/yellow]")
+        console.print("Install one with: [cyan]specify integration install <key>[/cyan]")
+
+
+@integration_app.command("use")
+def integration_use(
+    key: str = typer.Argument(help="Installed integration key to make the default"),
+    force: bool = typer.Option(False, "--force", help="Overwrite existing shared infrastructure files, including customizations, while changing the default"),
+):
+    """Set the default integration without uninstalling other integrations."""
+    from . import get_integration
+    from .. import _require_specify_project
+
+    project_root = _require_specify_project()
+    current = _read_integration_json(project_root)
+    installed_keys = _installed_integration_keys(current)
+    if key not in installed_keys:
+        console.print(f"[red]Error:[/red] Integration '{key}' is not installed.")
+        if installed_keys:
+            console.print(f"[yellow]Installed integrations:[/yellow] {', '.join(installed_keys)}")
+        else:
+            console.print("Install one with: [cyan]specify integration install <key>[/cyan]")
+        raise typer.Exit(1)
+
+    integration = get_integration(key)
+    if integration is None:
+        console.print(f"[red]Error:[/red] Unknown integration '{key}'")
+        raise typer.Exit(1)
+
+    raw_options, parsed_options = _resolve_integration_options(integration, current, key, None)
+    _set_default_integration_or_exit(
+        project_root,
+        current,
+        key,
+        integration,
+        installed_keys,
+        raw_options=raw_options,
+        parsed_options=parsed_options,
+        refresh_templates_force=force,
+        refresh_hint=(
+            "To overwrite customizations, re-run with "
+            f"[cyan]specify integration use {key} --force[/cyan]."
+        ),
+    )
+    console.print(f"[green]✓[/green] Default integration set to [bold]{key}[/bold].")
+
+
+# ===== Integration catalog discovery commands =====
+#
+# These commands mirror the workflow catalog CLI shape:
+#   - `search` / `info` for discovery over the active catalog stack
+#   - `catalog list/add/remove` for managing catalog sources
+#
+# They deliberately do NOT add `integration add/remove/enable/disable/
+# set-priority`: integrations are single-active (install / uninstall / switch),
+# not additive like extensions and presets.
+@integration_app.command("search")
+def integration_search(
+    query: Optional[str] = typer.Argument(None, help="Search query (optional)"),
+    tag: Optional[str] = typer.Option(None, "--tag", help="Filter by tag"),
+    author: Optional[str] = typer.Option(None, "--author", help="Filter by author"),
+):
+    """Search for integrations in the active catalog stack."""
+    from . import INTEGRATION_REGISTRY
+    from .catalog import (
+        IntegrationCatalog,
+        IntegrationCatalogError,
+        IntegrationValidationError,
+    )
+    from .. import _require_specify_project
+
+    project_root = _require_specify_project()
+    integration_config = _read_integration_json(project_root)
+    installed_key = _default_integration_key(integration_config)
+    catalog = IntegrationCatalog(project_root)
+
+    try:
+        results = catalog.search(query=query, tag=tag, author=author)
+    except IntegrationValidationError as exc:
+        console.print(f"[red]Error:[/red] {exc}")
+        console.print(
+            "\nTip: Check the configuration file path shown above for invalid catalog configuration "
+            "(for example, .specify/integration-catalogs.yml or ~/.specify/integration-catalogs.yml)."
+        )
+        raise typer.Exit(1)
+    except IntegrationCatalogError as exc:
+        console.print(f"[red]Error:[/red] {exc}")
+        if os.environ.get("SPECKIT_INTEGRATION_CATALOG_URL", "").strip():
+            console.print(
+                "\nTip: Check the SPECKIT_INTEGRATION_CATALOG_URL environment variable for an invalid "
+                "catalog URL, or unset it to use the configured catalog files "
+                "(.specify/integration-catalogs.yml or ~/.specify/integration-catalogs.yml)."
+            )
+        else:
+            console.print("\nTip: The catalog may be temporarily unavailable. Try again later.")
+        raise typer.Exit(1)
+
+    if not results:
+        console.print("\n[yellow]No integrations found matching criteria[/yellow]")
+        if query or tag or author:
+            console.print("\nTry:")
+            console.print("  • Broader search terms")
+            console.print("  • Remove filters")
+            console.print("  • specify integration search (show all)")
+        return
+
+    console.print(f"\n[green]Found {len(results)} integration(s):[/green]\n")
+    for integ in sorted(results, key=lambda e: e.get("id", "")):
+        iid = integ.get("id", "?")
+        name = integ.get("name", iid)
+        version = integ.get("version", "?")
+        console.print(f"[bold]{name}[/bold] ({iid}) v{version}")
+        desc = integ.get("description", "")
+        if desc:
+            console.print(f"  {desc}")
+
+        console.print(f"\n  [dim]Author:[/dim] {integ.get('author', 'Unknown')}")
+        tags = integ.get("tags", [])
+        if isinstance(tags, list) and tags:
+            console.print(f"  [dim]Tags:[/dim] {', '.join(str(t) for t in tags)}")
+
+        cat_name = integ.get("_catalog_name", "")
+        install_allowed = integ.get("_install_allowed", True)
+        if cat_name:
+            if install_allowed:
+                console.print(f"  [dim]Catalog:[/dim] {cat_name}")
+            else:
+                console.print(
+                    f"  [dim]Catalog:[/dim] {cat_name} "
+                    "[yellow](discovery only — not installable)[/yellow]"
+                )
+
+        if iid == installed_key:
+            console.print("\n  [green]✓ Installed[/green] (currently active)")
+        elif iid in INTEGRATION_REGISTRY:
+            console.print(f"\n  [cyan]Install:[/cyan] specify integration install {iid}")
+        elif install_allowed:
+            console.print(
+                "\n  [yellow]Found in catalog.[/yellow] Only built-in integration IDs "
+                "can be installed with 'specify integration install'."
+            )
+        else:
+            console.print(
+                f"\n  [yellow]⚠[/yellow]  Not directly installable from '{cat_name}'."
+            )
+        console.print()
+
+
+@integration_app.command("info")
+def integration_info(
+    integration_id: str = typer.Argument(..., help="Integration ID"),
+):
+    """Show catalog details for a single integration."""
+    from . import INTEGRATION_REGISTRY
+    from .catalog import (
+        IntegrationCatalog,
+        IntegrationCatalogError,
+        IntegrationValidationError,
+    )
+    from .. import _require_specify_project
+
+    project_root = _require_specify_project()
+    catalog = IntegrationCatalog(project_root)
+    installed_key = _default_integration_key(_read_integration_json(project_root))
+
+    try:
+        info = catalog.get_integration_info(integration_id)
+    except IntegrationCatalogError as exc:
+        info = None
+        # Keep the live exception so the fallback branch below can give
+        # different guidance for local-config vs. network failures.
+        catalog_error: Optional[IntegrationCatalogError] = exc
+    else:
+        catalog_error = None
+
+    if info:
+        name = info.get("name", integration_id)
+        version = info.get("version", "?")
+        console.print(f"\n[bold cyan]{name}[/bold cyan] ({integration_id}) v{version}")
+        if info.get("description"):
+            console.print(f"  {info['description']}")
+        console.print()
+
+        console.print(f"  [dim]Author:[/dim] {info.get('author', 'Unknown')}")
+        if info.get("license"):
+            console.print(f"  [dim]License:[/dim] {info['license']}")
+
+        tags = info.get("tags", [])
+        if isinstance(tags, list) and tags:
+            console.print(f"  [dim]Tags:[/dim] {', '.join(str(t) for t in tags)}")
+
+        cat_name = info.get("_catalog_name", "")
+        install_allowed = info.get("_install_allowed", True)
+        if cat_name:
+            install_note = "" if install_allowed else " [yellow](discovery only)[/yellow]"
+            console.print(f"  [dim]Source catalog:[/dim] {cat_name}{install_note}")
+
+        if info.get("repository"):
+            console.print(f"  [dim]Repository:[/dim] {info['repository']}")
+
+        if integration_id == installed_key:
+            console.print("\n  [green]✓ Installed[/green] (currently active)")
+        elif integration_id in INTEGRATION_REGISTRY:
+            console.print("\n  [dim]Built-in integration (not currently active)[/dim]")
+        return
+
+    if integration_id in INTEGRATION_REGISTRY:
+        integration = INTEGRATION_REGISTRY[integration_id]
+        cfg = integration.config or {}
+        name = cfg.get("name", integration_id)
+        console.print(f"\n[bold cyan]{name}[/bold cyan] ({integration_id})")
+        console.print("  [dim]Built-in integration (not listed in catalog)[/dim]")
+        if integration_id == installed_key:
+            console.print("\n  [green]✓ Installed[/green] (currently active)")
+        if catalog_error:
+            console.print(f"\n[yellow]Catalog unavailable:[/yellow] {catalog_error}")
+        return
+
+    if catalog_error:
+        console.print(f"[red]Error:[/red] Could not query integration catalog: {catalog_error}")
+        if isinstance(catalog_error, IntegrationValidationError):
+            console.print(
+                "\nCheck the configuration file path shown above "
+                "(.specify/integration-catalogs.yml or ~/.specify/integration-catalogs.yml), "
+                "or use a built-in integration ID directly."
+            )
+        elif os.environ.get("SPECKIT_INTEGRATION_CATALOG_URL", "").strip():
+            console.print(
+                "\nCheck whether SPECKIT_INTEGRATION_CATALOG_URL is set correctly and reachable, "
+                "or unset it to use the configured catalog files, or use a built-in integration ID directly."
+            )
+        else:
+            console.print("\nTry again when online, or use a built-in integration ID directly.")
+    else:
+        console.print(f"[red]Error:[/red] Integration '{integration_id}' not found")
+        console.print("\nTry: specify integration search")
+    raise typer.Exit(1)
+
+
+@integration_catalog_app.command("list")
+def integration_catalog_list():
+    """List configured integration catalog sources."""
+    from .catalog import IntegrationCatalog, IntegrationCatalogError
+    from .. import _require_specify_project
+
+    project_root = _require_specify_project()
+    catalog = IntegrationCatalog(project_root)
+    env_override = os.environ.get("SPECKIT_INTEGRATION_CATALOG_URL", "").strip()
+
+    try:
+        if env_override:
+            project_configs = None
+            configs = catalog.get_catalog_configs()
+        else:
+            project_configs = catalog.get_project_catalog_configs()
+            configs = project_configs if project_configs is not None else catalog.get_catalog_configs()
+    except IntegrationCatalogError as exc:
+        console.print(f"[red]Error:[/red] {exc}")
+        raise typer.Exit(1)
+
+    console.print("\n[bold cyan]Integration Catalog Sources:[/bold cyan]\n")
+    if env_override:
+        console.print(
+            "  SPECKIT_INTEGRATION_CATALOG_URL is set; it supersedes configured catalog files."
+        )
+        console.print(
+            "  Project/user catalog sources are not active while the env override is set.\n"
+        )
+        console.print("[bold]Active catalog source from environment (non-removable here):[/bold]\n")
+    elif project_configs is None:
+        console.print("  No project-level catalog sources configured.\n")
+        console.print("[bold]Active catalog sources (non-removable here):[/bold]\n")
+    else:
+        console.print("[bold]Project catalog sources (removable):[/bold]\n")
+
+    for i, cfg in enumerate(configs):
+        install_status = (
+            "[green]install allowed[/green]"
+            if cfg.get("install_allowed")
+            else "[yellow]discovery only[/yellow]"
+        )
+        raw_name = cfg.get("name")
+        display_name = str(raw_name).strip() if raw_name is not None else ""
+        if not display_name:
+            display_name = f"catalog-{i + 1}"
+        if env_override or project_configs is None:
+            console.print(f"  - [bold]{display_name}[/bold] — {install_status}")
+        else:
+            console.print(f"  [{i}] [bold]{display_name}[/bold] — {install_status}")
+        console.print(f"      {cfg.get('url', '')}")
+        if cfg.get("description"):
+            console.print(f"      [dim]{cfg['description']}[/dim]")
+        console.print()
+
+
+@integration_catalog_app.command("add")
+def integration_catalog_add(
+    url: str = typer.Argument(
+        ...,
+        help=(
+            "Catalog URL to add (HTTPS required, except http://localhost, "
+            "http://127.0.0.1, or http://[::1] for local testing)"
+        ),
+    ),
+    name: Optional[str] = typer.Option(None, "--name", help="Catalog name"),
+):
+    """Add an integration catalog source to the project config."""
+    from .catalog import IntegrationCatalog, IntegrationCatalogError
+    from .. import _require_specify_project
+
+    project_root = _require_specify_project()
+    catalog = IntegrationCatalog(project_root)
+
+    # Normalize once here so the success message reflects what was actually
+    # stored. ``IntegrationCatalog.add_catalog`` strips again defensively.
+    normalized_url = url.strip()
+
+    try:
+        catalog.add_catalog(normalized_url, name)
+    except IntegrationCatalogError as exc:
+        # Covers both URL validation (base class) and config-file validation
+        # (IntegrationValidationError subclass).
+        console.print(f"[red]Error:[/red] {exc}")
+        raise typer.Exit(1)
+
+    console.print(f"[green]✓[/green] Catalog source added: {normalized_url}")
+
+
+@integration_catalog_app.command("remove")
+def integration_catalog_remove(
+    index: int = typer.Argument(..., help="Catalog index to remove (from 'catalog list')"),
+):
+    """Remove an integration catalog source by 0-based index."""
+    from .catalog import IntegrationCatalog, IntegrationCatalogError
+    from .. import _require_specify_project
+
+    project_root = _require_specify_project()
+    catalog = IntegrationCatalog(project_root)
+
+    try:
+        removed_name = catalog.remove_catalog(index)
+    except IntegrationCatalogError as exc:
+        console.print(f"[red]Error:[/red] {exc}")
+        raise typer.Exit(1)
+
+    console.print(f"[green]✓[/green] Catalog source '{removed_name}' removed")

