feat(scripts): add --allow-existing-branch flag to create-new-feature (#1999)

* feat(scripts): add --allow-existing-branch flag to create-new-feature

Add an --allow-existing-branch / -AllowExistingBranch flag to both
bash and PowerShell create-new-feature scripts. When the target branch
already exists, the script switches to it instead of failing. The spec
directory and template are still created if missing, but existing
spec.md files are not overwritten (prevents data loss on re-runs).

The flag is opt-in, so existing behavior is completely unchanged
without it. This enables worktree-based workflows and CI/CD pipelines
that create branches externally before running speckit.specify.

Relates to #1931. Also addresses #1680, #841, #1921.

Assisted-By: 🤖 Claude Code

* fix: address PR review feedback for allow-existing-branch

- Make checkout failure fatal instead of suppressing with || true (bash)
- Check $LASTEXITCODE after git checkout in PowerShell
- Use Test-Path -PathType Leaf for spec file existence check (PS)
- Add PowerShell static assertion test for -AllowExistingBranch flag

Assisted-By: 🤖 Claude Code

.github/workflows/docs.yml

@@ -64,5 +64,5 @@ jobs:
     steps:
       - name: Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@v4
+        uses: actions/deploy-pages@v5
 

.github/workflows/lint.yml

@@ -15,7 +15,7 @@ jobs:
         uses: actions/checkout@v6
 
       - name: Run markdownlint-cli2
-        uses: DavidAnson/markdownlint-cli2-action@v19
+        uses: DavidAnson/markdownlint-cli2-action@v23
         with:
           globs: |
             '**/*.md'

.github/workflows/scripts/create-release-packages.ps1

@@ -497,13 +497,13 @@ $AllAgents = @('claude', 'gemini', 'copilot', 'cursor-agent', 'qwen', 'opencode'
 $AllScripts = @('sh', 'ps')
 
 function Normalize-List {
-    param([string]$Input)
+    param([string]$Value)
 
-    if ([string]::IsNullOrEmpty($Input)) {
+    if ([string]::IsNullOrEmpty($Value)) {
         return @()
     }
 
-    $items = $Input -split '[,\s]+' | Where-Object { $_ } | Select-Object -Unique
+    $items = $Value -split '[,\s]+' | Where-Object { $_ } | Select-Object -Unique
     return $items
 }
 
@@ -526,7 +526,7 @@ function Validate-Subset {
 
 # Determine agent list
 if (-not [string]::IsNullOrEmpty($Agents)) {
-    $AgentList = Normalize-List -Input $Agents
+    $AgentList = Normalize-List -Value $Agents
     if (-not (Validate-Subset -Type 'agent' -Allowed $AllAgents -Items $AgentList)) {
         exit 1
     }
@@ -536,7 +536,7 @@ if (-not [string]::IsNullOrEmpty($Agents)) {
 
 # Determine script list
 if (-not [string]::IsNullOrEmpty($Scripts)) {
-    $ScriptList = Normalize-List -Input $Scripts
+    $ScriptList = Normalize-List -Value $Scripts
     if (-not (Validate-Subset -Type 'script' -Allowed $AllScripts -Items $ScriptList)) {
         exit 1
     }

README.md

@@ -162,9 +162,18 @@ Want to see Spec Kit in action? Watch our [video overview](https://www.youtube.c
 
 The following community-contributed extensions are available in [`catalog.community.json`](extensions/catalog.community.json):
 
-**Categories:** `docs` — reads, validates, or generates spec artifacts · `code` — reviews, validates, or modifies source code · `process` — orchestrates workflow across phases · `integration` — syncs with external platforms · `visibility` — reports on project health or progress
+**Categories:**
 
-**Effect:** `Read-only` — produces reports without modifying files · `Read+Write` — modifies files, creates artifacts, or updates specs
+- `docs` — reads, validates, or generates spec artifacts
+- `code` — reviews, validates, or modifies source code
+- `process` — orchestrates workflow across phases
+- `integration` — syncs with external platforms
+- `visibility` — reports on project health or progress
+
+**Effect:**
+
+- `Read-only` — produces reports without modifying files
+- `Read+Write` — modifies files, creates artifacts, or updates specs
 