src/specify_cli/integrations/cline/__init__.py

@@ -0,0 +1,162 @@
+"""Cline IDE integration."""
+
+from __future__ import annotations
+
+import re
+from pathlib import Path
+from typing import Any
+
+from ..base import MarkdownIntegration
+from ..manifest import IntegrationManifest
+
+
+# Note injected into hook sections so Cline maps dot-notation command
+# names (from extensions.yml) to the hyphenated slash commands it uses.
+_HOOK_COMMAND_NOTE = (
+    "- When constructing slash commands from hook command names, "
+    "replace dots (`.`) with hyphens (`-`). "
+    "For example, `speckit.git.commit` → `/speckit-git-commit`.\n"
+)
+
+
+def format_cline_command_name(cmd_name: str) -> str:
+    """Convert command name to Cline-compatible hyphenated format.
+
+    Cline handles slash-commands optimally when they use hyphens instead of dots.
+    This function converts dot-notation command names to hyphenated format.
+
+    The function is idempotent: already-formatted names are returned unchanged.
+
+    Examples:
+        >>> format_cline_command_name("plan")
+        'speckit-plan'
+        >>> format_cline_command_name("speckit.plan")
+        'speckit-plan'
+        >>> format_cline_command_name("speckit.git.commit")
+        'speckit-git-commit'
+
+    Args:
+        cmd_name: Command name in dot notation (speckit.foo.bar),
+                  hyphenated format (speckit-foo-bar), or plain name (foo)
+
+    Returns:
+        Hyphenated command name with 'speckit-' prefix
+    """
+    cmd_name = cmd_name.replace(".", "-")
+
+    if not cmd_name.startswith("speckit-"):
+        cmd_name = f"speckit-{cmd_name}"
+
+    return cmd_name
+
+
+class ClineIntegration(MarkdownIntegration):
+    """Integration for Cline IDE."""
+
+    key = "cline"
+    config = {
+        "name": "Cline",
+        "folder": ".clinerules/",
+        "commands_subdir": "workflows",
+        "install_url": "https://github.com/cline/cline",
+        "requires_cli": False,
+    }
+    registrar_config = {
+        "dir": ".clinerules/workflows",
+        "format": "markdown",
+        "args": "$ARGUMENTS",
+        "extension": ".md",
+        "inject_name": True,
+        "format_name": format_cline_command_name,
+        "invoke_separator": "-",
+    }
+    context_file = ".clinerules/specify-rules.md"
+    invoke_separator = "-"
+    multi_install_safe = True
+
+    def command_filename(self, template_name: str) -> str:
+        """Cline uses hyphenated filenames (e.g. speckit-git-commit.md)."""
+        return format_cline_command_name(template_name) + ".md"
+
+    def process_template(self, *args, **kwargs):
+        """Ensure shared templates render Cline command references with hyphens."""
+        kwargs.setdefault("invoke_separator", self.invoke_separator)
+        return super().process_template(*args, **kwargs)
+
+    @staticmethod
+    def _inject_hook_command_note(content: str) -> str:
+        """Insert a dot-to-hyphen note before each hook output instruction.
+
+        Targets the line ``- For each executable hook, output the following``
+        and inserts the note on the line before it, matching its indentation.
+        Skips if the note is already present.
+        """
+        if "replace dots" in content:
+            return content
+
+        def repl(m: re.Match[str]) -> str:
+            indent = m.group(1)
+            instruction = m.group(2)
+            eol = m.group(3)
+            return (
+                indent
+                + _HOOK_COMMAND_NOTE.rstrip("\n")
+                + eol
+                + indent
+                + instruction
+                + eol
+            )
+
+        return re.sub(
+            r"(?m)^(\s*)(- For each executable hook, output the following[^\r\n]*)(\r\n|\n|$)",
+            repl,
+            content,
+        )
+
+    @staticmethod
+    def _rewrite_handoff_references(content: str) -> str:
+        """Replace dot-notation agent references in handoffs with hyphens."""
+        return re.sub(
+            r"(?m)^(\s*agent:\s*)(speckit\.[A-Za-z0-9-_]+(?:\.[A-Za-z0-9-_]+)*)",
+            lambda m: f"{m.group(1)}{format_cline_command_name(m.group(2))}",
+            content,
+        )
+
+    def post_process_content(self, content: str) -> str:
+        """Apply Cline-specific transformations to command content."""
+        updated = self._inject_hook_command_note(content)
+        updated = self._rewrite_handoff_references(updated)
+        return updated
+
+    def setup(
+        self,
+        project_root: Path,
+        manifest: IntegrationManifest,
+        parsed_options: dict[str, Any] | None = None,
+        **opts: Any,
+    ) -> list[Path]:
+        """Install Cline commands and apply post-processing transformations."""
+        created = super().setup(project_root, manifest, parsed_options, **opts)
+
+        # Post-process generated command files
+        dest_dir = self.commands_dest(project_root).resolve()
+
+        for path in created:
+            # Only touch .md files under the commands directory
+            try:
+                path.resolve().relative_to(dest_dir)
+            except ValueError:
+                continue
+            if path.suffix != ".md":
+                continue
+
+            content_bytes = path.read_bytes()
+            content = content_bytes.decode("utf-8")
+
+            updated = self.post_process_content(content)
+
+            if updated != content:
+                path.write_bytes(updated.encode("utf-8"))
+                self.record_file_in_manifest(path, project_root, manifest)
+
+        return created

src/specify_cli/integrations/copilot/__init__.py

@@ -283,58 +283,13 @@ class CopilotIntegration(IntegrationBase):
         return f"speckit.{template_name}.agent.md"
 
     def post_process_skill_content(self, content: str) -> str:
-        """Inject shared hook guidance and Copilot ``mode:`` frontmatter.
+        """Inject shared hook guidance into Copilot skill content.
 
-        Inserts ``mode: speckit.<stem>`` before the closing ``---`` so
-        Copilot can associate the skill with its agent mode.
+        Delegates to :class:`_CopilotSkillsHelper` for shared post-processing.
+        The ``mode:`` frontmatter field is intentionally omitted: VS Code
+        Copilot Agent Skills do not support it (see issue #2799).
         """
-        updated = _CopilotSkillsHelper().post_process_skill_content(content)
-        lines = updated.splitlines(keepends=True)
-
-        # Extract skill name from frontmatter to derive the mode value
-        dash_count = 0
-        skill_name = ""
-        for line in lines:
-            stripped = line.rstrip("\n\r")
-            if stripped == "---":
-                dash_count += 1
-                if dash_count == 2:
-                    break
-                continue
-            if dash_count == 1:
-                if stripped.startswith("mode:"):
-                    return updated  # already present
-                if stripped.startswith("name:"):
-                    # Parse: name: "speckit-plan" → speckit.plan
-                    val = stripped.split(":", 1)[1].strip().strip('"').strip("'")
-                    # Convert speckit-plan → speckit.plan
-                    if val.startswith("speckit-"):
-                        skill_name = "speckit." + val[len("speckit-"):]
-                    else:
-                        skill_name = val
-
-        if not skill_name:
-            return updated
-
-        # Inject mode: before the closing --- of frontmatter
-        out: list[str] = []
-        dash_count = 0
-        injected = False
-        for line in lines:
-            stripped = line.rstrip("\n\r")
-            if stripped == "---":
-                dash_count += 1
-                if dash_count == 2 and not injected:
-                    if line.endswith("\r\n"):
-                        eol = "\r\n"
-                    elif line.endswith("\n"):
-                        eol = "\n"
-                    else:
-                        eol = ""
-                    out.append(f"mode: {skill_name}{eol}")
-                    injected = True
-            out.append(line)
-        return "".join(out)
+        return _CopilotSkillsHelper().post_process_skill_content(content)
 
     def setup(
         self,

src/specify_cli/integrations/manifest.py

@@ -115,6 +115,7 @@ class IntegrationManifest:
         self.project_root = project_root.resolve()
         self.version = version
         self._files: dict[str, str] = {}  # rel_path → sha256 hex
+        self._recovered_files: set[str] = set()
         self._installed_at: str = ""
 
     # -- Manifest file location -------------------------------------------
@@ -131,6 +132,9 @@ class IntegrationManifest:
 
         Creates parent directories as needed.  Returns the absolute path
         of the written file.
+        If the path was previously marked as recovered via
+        ``record_existing(recovered=True)``, the recovered marker is
+        cleared because the bytes are now produced, not merely observed.
 
         Raises ``ValueError`` if *rel_path* resolves outside the project root.
         """
@@ -144,17 +148,77 @@ class IntegrationManifest:
 
         normalized = abs_path.relative_to(self.project_root).as_posix()
         self._files[normalized] = hashlib.sha256(content).hexdigest()
+        # ``record_file`` writes *produced* content, so any prior
+        # recovered marker for this path is no longer accurate.
+        self._recovered_files.discard(normalized)
         return abs_path
 
-    def record_existing(self, rel_path: str | Path) -> None:
-        """Record the hash of an already-existing file at *rel_path*.
+    def record_existing(self, rel_path: str | Path, *, recovered: bool = False) -> None:
+        """Record the hash of an already-existing regular file at *rel_path*.
 
-        Raises ``ValueError`` if *rel_path* resolves outside the project root.
+        When ``recovered=True``, the path is also marked in the manifest's
+        ``recovered_files`` list to signal that the file's on-disk hash was
+        *observed* during install (because the file already existed and was not
+        overwritten), not *produced* by the install. Future ``refresh_managed``
+        runs should consult ``is_recovered`` before treating the recorded hash
+        as a managed baseline.
+
+        Raises:
+            ValueError: if *rel_path* resolves outside the project root, is
+                a symlink, or is not a regular file. A directory or other
+                non-file path cannot be silently recorded — its hash would
+                be meaningless and ``check_modified``/``uninstall`` would
+                treat the entry as permanently broken.
+            OSError: if the underlying filesystem call (``is_symlink``,
+                ``is_file``, or the file-read used to compute the hash)
+                fails — for example a ``PermissionError`` on the path.
+                Callers should be prepared to handle ``OSError`` (and its
+                subclasses such as ``PermissionError``) in addition to
+                ``ValueError``.
         """
         rel = Path(rel_path)
+        # Cheap lexical pre-check first so absolute / parent-traversal paths
+        # don't trigger a filesystem stat outside the project root before
+        # ``_validate_rel_path`` raises. ``_validate_rel_path`` produces the
+        # canonical error messages used elsewhere.
+        if rel.is_absolute() or ".." in rel.parts:
+            _validate_rel_path(rel, self.project_root)
+            # _validate_rel_path raised for any actually-escaping path. If we reach
+            # here the path normalizes inside root (e.g. ``dir/../file.txt``).
+            # Reject anyway: manifest keys must be canonical so ``check_modified``
+            # and ``uninstall`` cannot key the same file under two paths.
+            raise ValueError(
+                f"Manifest paths must be canonical; '..' segments are not "
+                f"allowed (got {rel})"
+            )
+        # Walk each path component before resolution so a symlinked ancestor
+        # (e.g. ``linked_dir/file.txt`` where ``linked_dir`` is a symlink)
+        # cannot be silently followed by ``_validate_rel_path().resolve()``
+        # down to a target outside the project root. ``_ensure_safe_manifest_directory``
+        # uses the same pattern.
+        _walk = self.project_root
+        for part in rel.parts:
+            _walk = _walk / part
+            if _walk.is_symlink():
+                raise ValueError(
+                    f"Refusing to record symlinked manifest path: {rel} "
+                    f"(symlinked at {_walk.relative_to(self.project_root).as_posix()})"
+                )
         abs_path = _validate_rel_path(rel, self.project_root)
+        if not abs_path.is_file():
+            raise ValueError(
+                f"Manifest path is not a regular file: {rel}"
+            )
         normalized = abs_path.relative_to(self.project_root).as_posix()
         self._files[normalized] = _sha256(abs_path)
+        if recovered:
+            self._recovered_files.add(normalized)
+        else:
+            # ``recovered=False`` means the caller is asserting this path is
+            # managed-baseline now, not merely observed; drop any stale
+            # recovered marker so future is_recovered() queries reflect the
+            # transition. ``discard`` is a no-op when the key is absent.
+            self._recovered_files.discard(normalized)
 
     # -- Querying ---------------------------------------------------------
 
@@ -163,6 +227,37 @@ class IntegrationManifest:
         """Return a copy of the ``{rel_path: sha256}`` mapping."""
         return dict(self._files)
 
+    @property
+    def recovered_files(self) -> set[str]:
+        """Return a copy of the set of paths recorded with ``recovered=True``.
+
+        These entries had their hashes observed (not produced) during install
+        because the file already existed on disk and the install skipped it.
+        Their on-disk bytes may be user customizations — callers that would
+        overwrite based on hash equality (e.g. ``refresh_managed``) MUST check
+        ``is_recovered`` first.
+        """
+        return set(self._recovered_files)
+
+    def is_recovered(self, rel_path: str | Path) -> bool:
+        """Return True if *rel_path* was recorded via ``record_existing(recovered=True)``.
+
+        Input is normalized through the same pipeline as ``record_existing``:
+        absolute paths, paths escaping the project root, AND paths containing
+        ``'..'`` segments are rejected (returned as ``False``). This mirrors
+        ``record_existing``'s canonicalization guard — such paths can never
+        appear as stored keys, so the answer is always ``False``.
+        """
+        rel = Path(rel_path)
+        if rel.is_absolute() or ".." in rel.parts:
+            return False
+        try:
+            abs_path = _validate_rel_path(rel, self.project_root)
+            normalized = abs_path.relative_to(self.project_root).as_posix()
+        except ValueError:
+            return False
+        return normalized in self._recovered_files
+
     def check_modified(self) -> list[str]:
         """Return relative paths of tracked files whose content changed on disk."""
         modified: list[str] = []
@@ -269,6 +364,11 @@ class IntegrationManifest:
             "version": self.version,
             "installed_at": self._installed_at,
             "files": self._files,
+            **(
+                {"recovered_files": sorted(self._recovered_files)}
+                if self._recovered_files
+                else {}
+            ),
         }
         path = self.manifest_path
         content = json.dumps(data, indent=2) + "\n"
@@ -320,6 +420,20 @@ class IntegrationManifest:
         inst._installed_at = data.get("installed_at", "")
         inst._files = files
 
+        recovered = data.get("recovered_files", [])
+        if not isinstance(recovered, list) or not all(
+            isinstance(p, str) for p in recovered
+        ):
+            raise ValueError(
+                f"Integration manifest 'recovered_files' at {path} must be a "
+                "list of string paths"
+            )
+        inst._recovered_files = set(recovered)
+        # Drop any recovered_files entries that don't correspond to tracked
+        # files — defensive against externally-edited or partially-corrupted
+        # manifests. Inconsistent state self-corrects on next save().
+        inst._recovered_files &= set(inst._files.keys())
+
         stored_key = data.get("integration", "")
         if stored_key and stored_key != key:
             raise ValueError(

src/specify_cli/shared_infra.py

@@ -365,6 +365,23 @@ def install_shared_infra(
                                 preserved_user_files.append(rel)
                             else:
                                 skipped_files.append(rel)
+                                # Record the existing-on-disk file in the manifest so a
+                                # fresh manifest run against an already-populated
+                                # ``.specify/`` tree does not silently drop it (#2107).
+                                # ``prior_hashes`` is the function-scope snapshot taken
+                                # at entry, so this membership check is O(1) and avoids
+                                # the repeated ``dict(self._files)`` copy that
+                                # ``manifest.files`` performs on every access.
+                                if dst_path.is_file() and rel not in prior_hashes:
+                                    try:
+                                        manifest.record_existing(rel, recovered=True)
+                                    except (OSError, ValueError) as exc:
+                                        # Tolerate races / permission issues / non-file
+                                        # collisions so one weird path does not abort
+                                        # the whole install.
+                                        console.print(
+                                            f"[yellow]⚠[/yellow]  could not record {rel} in manifest: {exc}"
+                                        )
                             continue
 
                         if not _ensure_or_bucket_dir(dst_path.parent):
@@ -398,6 +415,23 @@ def install_shared_infra(
                         preserved_user_files.append(rel)
                     else:
                         skipped_files.append(rel)
+                        # Record the existing-on-disk template in the manifest so a
+                        # fresh manifest run against an already-populated
+                        # ``.specify/`` tree does not silently drop it (#2107).
+                        # ``prior_hashes`` is the function-scope snapshot taken at
+                        # entry, so this membership check is O(1) and avoids the
+                        # repeated ``dict(self._files)`` copy that ``manifest.files``
+                        # performs on every access.
+                        if dst.is_file() and rel not in prior_hashes:
+                            try:
+                                manifest.record_existing(rel, recovered=True)
+                            except (OSError, ValueError) as exc:
+                                # Tolerate races / permission issues / non-file
+                                # collisions so one weird path does not abort
+                                # the whole install.
+                                console.print(
+                                    f"[yellow]⚠[/yellow]  could not record {rel} in manifest: {exc}"
+                                )
                     continue
 
                 content = src.read_text(encoding="utf-8")
@@ -416,7 +450,7 @@ def install_shared_infra(
 
     if skipped_files:
         console.print(
-            f"[yellow]⚠[/yellow]  {len(skipped_files)} shared infrastructure file(s) already exist and were not updated:"
+            f"[yellow]⚠[/yellow]  {len(skipped_files)} shared infrastructure path(s) already exist and were not updated:"
         )
         for path in skipped_files:
             console.print(f"    {path}")

src/specify_cli/workflows/engine.py

@@ -232,6 +232,22 @@ def _validate_steps(
             step_errors = step_impl.validate(step_config)
             errors.extend(step_errors)
 
+        # Validate optional `continue_on_error` field. The engine honours
+        # this on any step that returns StepStatus.FAILED so the pipeline can route
+        # around the failure via a downstream `if` or `switch` (or a
+        # `gate` that surfaces the failure to the operator via message
+        # interpolation). The field must be a literal boolean —
+        # coercion from truthy strings is deliberately not supported so
+        # authoring mistakes surface at validation time rather than
+        # silently changing run semantics.
+        if "continue_on_error" in step_config:
+            coe = step_config["continue_on_error"]
+            if not isinstance(coe, bool):
+                errors.append(
+                    f"Step {step_id!r}: 'continue_on_error' must be a "
+                    f"boolean, got {type(coe).__name__}."
+                )
+
         # Recursively validate nested steps
         for nested_key in ("then", "else", "steps"):
             nested = step_config.get(nested_key)
@@ -629,7 +645,10 @@ class WorkflowEngine:
 
             # Handle failures
             if result.status == StepStatus.FAILED:
-                # Gate abort (output.aborted) maps to ABORTED status
+                # Gate abort (output.aborted) maps to ABORTED status.
+                # Aborts are deliberate operator decisions, so
+                # `continue_on_error` does NOT override them — that flag
+                # is for transient/expected step failures only.
                 if result.output.get("aborted"):
                     state.status = RunStatus.ABORTED
                     state.append_log(
@@ -638,15 +657,49 @@ class WorkflowEngine:
                             "step_id": step_id,
                         }
                     )
-                else:
-                    state.status = RunStatus.FAILED
+                    state.save()
+                    return
+
+                # `continue_on_error: true` lets the pipeline route
+                # around the failure instead of halting. The step
+                # result (including exit_code, stderr, status) is
+                # still recorded so a downstream `if` or `switch`
+                # can branch on it (or a `gate` can surface it to the
+                # operator via message interpolation). Log a single,
+                # unambiguous event per failure resolution — either
+                # the run continued past it, or it halted.
+                #
+                # Use identity comparison (`is True`) rather than
+                # truthiness so that only a literal boolean enables
+                # the behaviour, even if validation was skipped.
+                # Validation rejects non-bool values at parse time,
+                # but `WorkflowEngine.execute()` does not auto-validate
+                # (see `WorkflowEngine.load_workflow`, whose docstring
+                # explicitly notes "not yet validated; call
+                # `validate_workflow()` or `engine.validate()`
+                # separately"), so a caller passing an unvalidated
+                # definition could otherwise see truthy non-bool
+                # values like the string `"true"` silently change
+                # run semantics.
+                if step_config.get("continue_on_error") is True:
                     state.append_log(
                         {
-                            "event": "step_failed",
+                            "event": "step_continue_on_error",
                             "step_id": step_id,
                             "error": result.error,
                         }
                     )
+                    state.save()
+                    continue
+
+                state.status = RunStatus.FAILED
+                state.append_log(
+                    {
+                        "event": "step_failed",
+                        "step_id": step_id,
+                        "error": result.error,
+                    }
+                )
                 state.save()
                 return
 

templates/commands/specify.md

@@ -91,7 +91,8 @@ Given that feature description, do this:
 
    **Create the directory and spec file**:
    - `mkdir -p SPECIFY_FEATURE_DIRECTORY`
-   - Copy `templates/spec-template.md` to `SPECIFY_FEATURE_DIRECTORY/spec.md` as the starting point
+   - Resolve the active `spec-template` through the Spec Kit preset/template resolution stack (equivalent to `specify preset resolve spec-template`)
+   - Copy the resolved `spec-template` file to `SPECIFY_FEATURE_DIRECTORY/spec.md` as the starting point
    - Set `SPEC_FILE` to `SPECIFY_FEATURE_DIRECTORY/spec.md`
    - Persist the resolved path to `.specify/feature.json`:
      ```json
@@ -107,7 +108,7 @@ Given that feature description, do this:
    - The spec directory name and the git branch name are independent — they may be the same but that is the user's choice
    - The spec directory and file are always created by this command, never by the hook
 
-4. Load `templates/spec-template.md` to understand required sections.
+4. Load the resolved active `spec-template` file to understand required sections.
 
 5. **IF EXISTS**: Load `/memory/constitution.md` for project principles and governance constraints.
 

tests/integrations/test_cli.py

@@ -330,6 +330,7 @@ class TestInitIntegrationFlag:
     def test_shared_infra_skip_warning_displayed(self, tmp_path, capsys):
         """Console warning is displayed when files are skipped."""
         from specify_cli import _install_shared_infra
+        from tests.conftest import strip_ansi
 
         project = tmp_path / "warn-test"
         project.mkdir()

tests/integrations/test_integration_claude.py

@@ -3,6 +3,7 @@
 import codecs
 import json
 import os
+from pathlib import Path
 from unittest.mock import patch
 
 import yaml
@@ -577,3 +578,204 @@ class TestClaudeHookCommandNote:
         assert "user-invocable: true" in result
         assert "disable-model-invocation: false" in result
         assert "replace dots" in result
+
+
+class TestSpeckitManifestRecordsSkippedFiles:
+    """Regression test for issue #2107.
+
+    ``install_shared_infra`` must record every shared-infrastructure file
+    under ``.specify/`` in ``speckit.manifest.json``, including files that
+    were *skipped* because they already existed on disk and ``force=False``.
+
+    Before the fix, the skip branches in the scripts and templates loops
+    appended to ``skipped_files`` without calling ``manifest.record_existing``.
+    So when ``install_shared_infra`` ran with a fresh (or lost) manifest
+    against an already-populated ``.specify/`` tree, every file went down the
+    skip path, ``planned_copies`` and ``planned_templates`` stayed empty, and
+    ``manifest.save()`` wrote an empty ``files`` field — leaving the
+    integration believing nothing was installed.
+
+    Reproduction (without the fix) using ``install_shared_infra`` directly:
+
+        install_shared_infra(p, "sh", ..., force=False)   # 1st run → 10 files
+        (p / ".specify/integrations/speckit.manifest.json").unlink()
+        install_shared_infra(p, "sh", ..., force=False)   # 2nd run → 0 files
+                                                          # ^^ BUG: empty
+    """
+
+    def _read_manifest_files(self, project_path: Path) -> dict:
+        manifest_path = (
+            project_path / ".specify" / "integrations" / "speckit.manifest.json"
+        )
+        assert manifest_path.exists(), (
+            f"speckit.manifest.json not written at {manifest_path}"
+        )
+        data = json.loads(manifest_path.read_text(encoding="utf-8"))
+        # ``IntegrationManifest.save`` serialises a ``files`` dict — assert
+        # the schema explicitly so a regression to a different key (e.g.
+        # the internal ``_files`` attribute name) fails loudly instead of
+        # being masked by a silent fallback.
+        assert isinstance(data, dict), (
+            f"manifest root is not a dict, got {type(data).__name__}"
+        )
+        assert "files" in data, (
+            f"manifest missing 'files' key, got keys: {sorted(data.keys())}"
+        )
+        files = data["files"]
+        assert isinstance(files, dict), (
+            f"manifest 'files' is not a dict, got {type(files).__name__}"
+        )
+        return files
+
+    def test_install_shared_infra_records_skipped_files(self, tmp_path):
+        """With ``force=False`` and ``.specify/`` already populated, the
+        manifest must still record every file — the skip branches are not
+        allowed to drop files from the manifest."""
+        from rich.console import Console
+        from specify_cli.shared_infra import install_shared_infra
+
+        # Resolve the project's own packaged sources by walking up from this
+        # test file to the repo root (which contains ``scripts/`` and
+        # ``templates/`` that ``shared_scripts_source`` looks for).
+        repo_root = Path(__file__).resolve().parents[2]
+        console = Console(quiet=True)
+
+        # First run — fresh project, manifest gets populated normally.
+        install_shared_infra(
+            tmp_path,
+            "sh",
+            version="0.0.0",
+            core_pack=None,
+            repo_root=repo_root,
+            console=console,
+            force=False,
+        )
+        first_files = self._read_manifest_files(tmp_path)
+        assert first_files, "first install produced an empty manifest"
+
+        # Simulate a lost manifest while ``.specify/`` is still on disk
+        # (e.g. the manifest was deleted, corrupted, or the layout was
+        # extracted out-of-band).
+        manifest_path = (
+            tmp_path / ".specify" / "integrations" / "speckit.manifest.json"
+        )
+        manifest_path.unlink()
+
+        # Second run — every file already exists, so every iteration takes
+        # the skip branch. With the fix, those files are still recorded.
+        install_shared_infra(
+            tmp_path,
+            "sh",
+            version="0.0.0",
+            core_pack=None,
+            repo_root=repo_root,
+            console=console,
+            force=False,
+        )
+        second_files = self._read_manifest_files(tmp_path)
+        assert second_files, (
+            "speckit.manifest.json files dict is empty after install with "
+            "skipped files (issue #2107) — every file went down the skip "
+            "branch but none were recorded"
+        )
+
+        # The recovered manifest must cover everything the first run tracked.
+        missing = set(first_files) - set(second_files)
+        assert not missing, (
+            f"these files were tracked on the first install but missing after "
+            f"the skipped-files re-install: {sorted(missing)[:5]}"
+        )
+
+    def test_install_shared_infra_handles_directory_at_script_destination(
+        self, tmp_path
+    ):
+        """A non-file (directory) at a script's destination must NOT crash
+        ``install_shared_infra`` and must NOT be recorded in the manifest —
+        the path still appears in the user-visible skipped-paths warning.
+        """
+        from io import StringIO
+        from rich.console import Console
+        from specify_cli.shared_infra import install_shared_infra
+
+        repo_root = Path(__file__).resolve().parents[2]
+        output = StringIO()
+        console = Console(file=output, force_terminal=False, width=200)
+
+        # Pre-create the .specify/scripts/bash tree, then plant a directory
+        # where a script file is expected so the skip branch hits a
+        # non-regular-file path.
+        bash_dir = tmp_path / ".specify" / "scripts" / "bash"
+        bash_dir.mkdir(parents=True)
+        (bash_dir / "common.sh").mkdir()  # collision: dir where file expected
+
+        # Must not crash.
+        install_shared_infra(
+            tmp_path,
+            "sh",
+            version="0.0.0",
+            core_pack=None,
+            repo_root=repo_root,
+            console=console,
+            force=False,
+        )
+
+        files = self._read_manifest_files(tmp_path)
+        assert ".specify/scripts/bash/common.sh" not in files, (
+            "directory at script dst must not be recorded in the manifest"
+        )
+        text = output.getvalue()
+        assert "common.sh" in text, (
+            "directory-at-script-dst path must surface in the skipped warning"
+        )
+
+    def test_install_shared_infra_handles_directory_at_template_destination(
+        self, tmp_path
+    ):
+        """Symmetric coverage for the templates loop: a directory at a
+        template's destination must NOT crash install nor be recorded."""
+        from io import StringIO
+        from rich.console import Console
+        from specify_cli.shared_infra import install_shared_infra
+
+        repo_root = Path(__file__).resolve().parents[2]
+        output = StringIO()
+        console = Console(file=output, force_terminal=False, width=200)
+
+        templates_dir = tmp_path / ".specify" / "templates"
+        templates_dir.mkdir(parents=True)
+
+        src_templates = repo_root / "templates"
+        real_template = next(
+            (
+                p.name
+                for p in src_templates.iterdir()
+                if p.is_file()
+                and not p.name.startswith(".")
+                and p.name != "vscode-settings.json"
+            ),
+            None,
+        )
+        assert real_template, (
+            "no real template found in repo to collide against"
+        )
+        (templates_dir / real_template).mkdir()  # collision
+
+        install_shared_infra(
+            tmp_path,
+            "sh",
+            version="0.0.0",
+            core_pack=None,
+            repo_root=repo_root,
+            console=console,
+            force=False,
+        )
+
+        files = self._read_manifest_files(tmp_path)
+        template_rel = f".specify/templates/{real_template}"
+        assert template_rel not in files, (
+            "directory at template dst must not be recorded in manifest"
+        )
+        text = output.getvalue()
+        assert real_template in text, (
+            "directory-at-template-dst path must surface in the skipped warning"
+        )