 | Extension | Purpose | Category | Effect | URL |
 |-----------|---------|----------|--------|-----|
@@ -181,6 +190,15 @@ 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) |
+| 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) |
+| MAQA GitHub Projects Integration | GitHub Projects v2 integration for MAQA — syncs draft issues and Status columns as features progress | `integration` | Read+Write | [spec-kit-maqa-github-projects](https://github.com/GenieRobot/spec-kit-maqa-github-projects) |
+| MAQA Jira Integration | Jira integration for MAQA — syncs Stories and Subtasks as features progress through the board | `integration` | Read+Write | [spec-kit-maqa-jira](https://github.com/GenieRobot/spec-kit-maqa-jira) |
+| MAQA Linear Integration | Linear integration for MAQA — syncs issues and sub-issues across workflow states as features progress | `integration` | Read+Write | [spec-kit-maqa-linear](https://github.com/GenieRobot/spec-kit-maqa-linear) |
+| MAQA Trello Integration | Trello board integration for MAQA — populates board from specs, moves cards, real-time checklist ticking | `integration` | Read+Write | [spec-kit-maqa-trello](https://github.com/GenieRobot/spec-kit-maqa-trello) |
+| Onboard | Contextual onboarding and progressive growth for developers new to spec-kit projects. Explains specs, maps dependencies, validates understanding, and guides the next step | `process` | Read+Write | [spec-kit-onboard](https://github.com/dmux/spec-kit-onboard) |
+| 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) |
 | Presetify | Create and validate presets and preset catalogs | `process` | Read+Write | [presetify](https://github.com/mnriem/spec-kit-extensions/tree/main/presetify) |
 | Project Health Check | Diagnose a Spec Kit project and report health issues across structure, agents, features, scripts, extensions, and git | `visibility` | Read-only | [spec-kit-doctor](https://github.com/KhawarHabibKhan/spec-kit-doctor) |
 | Project Status | Show current SDD workflow progress — active feature, artifact status, task completion, workflow phase, and extensions summary | `visibility` | Read-only | [spec-kit-status](https://github.com/KhawarHabibKhan/spec-kit-status) |

extensions/EXTENSION-API-REFERENCE.md

@@ -44,7 +44,7 @@ provides:
     - name: string       # Required, pattern: ^speckit\.[a-z0-9-]+\.[a-z0-9-]+$
       file: string       # Required, relative path to command file
       description: string # Required
-      aliases: [string]  # Optional, array of alternate names
+      aliases: [string]  # Optional, same pattern as name; namespace must match extension.id and must not shadow core or installed extension commands
 
   config:                # Optional, array of config files
     - name: string       # Config file name

extensions/EXTENSION-DEVELOPMENT-GUIDE.md

@@ -41,7 +41,7 @@ provides:
     - name: "speckit.my-ext.hello"      # Must follow pattern: speckit.{ext-id}.{cmd}
       file: "commands/hello.md"
       description: "Say hello"
-      aliases: ["speckit.hello"]        # Optional aliases
+      aliases: ["speckit.my-ext.hi"]    # Optional aliases, same pattern
 
   config:                               # Optional: Config files
     - name: "my-ext-config.yml"
@@ -186,7 +186,7 @@ What the extension provides.
 - `name`: Command name (must match `speckit.{ext-id}.{command}`)
 - `file`: Path to command file (relative to extension root)
 - `description`: Command description (optional)
-- `aliases`: Alternative command names (optional, array)
+- `aliases`: Alternative command names (optional, array; each must match `speckit.{ext-id}.{command}`)
 
 ### Optional Fields
 

extensions/EXTENSION-USER-GUIDE.md

@@ -214,8 +214,8 @@ Extensions add commands that appear in your AI agent (Claude Code):
 # In Claude Code
 > /speckit.jira.specstoissues
 
-# Or use short alias (if provided)
+# Or use a namespaced alias (if provided)
-> /speckit.specstoissues
+> /speckit.jira.sync
 ```
 
 ### Extension Configuration

extensions/RFC-EXTENSION-SYSTEM.md

@@ -223,7 +223,7 @@ provides:
     - name: "speckit.jira.specstoissues"
       file: "commands/specstoissues.md"
       description: "Create Jira hierarchy from spec and tasks"
-      aliases: ["speckit.specstoissues"]  # Alternate names
+      aliases: ["speckit.jira.sync"]  # Alternate names
 
     - name: "speckit.jira.discover-fields"
       file: "commands/discover-fields.md"
@@ -1517,7 +1517,7 @@ specify extension add github-projects
 /speckit.github.taskstoissues
 ```
 
-**Compatibility shim** (if needed):
+**Migration alias** (if needed):
 
 ```yaml
 # extension.yml
@@ -1525,10 +1525,10 @@ provides:
   commands:
     - name: "speckit.github.taskstoissues"
       file: "commands/taskstoissues.md"
-      aliases: ["speckit.taskstoissues"]  # Backward compatibility
+      aliases: ["speckit.github.sync-taskstoissues"]  # Alternate namespaced entry point
 ```
 
-AI agent registers both names, so old scripts work.
+AI agents register both names, so callers can migrate to the alternate alias without relying on deprecated global shortcuts like `/speckit.taskstoissues`.
 
 ---
 

extensions/catalog.community.json

@@ -1,12 +1,12 @@
 {
   "schema_version": "1.0",
-  "updated_at": "2026-03-19T12:08:20Z",
+  "updated_at": "2026-03-27T08:22:30Z",
   "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/extensions/catalog.community.json",
   "extensions": {
     "aide": {
       "name": "AI-Driven Engineering (AIDE