tests/integrations/test_integration_cline.py

@@ -0,0 +1,223 @@
+"""Tests for ClineIntegration."""
+
+import os
+import pytest
+
+from specify_cli.integrations import get_integration
+from specify_cli.integrations.cline import format_cline_command_name
+from .test_integration_base_markdown import MarkdownIntegrationTests
+
+
+class TestClineCommandNameFormatter:
+    """Test the Cline command name formatter."""
+
+    def test_simple_name_without_prefix(self):
+        """Test formatting a simple name without 'speckit.' prefix."""
+        assert format_cline_command_name("plan") == "speckit-plan"
+        assert format_cline_command_name("tasks") == "speckit-tasks"
+        assert format_cline_command_name("specify") == "speckit-specify"
+
+    def test_name_with_speckit_prefix(self):
+        """Test formatting a name that already has 'speckit.' prefix."""
+        assert format_cline_command_name("speckit.plan") == "speckit-plan"
+        assert format_cline_command_name("speckit.tasks") == "speckit-tasks"
+
+    def test_extension_command_name(self):
+        """Test formatting extension command names with dots."""
+        assert (
+            format_cline_command_name("speckit.my-extension.example")
+            == "speckit-my-extension-example"
+        )
+        assert (
+            format_cline_command_name("my-extension.example")
+            == "speckit-my-extension-example"
+        )
+
+    def test_idempotent_already_hyphenated(self):
+        """Test that already-hyphenated names are returned unchanged (idempotent)."""
+        assert format_cline_command_name("speckit-plan") == "speckit-plan"
+        assert (
+            format_cline_command_name("speckit-my-extension-example")
+            == "speckit-my-extension-example"
+        )
+
+
+class TestClineIntegration(MarkdownIntegrationTests):
+    KEY = "cline"
+    FOLDER = ".clinerules/"
+    COMMANDS_SUBDIR = "workflows"
+    REGISTRAR_DIR = ".clinerules/workflows"
+    CONTEXT_FILE = ".clinerules/specify-rules.md"
+
+    @pytest.mark.parametrize(
+        "cmd_name, expected_filename",
+        [
+            ("plan", "speckit-plan.md"),
+            ("speckit.plan", "speckit-plan.md"),
+            ("speckit.git.commit", "speckit-git-commit.md"),
+            ("speckit", "speckit-speckit.md"),
+            ("speckitfoo", "speckit-speckitfoo.md"),
+        ],
+    )
+    def test_cline_command_filename(self, cmd_name, expected_filename):
+        """Verify Cline uses hyphenated filenames."""
+        cline = get_integration("cline")
+        assert cline.command_filename(cmd_name) == expected_filename
+
+    def test_cline_invoke_separator(self):
+        """Verify Cline uses hyphen as invoke separator."""
+        cline = get_integration("cline")
+        assert cline.invoke_separator == "-"
+        assert cline.registrar_config["invoke_separator"] == "-"
+
+    def test_cline_name_injection_and_formatting(self):
+        """Verify Cline has inject_name and format_name configured."""
+        cline = get_integration("cline")
+        assert cline.registrar_config["inject_name"] is True
+        assert cline.registrar_config["format_name"] == format_cline_command_name
+
+    def test_cline_handoff_rewrite(self):
+        """Verify Cline rewrites agent: speckit.foo to agent: speckit-foo."""
+        cline = get_integration("cline")
+        content = "---\nagent: speckit.plan\n---\n"
+        rewritten = cline._rewrite_handoff_references(content)
+        assert rewritten == "---\nagent: speckit-plan\n---\n"
+
+    def test_cline_hook_instruction_injection(self):
+        """Verify Cline injects the dot-to-hyphen note for hooks."""
+        cline = get_integration("cline")
+        content = "- For each executable hook, output the following:\n"
+        injected = cline._inject_hook_command_note(content)
+        assert "replace dots (`.`) with hyphens (`-`)" in injected
+        assert "- For each executable hook, output the following:" in injected
+
+    # -- Overrides for MarkdownIntegrationTests ---------------------------
+
+    def test_setup_creates_files(self, tmp_path):
+        from specify_cli.integrations.manifest import IntegrationManifest
+
+        i = get_integration(self.KEY)
+        m = IntegrationManifest(self.KEY, tmp_path)
+        created = i.setup(tmp_path, m)
+        assert len(created) > 0
+        cmd_files = [
+            f
+            for f in created
+            if "scripts" not in f.parts
+            and f.suffix == ".md"
+            and f.name != i.context_file
+        ]
+        for f in cmd_files:
+            assert f.exists()
+            assert f.name.startswith("speckit-")
+            assert f.name.endswith(".md")
+
+        specify_file = next(
+            (f for f in cmd_files if f.name == "speckit-specify.md"), None
+        )
+        assert specify_file is not None
+        specify_contents = specify_file.read_text(encoding="utf-8")
+        assert "/speckit-plan" in specify_contents
+        assert "/speckit.plan" not in specify_contents
+
+    def test_integration_flag_creates_files(self, tmp_path):
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        project = tmp_path / f"int-{self.KEY}"
+        project.mkdir()
+        old_cwd = os.getcwd()
+        try:
+            os.chdir(project)
+            runner = CliRunner()
+            result = runner.invoke(
+                app,
+                [
+                    "init",
+                    "--here",
+                    "--integration",
+                    self.KEY,
+                    "--script",
+                    "sh",
+                    "--no-git",
+                    "--ignore-agent-tools",
+                ],
+                catch_exceptions=False,
+            )
+        finally:
+            os.chdir(old_cwd)
+        assert result.exit_code == 0
+        i = get_integration(self.KEY)
+        cmd_dir = i.commands_dest(project)
+        assert cmd_dir.is_dir()
+        commands = sorted(cmd_dir.glob("speckit-*"))
+        assert len(commands) > 0
+
+    def _expected_files(self, script_variant: str) -> list[str]:
+        """Override to expect hyphenated speckit- prefix."""
+        i = get_integration(self.KEY)
+        cmd_dir = i.registrar_config["dir"]
+        files = []
+
+        # Command files
+        for stem in (
+            self.COMMANDS_SUBDIR_STEMS
+            if hasattr(self, "COMMANDS_SUBDIR_STEMS")
+            else self.COMMAND_STEMS
+        ):
+            files.append(f"{cmd_dir}/speckit-{stem.replace('.', '-')}.md")
+
+        # Framework files
+        files.append(".specify/integration.json")
+        files.append(".specify/init-options.json")
+        files.append(f".specify/integrations/{self.KEY}.manifest.json")
+        files.append(".specify/integrations/speckit.manifest.json")
+
+        if script_variant == "sh":
+            for name in [
+                "check-prerequisites.sh",
+                "common.sh",
+                "create-new-feature.sh",
+                "setup-plan.sh",
+                "setup-tasks.sh",
+            ]:
+                files.append(f".specify/scripts/bash/{name}")
+        else:
+            for name in [
+                "check-prerequisites.ps1",
+                "common.ps1",
+                "create-new-feature.ps1",
+                "setup-plan.ps1",
+                "setup-tasks.ps1",
+            ]:
+                files.append(f".specify/scripts/powershell/{name}")
+
+        for name in [
+            "checklist-template.md",
+            "constitution-template.md",
+            "plan-template.md",
+            "spec-template.md",
+            "tasks-template.md",
+        ]:
+            files.append(f".specify/templates/{name}")
+
+        files.append(".specify/memory/constitution.md")
+        # Bundled workflow
+        files.append(".specify/workflows/speckit/workflow.yml")
+        files.append(".specify/workflows/workflow-registry.json")
+
+        # Bundled agent-context extension
+        files.append(".specify/extensions.yml")
+        files.append(".specify/extensions/.registry")
+        files.append(".specify/extensions/agent-context/README.md")
+        files.append(".specify/extensions/agent-context/agent-context-config.yml")
+        files.append(".specify/extensions/agent-context/commands/speckit.agent-context.update.md")
+        files.append(".specify/extensions/agent-context/extension.yml")
+        files.append(".specify/extensions/agent-context/scripts/bash/update-agent-context.sh")
+        files.append(".specify/extensions/agent-context/scripts/powershell/update-agent-context.ps1")
+
+        # Agent context file (if set)
+        if i.context_file:
+            files.append(i.context_file)
+
+        return sorted(files)

tests/integrations/test_integration_copilot.py

@@ -147,6 +147,21 @@ class TestCopilotIntegration:
             assert "__SPECKIT_COMMAND_" not in content, f"{agent_file.name} has unprocessed __SPECKIT_COMMAND_*__"
             assert "\nscripts:\n" not in content
 
+    def test_specify_agent_resolves_active_spec_template(self, tmp_path):
+        """Generated specify agent must not hardcode the core spec template."""
+        from specify_cli.integrations.copilot import CopilotIntegration
+        copilot = CopilotIntegration()
+        m = IntegrationManifest("copilot", tmp_path)
+        copilot.setup(tmp_path, m)
+
+        specify_file = tmp_path / ".github" / "agents" / "speckit.specify.agent.md"
+        content = specify_file.read_text(encoding="utf-8")
+
+        assert "specify preset resolve spec-template" in content
+        assert "resolved active `spec-template`" in content
+        assert "Copy `.specify/templates/spec-template.md`" not in content
+        assert "Load `.specify/templates/spec-template.md`" not in content
+
     def test_plan_references_correct_context_file(self, tmp_path):
         """The generated plan command must reference copilot's context file."""
         from specify_cli.integrations.copilot import CopilotIntegration
@@ -411,8 +426,8 @@ class TestCopilotSkillsMode:
 
     # -- Copilot-specific post-processing ---------------------------------
 
-    def test_post_process_skill_content_injects_mode(self):
-        """post_process_skill_content() should inject mode: field."""
+    def test_post_process_skill_content_does_not_inject_mode(self):
+        """post_process_skill_content() must NOT inject mode: — VS Code Copilot does not support it."""
         copilot = self._make_copilot()
         content = (
             "---\n"
@@ -422,10 +437,10 @@ class TestCopilotSkillsMode:
             "\nBody content\n"
         )
         updated = copilot.post_process_skill_content(content)
-        assert "mode: speckit.plan" in updated
+        assert "mode:" not in updated
 
     def test_post_process_skill_content_injects_hook_note(self):
-        """post_process_skill_content() should inject shared hook guidance."""
+        """post_process_skill_content() should inject shared hook guidance but not mode:."""
         copilot = self._make_copilot()
         content = (
             "---\n"
@@ -436,7 +451,7 @@ class TestCopilotSkillsMode:
         )
         updated = copilot.post_process_skill_content(content)
         assert "replace dots" in updated
-        assert "mode: speckit.specify" in updated
+        assert "mode:" not in updated
 
     def test_post_process_idempotent(self):
         """post_process_skill_content() must be idempotent."""
@@ -452,8 +467,8 @@ class TestCopilotSkillsMode:
         second = copilot.post_process_skill_content(first)
         assert first == second
 
-    def test_skills_have_mode_in_frontmatter(self, tmp_path):
-        """Generated SKILL.md files should have mode: field from post-processing."""
+    def test_skills_do_not_have_mode_in_frontmatter(self, tmp_path):
+        """Generated SKILL.md files must NOT contain mode: — VS Code Copilot does not support it."""
         copilot = self._make_copilot()
         created, _ = self._setup_skills(copilot, tmp_path)
         skill_files = [f for f in created if f.name == "SKILL.md"]
@@ -462,11 +477,7 @@ class TestCopilotSkillsMode:
             content = f.read_text(encoding="utf-8")
             parts = content.split("---", 2)
             fm = yaml.safe_load(parts[1])
-            assert "mode" in fm, f"{f} frontmatter missing 'mode'"
-            # mode should be speckit.<stem>
-            skill_dir_name = f.parent.name
-            stem = skill_dir_name.removeprefix("speckit-")
-            assert fm["mode"] == f"speckit.{stem}"
+            assert "mode" not in fm, f"{f} frontmatter must not contain unsupported 'mode' field"
 
     def test_skills_hook_sections_explain_dotted_command_conversion(self, tmp_path):
         """Generated skills with hook sections should include shared hook guidance."""

tests/integrations/test_integration_forge.py

@@ -330,7 +330,7 @@ class TestForgeCommandRegistrar:
         assert "speckit.my-extension.example" in registered
         
         # Check the generated file has hyphenated name in frontmatter
-        forge_cmd = tmp_path / ".forge" / "commands" / "speckit.my-extension.example.md"
+        forge_cmd = tmp_path / ".forge" / "commands" / "speckit-my-extension-example.md"
         assert forge_cmd.exists()
         
         content = forge_cmd.read_text(encoding="utf-8")
@@ -378,7 +378,7 @@ class TestForgeCommandRegistrar:
         )
         
         # Check the alias file has hyphenated name in frontmatter
-        alias_file = tmp_path / ".forge" / "commands" / "speckit.my-extension.ex.md"
+        alias_file = tmp_path / ".forge" / "commands" / "speckit-my-extension-ex.md"
         assert alias_file.exists()
         
         content = alias_file.read_text(encoding="utf-8")
@@ -467,7 +467,7 @@ class TestForgeCommandRegistrar:
 
         assert "speckit.git.feature" in registered
 
-        forge_cmd = tmp_path / ".forge" / "commands" / "speckit.git.feature.md"
+        forge_cmd = tmp_path / ".forge" / "commands" / "speckit-git-feature.md"
         assert forge_cmd.exists(), "Expected Forge command file was not created"
 
         content = forge_cmd.read_text(encoding="utf-8")

tests/integrations/test_integration_subcommand.py

@@ -185,7 +185,8 @@ class TestIntegrationInstall:
         finally:
             os.chdir(old_cwd)
         assert result.exit_code == 0
-        normalized = " ".join(result.output.split())
+        output = strip_ansi(result.output)
+        normalized = " ".join(output.split())
         assert "already installed" in normalized
         assert "specify integration use codex" in normalized
         assert "specify integration upgrade codex" in normalized
@@ -241,9 +242,9 @@ class TestIntegrationInstall:
         opts["speckit_version"] = "0.6.1"
         init_options.write_text(json.dumps(opts), encoding="utf-8")
 
-        import specify_cli
+        import specify_cli.integrations._commands as _int_cmds
 
-        monkeypatch.setattr(specify_cli, "get_speckit_version", lambda: "0.8.11")
+        monkeypatch.setattr(_int_cmds, "get_speckit_version", lambda: "0.8.11")
 
         result = _run_in_project(project, [
             "integration", "install", "codex",
@@ -897,11 +898,10 @@ class TestIntegrationSwitch:
         assert copilot_git_feature.exists(), "Git extension skill should exist for Copilot skills mode"
         assert not copilot_agent_file.exists(), "Copilot skills mode should not create extension .agent.md files"
 
-        # Verify Copilot-specific frontmatter: mode field should map from
-        # skill name (speckit-git-feature) back to dot notation (speckit.git-feature)
+        # Verify Copilot skill frontmatter does NOT contain mode: — VS Code Copilot does not support it
         skill_content = copilot_git_feature.read_text(encoding="utf-8")
-        assert "mode: speckit.git-feature" in skill_content, (
-            "Copilot skill frontmatter should contain mode mapped from skill name"
+        assert "mode:" not in skill_content, (
+            "Copilot skill frontmatter must not contain unsupported 'mode' field"
         )
 
         registry = json.loads(
@@ -1209,9 +1209,9 @@ class TestIntegrationUpgrade:
         opts["speckit_version"] = "0.6.1"
         init_options.write_text(json.dumps(opts), encoding="utf-8")
 
-        import specify_cli
+        import specify_cli.integrations._commands as _int_cmds
 
-        monkeypatch.setattr(specify_cli, "get_speckit_version", lambda: "0.8.11")
+        monkeypatch.setattr(_int_cmds, "get_speckit_version", lambda: "0.8.11")
 
         result = _run_in_project(project, [
             "integration", "upgrade", "claude",
@@ -1235,9 +1235,9 @@ class TestIntegrationUpgrade:
         opts["speckit_version"] = "0.6.1"
         init_options.write_text(json.dumps(opts), encoding="utf-8")
 
-        import specify_cli
+        import specify_cli.integrations._commands as _int_cmds
 
-        monkeypatch.setattr(specify_cli, "get_speckit_version", lambda: "0.8.11")
+        monkeypatch.setattr(_int_cmds, "get_speckit_version", lambda: "0.8.11")
 
         result = _run_in_project(project, [
             "integration", "upgrade", "claude",
@@ -1471,7 +1471,7 @@ class TestScriptTypeValidation:
 class TestParseIntegrationOptionsEqualsForm:
     def test_equals_form_parsed(self):
         """--commands-dir=./x should be parsed the same as --commands-dir ./x."""
-        from specify_cli import _parse_integration_options
+        from specify_cli.integrations._commands import _parse_integration_options
         from specify_cli.integrations import get_integration
 
         integration = get_integration("generic")

tests/integrations/test_manifest.py

@@ -34,6 +34,57 @@ class TestManifestRecordFile:
         assert m.files["existing.txt"] == _sha256(f)
 
 
+class TestManifestRecordExistingErrors:
+    """Error-case coverage for ``record_existing`` symlink + non-file guards.
+
+    Added in #2483 — Copilot review flagged these as un-tested regressions
+    after the ``is_symlink``/``is_file`` guards were introduced.
+    """
+
+    def test_rejects_symlink_target(self, tmp_path):
+        target = tmp_path / "target.txt"
+        target.write_text("target content", encoding="utf-8")
+        link = tmp_path / "link.txt"
+        link.symlink_to(target)
+        m = IntegrationManifest("test", tmp_path)
+        with pytest.raises(ValueError, match="symlinked"):
+            m.record_existing("link.txt")
+
+    def test_rejects_dangling_symlink(self, tmp_path):
+        # A symlink pointing nowhere should still be rejected before the
+        # ``is_file()`` check (which would itself be False on a dangler).
+        link = tmp_path / "dangler.txt"
+        link.symlink_to(tmp_path / "no-such-target.txt")
+        m = IntegrationManifest("test", tmp_path)
+        with pytest.raises(ValueError, match="symlinked"):
+            m.record_existing("dangler.txt")
+
+    def test_rejects_directory_path(self, tmp_path):
+        (tmp_path / "a_dir").mkdir()
+        m = IntegrationManifest("test", tmp_path)
+        with pytest.raises(ValueError, match="not a regular file"):
+            m.record_existing("a_dir")
+
+    def test_rejects_missing_path(self, tmp_path):
+        # ``is_file()`` is False for non-existent paths too; the same error
+        # surface keeps callers from having to distinguish "missing" from
+        # "wrong kind" — both mean "cannot hash this".
+        m = IntegrationManifest("test", tmp_path)
+        with pytest.raises(ValueError, match="not a regular file"):
+            m.record_existing("never-existed.txt")
+
+    def test_lexical_prevalidation_for_absolute_path(self, tmp_path):
+        # ``record_existing`` must reject absolute paths via the lexical
+        # pre-check, NOT via the filesystem-touching ``is_symlink()`` call.
+        # Verified by passing an absolute path that points to a directory
+        # outside the project root — the canonical "Absolute paths" error
+        # must surface before any stat on the absolute path.
+        m = IntegrationManifest("test", tmp_path)
+        abs_path = "C:\\tmp\\escape.txt" if sys.platform == "win32" else "/tmp/escape.txt"
+        with pytest.raises(ValueError, match="Absolute paths"):
+            m.record_existing(abs_path)
+
+
 class TestManifestPathTraversal:
     def test_record_file_rejects_parent_traversal(self, tmp_path):
         m = IntegrationManifest("test", tmp_path)
@@ -245,3 +296,160 @@ class TestManifestLoadValidation:
         path.write_text("{not valid json", encoding="utf-8")
         with pytest.raises(ValueError, match="invalid JSON"):
             IntegrationManifest.load("bad", tmp_path)
+
+    def test_load_filters_recovered_files_not_in_files(self, tmp_path):
+        # Finding B (Round-9): a recovered_files entry referencing a path
+        # not present in files indicates an internally-inconsistent manifest
+        # (e.g. external edit). load() filters those entries silently so the
+        # manifest self-heals on next save(); is_recovered then returns the
+        # truthful False for the orphan.
+        path = tmp_path / ".specify" / "integrations" / "test.manifest.json"
+        path.parent.mkdir(parents=True)
+        path.write_text(json.dumps({
+            "integration": "test",
+            "files": {"kept.txt": "abc123"},
+            "recovered_files": ["kept.txt", "orphan.txt"],
+        }), encoding="utf-8")
+        m = IntegrationManifest.load("test", tmp_path)
+        assert m.recovered_files == {"kept.txt"}
+        assert m.is_recovered("kept.txt") is True
+        assert m.is_recovered("orphan.txt") is False
+
+
+class TestManifestRecoveredFiles:
+    """Coverage for the ``recovered_files`` channel added in #2483.
+
+    When ``shared_infra`` skips an existing file (because the user already has
+    it on disk) it now records the file with ``recovered=True``. The path
+    appears in ``manifest.recovered_files`` and ``is_recovered(path)`` returns
+    True. ``refresh_managed`` (out of scope for this PR) consults this list
+    before treating the recorded hash as a managed baseline, defending against
+    silent overwrite of user customizations after manifest loss.
+    """
+
+    def test_record_existing_default_is_not_recovered(self, tmp_path):
+        (tmp_path / "f.txt").write_text("x", encoding="utf-8")
+        m = IntegrationManifest("test", tmp_path)
+        m.record_existing("f.txt")
+        assert m.is_recovered("f.txt") is False
+        assert m.recovered_files == set()
+
+    def test_record_existing_with_recovered_flag(self, tmp_path):
+        (tmp_path / "f.txt").write_text("x", encoding="utf-8")
+        m = IntegrationManifest("test", tmp_path)
+        m.record_existing("f.txt", recovered=True)
+        assert m.is_recovered("f.txt") is True
+        assert m.recovered_files == {"f.txt"}
+        # File still hashed normally so check_modified/uninstall keep working
+        assert m.files["f.txt"] == _sha256(tmp_path / "f.txt")
+
+    def test_recovered_files_round_trips_through_save_load(self, tmp_path):
+        (tmp_path / "a.txt").write_text("aaa", encoding="utf-8")
+        (tmp_path / "b.txt").write_text("bbb", encoding="utf-8")
+        m = IntegrationManifest("test", tmp_path, version="9.9")
+        m.record_existing("a.txt", recovered=True)
+        m.record_existing("b.txt")  # not recovered
+        m.save()
+        loaded = IntegrationManifest.load("test", tmp_path)
+        assert loaded.is_recovered("a.txt") is True
+        assert loaded.is_recovered("b.txt") is False
+        assert loaded.recovered_files == {"a.txt"}
+
+    def test_save_omits_empty_recovered_files(self, tmp_path):
+        m = IntegrationManifest("test", tmp_path)
+        m.record_file("f.txt", "x")
+        path = m.save()
+        data = json.loads(path.read_text(encoding="utf-8"))
+        assert "recovered_files" not in data
+
+    def test_load_rejects_non_list_recovered_files(self, tmp_path):
+        path = tmp_path / ".specify" / "integrations" / "bad.manifest.json"
+        path.parent.mkdir(parents=True)
+        path.write_text(
+            json.dumps({"files": {}, "recovered_files": "not-a-list"}),
+            encoding="utf-8",
+        )
+        with pytest.raises(ValueError, match="recovered_files"):
+            IntegrationManifest.load("bad", tmp_path)
+
+    def test_is_recovered_absolute_path_returns_false(self, tmp_path):
+        # Copilot round-5 finding: passing an absolute path silently returned
+        # False because the stored keys are relative POSIX strings. Round-7
+        # made this explicit: ``is_recovered`` now rejects absolute paths
+        # up front via a lexical ``rel.is_absolute()`` guard and returns
+        # False without calling ``_validate_rel_path`` at all — matching
+        # ``record_existing``'s canonical-key guard so the two methods
+        # agree on which inputs can ever be stored keys.
+        (tmp_path / "f.txt").write_text("x", encoding="utf-8")
+        m = IntegrationManifest("test", tmp_path)
+        m.record_existing("f.txt", recovered=True)
+        import sys
+        abs_input = "C:\\tmp\\f.txt" if sys.platform == "win32" else "/tmp/f.txt"
+        assert m.is_recovered(abs_input) is False
+
+    def test_is_recovered_escaping_path_returns_false(self, tmp_path):
+        # A relative path containing ``..`` segments cannot be a stored key:
+        # Round-7 added the same lexical ``".." in rel.parts`` guard to
+        # ``is_recovered`` that ``record_existing`` already enforces, so the
+        # method returns False immediately without reaching
+        # ``_validate_rel_path``. The try/except around ``_validate_rel_path``
+        # remains as defense-in-depth for paths that pass the lexical guard
+        # but still resolve outside the project root via a symlinked
+        # ancestor.
+        m = IntegrationManifest("test", tmp_path)
+        # Don't record anything — the path is impossible to record anyway.
+        assert m.is_recovered("../escape.txt") is False
+
+    def test_record_existing_clears_recovered_when_false(self, tmp_path):
+        # Finding A: re-recording the same path with recovered=False must
+        # drop the prior recovered marker (transition to managed baseline).
+        f = tmp_path / "x.txt"
+        f.write_text("v1", encoding="utf-8")
+        m = IntegrationManifest("test", tmp_path)
+        m.record_existing("x.txt", recovered=True)
+        assert m.is_recovered("x.txt") is True
+        m.record_existing("x.txt", recovered=False)
+        assert m.is_recovered("x.txt") is False
+
+    def test_record_file_clears_recovered(self, tmp_path):
+        # Finding A: record_file writes produced content; the path can no
+        # longer be considered "merely observed" once we wrote bytes.
+        (tmp_path / "y.txt").write_text("observed", encoding="utf-8")
+        m = IntegrationManifest("test", tmp_path)
+        m.record_existing("y.txt", recovered=True)
+        assert m.is_recovered("y.txt") is True
+        m.record_file("y.txt", "produced")
+        assert m.is_recovered("y.txt") is False
+
+    def test_is_recovered_rejects_dotdot_segment(self, tmp_path):
+        # Finding B: record_existing rejects ``..`` segments via the lexical
+        # pre-check; is_recovered must match that behavior and return False
+        # without raising, mirroring the canonicalization guard.
+        (tmp_path / "z.txt").write_text("v1", encoding="utf-8")
+        m = IntegrationManifest("test", tmp_path)
+        m.record_existing("z.txt", recovered=True)
+        # Same file via dotdot-normalizing path — must be False, not raise.
+        assert m.is_recovered("subdir/../z.txt") is False
+
+
+class TestRecordExistingNewGuards:
+    """Coverage for the two new guards added by Copilot's 2026-05-18 review."""
+
+    def test_rejects_symlinked_ancestor(self, tmp_path):
+        real_dir = tmp_path / "real_dir"
+        real_dir.mkdir()
+        (real_dir / "file.txt").write_text("payload", encoding="utf-8")
+        (tmp_path / "linked_dir").symlink_to(real_dir, target_is_directory=True)
+        m = IntegrationManifest("test", tmp_path)
+        with pytest.raises(ValueError, match="symlinked"):
+            m.record_existing("linked_dir/file.txt")
+
+    def test_rejects_inside_root_dotdot_with_explicit_message(self, tmp_path):
+        # ``dir/../file.txt`` normalizes inside root, so the old "escapes
+        # project root" message was misleading. The new message names the
+        # actual reason: canonicalization.
+        (tmp_path / "dir").mkdir()
+        (tmp_path / "file.txt").write_text("x", encoding="utf-8")
+        m = IntegrationManifest("test", tmp_path)
+        with pytest.raises(ValueError, match=r"canonical|'\.\.' segments"):
+            m.record_existing("dir/../file.txt")

tests/test_commands_package.py

@@ -13,12 +13,6 @@ def test_commands_init_importable():
     assert callable(mod.register)
 
 
-def test_commands_stubs_importable():
-    for name in ("integration", "preset", "extension", "workflow"):
-        mod = importlib.import_module(f"specify_cli.commands.{name}")
-        assert mod is not None
-
-
 def test_agent_config_importable():
     from specify_cli._agent_config import (
         AGENT_CONFIG,

tests/test_extensions.py

@@ -1315,6 +1315,42 @@ $ARGUMENTS
         assert not (skills_dir / "speckit-specify" / "SKILL.md").exists()
         assert not (skills_dir / "speckit-shortcut" / "SKILL.md").exists()
 
+    def test_unregister_commands_handles_legacy_dot_notated_files(self, project_dir):
+        """Unregister should clean up both legacy dot-notated and new hyphenated files."""
+        # 1. Mock an agent that uses hyphenated/formatted names (e.g. Cline)
+        from specify_cli.agents import CommandRegistrar as AgentCommandRegistrar
+        registrar = AgentCommandRegistrar()
+
+        # We'll use "cline" since it has format_name
+        assert "cline" in registrar.AGENT_CONFIGS
+        cline_config = registrar.AGENT_CONFIGS["cline"]
+        cline_dir = project_dir / cline_config["dir"]
+        cline_dir.mkdir(parents=True, exist_ok=True)
+
+        # 2. Create both legacy and new files
+        # Command name: speckit.git.commit
+        # Formatted name: speckit-git-commit
+        cmd_name = "speckit.git.commit"
+        formatted_name = "speckit-git-commit"
+
+        legacy_file = cline_dir / f"{cmd_name}.md"
+        formatted_file = cline_dir / f"{formatted_name}.md"
+
+        legacy_file.write_text("legacy body")
+        formatted_file.write_text("formatted body")
+
+        assert legacy_file.exists()
+        assert formatted_file.exists()
+
+        # 3. Call unregister
+        registrar.unregister_commands({"cline": [cmd_name]}, project_dir)
+
+        # 4. Verify both are gone
+        assert not legacy_file.exists(), "Legacy dot-notated file should be removed"
+        assert (
+            not formatted_file.exists()
+        ), "Formatted hyphenated file should be removed"
+
     def test_register_commands_for_all_agents_distinguishes_codex_from_amp(self, extension_dir, project_dir):
         """A Codex project under .agents/skills should not implicitly activate Amp."""
         skills_dir = project_dir / ".agents" / "skills"
@@ -2768,17 +2804,33 @@ class TestExtensionCatalog:
             zf.writestr("extension.yml", "id: test-ext\nname: Test\nversion: 1.0.0\n")
         zip_bytes = zip_buf.getvalue()
 
-        mock_response = MagicMock()
-        mock_response.read.return_value = zip_bytes
-        mock_response.__enter__ = lambda s: s
-        mock_response.__exit__ = MagicMock(return_value=False)
+        release_response = MagicMock()
+        release_response.read.return_value = json.dumps(
+            {
+                "assets": [
+                    {
+                        "name": "test-ext.zip",
+                        "url": "https://api.github.com/repos/org/repo/releases/assets/1",
+                    }
+                ]
+            }
+        ).encode()
+        release_response.__enter__ = lambda s: s
+        release_response.__exit__ = MagicMock(return_value=False)
 
-        captured = {}
+        asset_response = MagicMock()
+        asset_response.read.return_value = zip_bytes
+        asset_response.__enter__ = lambda s: s
+        asset_response.__exit__ = MagicMock(return_value=False)
+
+        captured = []
         mock_opener = MagicMock()
 
         def fake_open(req, timeout=None):
-            captured["req"] = req
-            return mock_response
+            captured.append(req)
+            if req.full_url.endswith("/releases/tags/v1"):
+                return release_response
+            return asset_response
 
         mock_opener.open.side_effect = fake_open
 
@@ -2793,7 +2845,56 @@ class TestExtensionCatalog:
              patch("specify_cli.authentication.http.urllib.request.build_opener", return_value=mock_opener):
             catalog.download_extension("test-ext", target_dir=temp_dir)
 
-        assert captured["req"].get_header("Authorization") == "Bearer ghp_testtoken"
+        assert captured[0].full_url == "https://api.github.com/repos/org/repo/releases/tags/v1"
+        assert captured[0].get_header("Authorization") == "Bearer ghp_testtoken"
+        assert captured[1].full_url == "https://api.github.com/repos/org/repo/releases/assets/1"
+        assert captured[1].get_header("Authorization") == "Bearer ghp_testtoken"
+        assert captured[1].get_header("Accept") == "application/octet-stream"
+
+    def test_download_extension_accepts_direct_github_rest_asset_url(self, temp_dir, monkeypatch):
+        """download_extension can use a GitHub REST release asset URL directly."""
+        from unittest.mock import patch, MagicMock
+        import zipfile
+        import io
+
+        monkeypatch.setenv("GITHUB_TOKEN", "ghp_testtoken")
+        self._inject_github_config(monkeypatch, token_env="GITHUB_TOKEN")
+        catalog = self._make_catalog(temp_dir)
+
+        zip_buf = io.BytesIO()
+        with zipfile.ZipFile(zip_buf, "w") as zf:
+            zf.writestr("extension.yml", "id: test-ext\nname: Test\nversion: 1.0.0\n")
+        zip_bytes = zip_buf.getvalue()
+
+        asset_response = MagicMock()
+        asset_response.read.return_value = zip_bytes
+        asset_response.__enter__ = lambda s: s
+        asset_response.__exit__ = MagicMock(return_value=False)
+
+        captured = []
+        mock_opener = MagicMock()
+
+        def fake_open(req, timeout=None):
+            captured.append(req)
+            return asset_response
+
+        mock_opener.open.side_effect = fake_open
+
+        ext_info = {
+            "id": "test-ext",
+            "name": "Test Extension",
+            "version": "1.0.0",
+            "download_url": "https://api.github.com/repos/org/repo/releases/assets/1",
+        }
+
+        with patch.object(catalog, "get_extension_info", return_value=ext_info), \
+             patch("specify_cli.authentication.http.urllib.request.build_opener", return_value=mock_opener):
+            catalog.download_extension("test-ext", target_dir=temp_dir)
+
+        assert len(captured) == 1
+        assert captured[0].full_url == "https://api.github.com/repos/org/repo/releases/assets/1"
+        assert captured[0].get_header("Authorization") == "Bearer ghp_testtoken"
+        assert captured[0].get_header("Accept") == "application/octet-stream"
 
 
 
@@ -3322,9 +3423,13 @@ class TestExtensionIgnore:
                 else:
                     p.write_text(content)
 
-        # Write .extensionignore
+        # Write .extensionignore. Pinned to UTF-8 so non-ASCII patterns
+        # in tests (see ``test_extensionignore_utf8_patterns``) survive
+        # the round-trip on Windows runners with non-UTF-8 default locales.
         if ignore_content is not None:
-            (ext_dir / ".extensionignore").write_text(ignore_content)
+            (ext_dir / ".extensionignore").write_text(
+                ignore_content, encoding="utf-8"
+            )
 
         return ext_dir
 
@@ -3554,6 +3659,73 @@ class TestExtensionIgnore:
         assert (dest / "docs" / "guide.md").exists()
         assert not (dest / "docs" / "internal" / "draft.md").exists()
 
+    def test_extensionignore_utf8_patterns(self, temp_dir, valid_manifest_data):
+        """Non-ASCII patterns in .extensionignore work on every locale.
+
+        ``Path.read_text`` defaults to the system locale codec on Windows
+        (cp1252 / gb2312 / cp932). Without an explicit ``encoding="utf-8"``,
+        a pattern like ``ドキュメント/`` written by a UTF-8 host becomes
+        mojibake on a cp1252 host and silently fails to match — leaking
+        files the author intended to exclude. The existing
+        ``test_extensionignore_windows_backslash_patterns`` already shows
+        the codebase treats this as a Windows-author-friendly file; UTF-8
+        is part of that same contract.
+        """
+        ext_dir = self._make_extension(
+            temp_dir,
+            valid_manifest_data,
+            extra_files={
+                "ドキュメント/private.md": "secret",
+                "ドキュメント/public.md": "public",
+                "docs/guide.md": "# Guide",
+                "café/résumé.txt": "draft",
+            },
+            ignore_content="ドキュメント/\ncafé/\n",
+        )
+
+        proj_dir = temp_dir / "project"
+        proj_dir.mkdir()
+        (proj_dir / ".specify").mkdir()
+
+        manager = ExtensionManager(proj_dir)
+        manager.install_from_directory(ext_dir, "0.1.0", register_commands=False)
+
+        dest = proj_dir / ".specify" / "extensions" / "test-ext"
+        # Multibyte patterns excluded.
+        assert not (dest / "ドキュメント").exists()
+        assert not (dest / "café").exists()
+        # ASCII path with no matching pattern is unaffected.
+        assert (dest / "docs" / "guide.md").exists()
+
+    def test_extensionignore_invalid_utf8_raises_validation_error(
+        self, temp_dir, valid_manifest_data
+    ):
+        """A non-UTF-8 ``.extensionignore`` surfaces as ``ValidationError``.
+
+        Pinning ``encoding="utf-8"`` on the reader means an
+        ``.extensionignore`` written in some other codec (cp1252, etc.)
+        now triggers ``UnicodeDecodeError`` instead of silently
+        mojibake-ing patterns. Wrap that exception as ``ValidationError``
+        with a pointer to the offending byte — the same pattern
+        ``ExtensionManifest._load_yaml`` uses for ``extension.yml`` —
+        so installation aborts with a user-friendly message instead of a
+        raw Python traceback.
+        """
+        ext_dir = self._make_extension(temp_dir, valid_manifest_data)
+        # Write an .extensionignore whose bytes are not valid UTF-8.
+        # 0xE9 is 'é' in cp1252 but an invalid lead byte in UTF-8.
+        (ext_dir / ".extensionignore").write_bytes(b"caf\xe9/\n")
+
+        proj_dir = temp_dir / "project"
+        proj_dir.mkdir()
+        (proj_dir / ".specify").mkdir()
+
+        manager = ExtensionManager(proj_dir)
+        with pytest.raises(
+            ValidationError, match=r"\.extensionignore is not valid UTF-8"
+        ):
+            manager.install_from_directory(ext_dir, "0.1.0", register_commands=False)
+
     def test_extensionignore_star_does_not_cross_directories(self, temp_dir, valid_manifest_data):
         """'*' should NOT match across directory boundaries (gitignore semantics)."""
         ext_dir = self._make_extension(
@@ -4616,6 +4788,43 @@ class TestHookInvocationRendering:
         assert execution["command"] == "speckit.tasks"
         assert execution["invocation"] == "$speckit-tasks"
 
+    def test_cline_hooks_render_hyphenated_invocation(self, project_dir):
+        """Cline projects should render /speckit-* invocations."""
+        init_options = project_dir / ".specify" / "init-options.json"
+        init_options.parent.mkdir(parents=True, exist_ok=True)
+        init_options.write_text(json.dumps({"ai": "cline"}))
+
+        hook_executor = HookExecutor(project_dir)
+        execution = hook_executor.execute_hook(
+            {
+                "extension": "test-ext",
+                "command": "speckit.tasks",
+                "optional": False,
+            }
+        )
+
+        assert execution["command"] == "speckit.tasks"
+        assert execution["invocation"] == "/speckit-tasks"
+
+    def test_cline_hooks_render_extension_command(self, project_dir):
+        """Cline projects should render /speckit-my-ext-cmd for extension hooks."""
+        init_options = project_dir / ".specify" / "init-options.json"
+        init_options.parent.mkdir(parents=True, exist_ok=True)
+        init_options.write_text(json.dumps({"ai": "cline"}))
+
+        hook_executor = HookExecutor(project_dir)
+        # Test with a non-speckit. command
+        execution = hook_executor.execute_hook(
+            {
+                "extension": "test-ext",
+                "command": "my-extension.do-something",
+                "optional": False,
+            }
+        )
+
+        assert execution["command"] == "my-extension.do-something"
+        assert execution["invocation"] == "/speckit-my-extension-do-something"
+
     def test_non_skill_command_keeps_slash_invocation(self, project_dir):
         """Custom hook commands should keep slash invocation style."""
         init_options = project_dir / ".specify" / "init-options.json"
@@ -4751,3 +4960,157 @@ class TestExtensionRemoveCLI:
             )
 
         assert "2 commands" in result.output
+
+
+class TestClineExtensionHyphenation:
+    """Test that Cline integration uses hyphenated commands and frontmatter references."""
+
+    def _setup_mock_extension(self, tmp_path, ai_name):
+        import yaml
+        import json
+
+        # 1. Setup mock project
+        project_dir = tmp_path / "project"
+        project_dir.mkdir()
+        (project_dir / ".specify").mkdir()
+
+        init_options = project_dir / ".specify" / "init-options.json"
+        init_options.write_text(json.dumps({"ai": ai_name}), encoding="utf-8")
+
+        if ai_name == "cline":
+            commands_dest_dir = project_dir / ".clinerules" / "workflows"
+        else:
+            commands_dest_dir = project_dir / ".agents" / "commands"
+        commands_dest_dir.mkdir(parents=True, exist_ok=True)
+
+        # 2. Setup mock extension directory
+        ext_dir = tmp_path / "mock-ext"
+        ext_dir.mkdir()
+
+        manifest_data = {
+            "schema_version": "1.0",
+            "extension": {
+                "id": "mock-ext",
+                "name": "Mock Extension",
+                "version": "1.0.0",
+                "description": f"Mock extension for {ai_name} tests",
+                "author": "Tester",
+                "repository": "https://github.com/test/mock-ext",
+                "license": "MIT",
+            },
+            "requires": {
+                "speckit_version": ">=0.1.0",
+            },
+            "provides": {
+                "commands": [
+                    {
+                        "name": "speckit.mock-ext.hello",
+                        "file": "commands/hello.md",
+                        "description": "Test hello command",
+                        "aliases": ["speckit.mock-ext.greet"]
+                    }
+                ]
+            }
+        }
+
+        with open(ext_dir / "extension.yml", "w", encoding="utf-8") as f:
+            yaml.dump(manifest_data, f)
+
+        commands_dir = ext_dir / "commands"
+        commands_dir.mkdir()
+
+        # Command file with dotted speckit references in frontmatter and body
+        cmd_content = """---
+description: "Test hello command"
+agent: speckit.tasks
+handoffs:
+  - agent: speckit.iterate.start
+    message: "Hand off to start"
+---
+
+# Test Hello Command
+
+Please refer to speckit.mock-ext.greet for instructions.
+$ARGUMENTS
+"""
+        (commands_dir / "hello.md").write_text(cmd_content, encoding="utf-8")
+
+        return project_dir, ext_dir, commands_dest_dir
+
+    def test_cline_extension_hyphenation(self, tmp_path):
+        from typer.testing import CliRunner
+        from unittest.mock import patch
+        from specify_cli import app
+        from specify_cli.agents import CommandRegistrar
+
+        project_dir, ext_dir, cline_workflows_dir = self._setup_mock_extension(tmp_path, "cline")
+
+        # 3. Run specify extension add
+        runner = CliRunner()
+        with patch.object(Path, "cwd", return_value=project_dir):
+            result = runner.invoke(
+                app, ["extension", "add", str(ext_dir), "--dev"], catch_exceptions=False
+            )
+
+        # Verify CLI printed hyphenated commands
+        # Note: We assert that the primary command 'speckit-mock-ext-hello' is printed,
+        # but we do not assert that the alias 'speckit-mock-ext-greet' is printed in the console
+        # because manifest.commands only lists primary commands.
+        assert "speckit-mock-ext-hello" in result.output
+        assert "speckit.mock-ext.hello" not in result.output
+
+        # Verify on-disk command names are hyphenated
+        hello_file = cline_workflows_dir / "speckit-mock-ext-hello.md"
+        greet_file = cline_workflows_dir / "speckit-mock-ext-greet.md"
+
+        assert hello_file.exists()
+        assert greet_file.exists()
+
+        # Verify frontmatter in the generated files is recursively hyphenated
+        hello_text = hello_file.read_text(encoding="utf-8")
+        hello_fm, hello_body = CommandRegistrar.parse_frontmatter(hello_text)
+        assert hello_fm["agent"] == "speckit-tasks"
+        assert hello_fm["handoffs"][0]["agent"] == "speckit-iterate-start"
+
+        # Verify body references are hyphenated for Cline
+        assert "speckit-mock-ext-greet" in hello_body
+        assert "speckit.mock-ext.greet" not in hello_body
+
+    def test_non_cline_extension_no_hyphenation(self, tmp_path):
+        from typer.testing import CliRunner
+        from unittest.mock import patch
+        from specify_cli import app
+        from specify_cli.agents import CommandRegistrar
+
+        project_dir, ext_dir, claude_commands_dir = self._setup_mock_extension(tmp_path, "claude")
+
+        # 3. Run specify extension add
+        runner = CliRunner()
+        with patch.object(Path, "cwd", return_value=project_dir):
+            result = runner.invoke(
+                app, ["extension", "add", str(ext_dir), "--dev"], catch_exceptions=False
+            )
+
+        # Verify CLI printed dotted commands
+        # Note: We assert that the primary command 'speckit.mock-ext.hello' is printed,
+        # but we do not assert that the alias 'speckit.mock-ext.greet' is printed in the console
+        # because manifest.commands only lists primary commands.
+        assert "speckit.mock-ext.hello" in result.output
+        assert "speckit-mock-ext-hello" not in result.output
+
+        # Verify on-disk command names are dotted
+        hello_file = claude_commands_dir / "speckit.mock-ext.hello.md"
+        greet_file = claude_commands_dir / "speckit.mock-ext.greet.md"
+
+        assert hello_file.exists()
+        assert greet_file.exists()
+
+        # Verify frontmatter references are still dotted
+        hello_text = hello_file.read_text(encoding="utf-8")
+        hello_fm, hello_body = CommandRegistrar.parse_frontmatter(hello_text)
+        assert hello_fm["agent"] == "speckit.tasks"
+        assert hello_fm["handoffs"][0]["agent"] == "speckit.iterate.start"
+
+        # Verify body references are still dotted for non-Cline
+        assert "speckit.mock-ext.greet" in hello_body
+        assert "speckit-mock-ext-greet" not in hello_body

tests/test_presets.py

@@ -2269,6 +2269,85 @@ class TestInitOptions:
 
         assert load_init_options(project_dir) == {}
 
+    @pytest.mark.parametrize(
+        "value",
+        ["名前-プロジェクト", "café-résumé", "Ωmega-Δelta", "🚀-launch"],
+    )
+    def test_save_load_round_trip_preserves_non_ascii(self, project_dir, value):
+        """Non-ASCII values round-trip via explicit UTF-8 encoding.
+
+        ``Path.write_text`` / ``Path.read_text`` default to the system
+        locale codec on Windows (cp1252 / gb2312 / cp932). Without
+        ``encoding="utf-8"`` pinned on both ends, a project name like
+        ``café`` written on a UTF-8 host becomes garbled or unreadable on
+        a cp1252 host (and vice versa). Pin UTF-8 explicitly so init
+        options round-trip across machines and CI.
+
+        Note: this test only meaningfully exercises the encoding pin
+        because ``save_init_options`` now writes JSON with
+        ``ensure_ascii=False`` — otherwise ``json.dumps`` would output
+        ASCII-only ``\\uXXXX`` escapes and the encoding pin would be a
+        no-op for any value here. ``test_save_writes_real_utf8_bytes``
+        below asserts that contract directly.
+        """
+        from specify_cli import save_init_options, load_init_options
+
+        save_init_options(project_dir, {"ai": "claude", "project_name": value})
+
+        loaded = load_init_options(project_dir)
+        assert loaded["project_name"] == value
+
+    def test_save_writes_real_utf8_bytes(self, project_dir):
+        """The on-disk file contains real UTF-8 bytes, not ``\\uXXXX`` escapes.
+
+        Pinning ``encoding="utf-8"`` on ``write_text`` only makes a
+        difference when the serialiser actually emits non-ASCII
+        characters. With ``ensure_ascii=False`` on ``json.dumps`` the
+        non-ASCII bytes hit the file, so the encoding pin is the thing
+        that decides between cp1252 garbage and clean UTF-8 on Windows.
+
+        This test pins that behaviour: the on-disk bytes are valid UTF-8
+        and contain the multi-byte encoding of ``café``, not its
+        ``\\u00e9`` escape form. Reviewers can verify that removing
+        ``ensure_ascii=False`` or ``encoding="utf-8"`` from the writer
+        breaks this test, which is what Copilot's review pointed out the
+        original round-trip test failed to do.
+        """
+        from specify_cli import save_init_options
+
+        save_init_options(project_dir, {"project_name": "café"})
+
+        opts_file = project_dir / ".specify" / "init-options.json"
+        raw = opts_file.read_bytes()
+        # 'café' in UTF-8 ends with bytes 0xC3 0xA9 ('é'). The cp1252
+        # encoding of 'é' is the single byte 0xE9. The JSON-escape form
+        # would be the 6-byte literal '\\u00e9'. We assert the UTF-8 form
+        # is present so the test pins the actual contract.
+        assert b"caf\xc3\xa9" in raw, (
+            "Expected UTF-8 bytes for 'café' in the on-disk file, "
+            f"got: {raw!r}"
+        )
+        # And the whole file decodes cleanly as UTF-8.
+        raw.decode("utf-8")
+
+    def test_load_returns_empty_on_locale_corrupted_file(self, project_dir):
+        """A file written in a non-UTF-8 codec falls back to {}, not crash.
+
+        Simulates a file produced by an old client (or by a peer machine
+        with a different default locale) that contains bytes invalid as
+        UTF-8. ``load_init_options`` should fall back to ``{}`` per the
+        existing contract — never propagate a raw ``UnicodeDecodeError``
+        to the CLI surface.
+        """
+        from specify_cli import load_init_options
+
+        opts_file = project_dir / ".specify" / "init-options.json"
+        opts_file.parent.mkdir(parents=True, exist_ok=True)
+        # 0xE9 is 'é' in cp1252 but an invalid lead byte in UTF-8.
+        opts_file.write_bytes(b'{"project_name": "caf\xe9"}')
+
+        assert load_init_options(project_dir) == {}
+
 
 class TestPresetSkills:
     """Tests for preset skill registration and unregistration.

tests/test_workflows.py

@@ -520,6 +520,7 @@ class TestCommandStep:
         assert result.output["integration"] == "gemini"
 
     def test_step_override_model(self):
+        from unittest.mock import patch
         from specify_cli.workflows.steps.command import CommandStep
         from specify_cli.workflows.base import StepContext
 
@@ -531,10 +532,12 @@ class TestCommandStep:
             "model": "opus-4",
             "input": {},
         }
-        result = step.execute(config, ctx)
+        with patch("specify_cli.workflows.steps.command.shutil.which", return_value=None):
+            result = step.execute(config, ctx)
         assert result.output["model"] == "opus-4"
 
     def test_options_merge(self):
+        from unittest.mock import patch
         from specify_cli.workflows.steps.command import CommandStep
         from specify_cli.workflows.base import StepContext
 
@@ -546,7 +549,8 @@ class TestCommandStep:
             "options": {"thinking-budget": 32768},
             "input": {},
         }
-        result = step.execute(config, ctx)
+        with patch("specify_cli.workflows.steps.command.shutil.which", return_value=None):
+            result = step.execute(config, ctx)
         assert result.output["options"]["max-tokens"] == 8000
         assert result.output["options"]["thinking-budget"] == 32768
 
@@ -2375,6 +2379,306 @@ steps:
         assert state.step_results["stamp"]["output"]["stdout"].strip() == "explicit-456"
 
 
+# ===== continue_on_error Tests =====
+#
+# Locks the contract documented in workflows/README.md "Error Handling"
+# section: when a step returns `StepResult(status=StepStatus.FAILED, ...)` and
+# `continue_on_error: true` is declared, the engine records the step's
+# `output` (with `exit_code` and `stderr` from the failure) and its
+# `status` (sibling key on `steps.<id>`, not nested under `output`)
+# and continues to the next sibling step instead of halting the run.
+# Gate aborts (`output.aborted`) still halt regardless of the flag.
+# Unhandled exceptions raised out of `step_impl.execute()` are out of
+# scope for this flag — they propagate to `WorkflowEngine.execute()`
+# and abort the run.
+
+
+class TestContinueOnError:
+    """Test the `continue_on_error` step-level field."""
+
+    def test_undeclared_failure_halts_run(self, project_dir):
+        """Default behaviour (no `continue_on_error`): a failing step
+        halts the workflow run with `status == StepStatus.FAILED`.
+
+        Locks the byte-equivalent default — workflows that do not
+        declare the flag must behave exactly as before this feature.
+        """
+        from specify_cli.workflows.engine import WorkflowDefinition, WorkflowEngine
+        from specify_cli.workflows.base import RunStatus
+
+        definition = WorkflowDefinition.from_string("""
+schema_version: "1.0"
+workflow:
+  id: "halt-on-fail"
+  name: "Halt On Fail"
+  version: "1.0.0"
+steps:
+  - id: fail-step
+    type: shell
+    run: "exit 7"
+  - id: after
+    type: shell
+    run: "echo should-not-run"
+""")
+        engine = WorkflowEngine(project_dir)
+        state = engine.execute(definition)
+
+        assert state.status == RunStatus.FAILED
+        assert "fail-step" in state.step_results
+        assert state.step_results["fail-step"]["output"]["exit_code"] == 7
+        # Subsequent step never executes when the flag is absent.
+        assert "after" not in state.step_results
+
+    def test_declared_and_fired_continues_run(self, project_dir):
+        """`continue_on_error: true` + failing step: the run keeps
+        going, the failed step's result is recorded, and the
+        downstream step runs.
+        """
+        from specify_cli.workflows.engine import WorkflowDefinition, WorkflowEngine
+        from specify_cli.workflows.base import RunStatus
+
+        definition = WorkflowDefinition.from_string("""
+schema_version: "1.0"
+workflow:
+  id: "continue-past-fail"
+  name: "Continue Past Fail"
+  version: "1.0.0"
+steps:
+  - id: flaky-step
+    type: shell
+    run: "exit 42"
+    continue_on_error: true
+  - id: after
+    type: shell
+    run: "echo did-run"
+""")
+        engine = WorkflowEngine(project_dir)
+        state = engine.execute(definition)
+
+        assert state.status == RunStatus.COMPLETED
+        # Failed step's exit_code is preserved so downstream branching
+        # can inspect it.
+        assert state.step_results["flaky-step"]["output"]["exit_code"] == 42
+        assert state.step_results["flaky-step"]["status"] == "failed"
+        # Downstream step ran successfully.
+        assert state.step_results["after"]["output"]["exit_code"] == 0
+
+    def test_declared_but_step_succeeded_is_noop(self, project_dir):
+        """`continue_on_error: true` on a step that succeeds is a
+        no-op — the flag only changes behaviour on StepStatus.FAILED status.
+        """
+        from specify_cli.workflows.engine import WorkflowDefinition, WorkflowEngine
+        from specify_cli.workflows.base import RunStatus
+
+        definition = WorkflowDefinition.from_string("""
+schema_version: "1.0"
+workflow:
+  id: "flag-but-success"
+  name: "Flag But Success"
+  version: "1.0.0"
+steps:
+  - id: ok-step
+    type: shell
+    run: "echo ok"
+    continue_on_error: true
+  - id: after
+    type: shell
+    run: "echo done"
+""")
+        engine = WorkflowEngine(project_dir)
+        state = engine.execute(definition)
+
+        assert state.status == RunStatus.COMPLETED
+        assert state.step_results["ok-step"]["status"] == "completed"
+        assert state.step_results["ok-step"]["output"]["exit_code"] == 0
+        assert state.step_results["after"]["output"]["exit_code"] == 0
+
+    def test_if_branch_routes_around_failure(self, project_dir):
+        """End-to-end: `continue_on_error` + `if` cleanly routes around
+        a failure. The recovery branch runs; the success branch does
+        not.
+
+        Mirrors the canonical usage pattern from the original feature
+        discussion in issue #2591.
+        """
+        from specify_cli.workflows.engine import WorkflowDefinition, WorkflowEngine
+        from specify_cli.workflows.base import RunStatus
+
+        definition = WorkflowDefinition.from_string("""
+schema_version: "1.0"
+workflow:
+  id: "route-around"
+  name: "Route Around Failure"
+  version: "1.0.0"
+steps:
+  - id: heavy-thing
+    type: shell
+    run: "exit 1"
+    continue_on_error: true
+  - id: check-result
+    type: if
+    condition: "{{ steps.heavy-thing.output.exit_code != 0 }}"
+    then:
+      - id: recovery
+        type: shell
+        run: "echo recovery-ran"
+    else:
+      - id: happy-path
+        type: shell
+        run: "echo happy-path-ran"
+""")
+        engine = WorkflowEngine(project_dir)
+        state = engine.execute(definition)
+
+        assert state.status == RunStatus.COMPLETED
+        assert "recovery" in state.step_results
+        assert "happy-path" not in state.step_results
+
+    def test_gate_abort_still_halts_with_continue_on_error(
+        self, project_dir, monkeypatch
+    ):
+        """`continue_on_error` does NOT override a deliberate gate
+        abort. `output.aborted` always halts the run with
+        `status == ABORTED`.
+
+        Aborts are explicit operator decisions; continue_on_error
+        is for transient/expected step failures only.
+        """
+        from specify_cli.workflows.engine import WorkflowDefinition, WorkflowEngine
+        from specify_cli.workflows.base import RunStatus
+        from specify_cli.workflows.steps.gate import GateStep
+        from specify_cli.workflows.steps import gate as gate_module
+
+        # Force the gate step into interactive mode and feed a "reject"
+        # choice so the abort path actually runs in the test env
+        # (default behaviour returns StepStatus.PAUSED when stdin is not a TTY).
+        # Swap sys.stdin itself for a stub: setattr on the real
+        # TextIOWrapper's `isatty` method is not assignable under some
+        # runners (e.g. pytest with capture disabled).
+        class _TTYStdin:
+            def isatty(self) -> bool:
+                return True
+
+        monkeypatch.setattr(gate_module.sys, "stdin", _TTYStdin())
+        monkeypatch.setattr(
+            GateStep, "_prompt", staticmethod(lambda _msg, _opts: "reject")
+        )
+
+        definition = WorkflowDefinition.from_string("""
+schema_version: "1.0"
+workflow:
+  id: "gate-abort-halts"
+  name: "Gate Abort Halts"
+  version: "1.0.0"
+steps:
+  - id: gate-step
+    type: gate
+    message: "Approve?"
+    options: [approve, reject]
+    on_reject: abort
+    continue_on_error: true
+  - id: should-not-run
+    type: shell
+    run: "echo nope"
+""")
+        engine = WorkflowEngine(project_dir)
+        state = engine.execute(definition)
+
+        assert state.status == RunStatus.ABORTED
+        assert "should-not-run" not in state.step_results
+
+    def test_validation_rejects_non_bool_continue_on_error(self):
+        """`continue_on_error` must be a literal boolean; coerced
+        strings like `"true"` are rejected at validation time so
+        authoring mistakes surface before execution.
+        """
+        from specify_cli.workflows.engine import (
+            WorkflowDefinition,
+            validate_workflow,
+        )
+
+        definition = WorkflowDefinition.from_string("""
+schema_version: "1.0"
+workflow:
+  id: "bad-coe"
+  name: "Bad COE"
+  version: "1.0.0"
+steps:
+  - id: step-one
+    type: shell
+    run: "true"
+    continue_on_error: "true"
+""")
+        errors = validate_workflow(definition)
+        assert any(
+            "continue_on_error" in e and "boolean" in e for e in errors
+        ), errors
+
+    def test_validation_accepts_bool_continue_on_error(self):
+        """Boolean values pass validation cleanly."""
+        from specify_cli.workflows.engine import (
+            WorkflowDefinition,
+            validate_workflow,
+        )
+
+        for value in (True, False):
+            yaml_value = "true" if value else "false"
+            definition = WorkflowDefinition.from_string(f"""
+schema_version: "1.0"
+workflow:
+  id: "good-coe"
+  name: "Good COE"
+  version: "1.0.0"
+steps:
+  - id: step-one
+    type: shell
+    run: "true"
+    continue_on_error: {yaml_value}
+""")
+            errors = validate_workflow(definition)
+            assert errors == [], errors
+
+    def test_engine_ignores_truthy_non_bool_continue_on_error(self, project_dir):
+        """Defense-in-depth: even if a caller bypasses
+        `validate_workflow()` and feeds the engine a definition with
+        `continue_on_error: "true"` (a string), the engine must NOT
+        honour the flag — only a literal boolean enables the
+        behaviour. `WorkflowEngine.execute()` does not auto-validate
+        (the `WorkflowEngine.load_workflow` docstring explicitly
+        notes the definition is "not yet validated; call
+        `validate_workflow()` or `engine.validate()` separately"),
+        so the engine guards against truthy non-bool values itself
+        via an identity check rather than truthiness.
+        """
+        from specify_cli.workflows.engine import WorkflowDefinition, WorkflowEngine
+        from specify_cli.workflows.base import RunStatus
+
+        # Bypass `validate_workflow()` — execute() is what would
+        # be called by a caller that skipped validation.
+        definition = WorkflowDefinition.from_string("""
+schema_version: "1.0"
+workflow:
+  id: "string-coe"
+  name: "String COE"
+  version: "1.0.0"
+steps:
+  - id: fail-step
+    type: shell
+    run: "exit 1"
+    continue_on_error: "true"
+  - id: should-not-run
+    type: shell
+    run: "echo should-not-run"
+""")
+        engine = WorkflowEngine(project_dir)
+        state = engine.execute(definition)
+
+        # String "true" is truthy but not a literal boolean, so the
+        # engine must treat the step as a halting failure.
+        assert state.status == RunStatus.FAILED
+        assert "should-not-run" not in state.step_results
+
+
 # ===== State Persistence Tests =====
 
 class TestRunState:

workflows/README.md

@@ -219,6 +219,83 @@ Aggregate results from fan-out steps:
   output: {}
 ```
 
+## Error Handling
+
+By default, any step that returns `StepResult(status=StepStatus.FAILED, ...)`
+at runtime halts the entire run — most commonly a `shell` or
+`command` step exiting non-zero. Set `continue_on_error: true` on
+a step to record its result and continue to the next sibling step
+instead. When the failure was a non-zero exit, the exit code
+remains available on `steps.<id>.output.exit_code` so a downstream
+`if` or `switch` can branch on it (or a `gate` can surface it to
+the operator via `{{ }}` interpolation in `message`):
+
+```yaml
+- id: heavy-thing
+  type: command
+  integration: claude
+  command: speckit.heavy-thing
+  continue_on_error: true
+
+- id: check-result
+  type: if
+  condition: "{{ steps.heavy-thing.output.exit_code != 0 }}"
+  then:
+    - id: review
+      type: gate
+      message: "Step failed (exit {{ steps.heavy-thing.output.exit_code }}). Approve to run the recovery path, or reject to leave the failure recorded and move on."
+      on_reject: skip
+    - id: recover
+      type: if
+      condition: "{{ steps.review.output.choice == 'approve' }}"
+      then:
+        - id: rerun
+          command: speckit.recovery
+  else:
+    - id: next-thing
+      command: speckit.next-thing
+```
+
+A few things worth knowing about that example:
+
+- Both gate options (`approve`, `reject`) return `StepStatus.COMPLETED`;
+  `on_reject: skip` controls only whether the engine aborts on reject
+  (it doesn't, with `skip`) — it does **not** auto-skip subsequent
+  sibling steps in the `then:` list. Downstream branching is the
+  workflow author's responsibility: read
+  `{{ steps.<gate-id>.output.choice }}` in a follow-up `if`, `switch`,
+  or expression, as the `recover` step above does.
+- `on_reject` has three values: `abort` (default — reject → `StepStatus.FAILED`
+  with `output.aborted = True`, halts the run), `skip` (reject →
+  `StepStatus.COMPLETED`, author handles branching as shown), and `retry`
+  (reject → `StepStatus.PAUSED` so the next `specify workflow resume` re-runs
+  the gate).
+- Gates do not automatically re-run the failed step. To express a
+  retry path, either define custom gate options and branch on the
+  choice downstream, or wrap the failing step in your own loop.
+
+**Notes:**
+
+- The field must be a literal boolean (`true` / `false`); coerced
+  strings like `"true"` are rejected at validation time.
+- **Scope: returned failures only.** The flag applies to step results
+  with `status=StepStatus.FAILED`. Unhandled exceptions raised out of a step's
+  `execute()` method are caught one level up by `WorkflowEngine.execute()`,
+  logged as `workflow_failed`, and abort the run regardless of
+  `continue_on_error`. If a step author wants the flag to cover an
+  exceptional path, the step must catch the exception internally and
+  return `StepResult(status=StepStatus.FAILED, ...)` with the failure encoded in
+  `output` (e.g. `exit_code`, `stderr`, or a custom field).
+- Gate aborts (`on_reject: abort` chosen by the operator) always halt
+  the run — `continue_on_error` does not override them. The flag is
+  for transient/expected step failures, not for overriding deliberate
+  operator decisions.
+- Structural validation runs up-front: `specify workflow run` rejects
+  invalid workflow definitions before the run is created, so
+  validation failures never reach this code path.
+- When the flag is omitted, behaviour is byte-equivalent to before
+  this feature.
+
 ## Expressions
 
 Workflow definitions use `{{ expression }}` syntax for dynamic values: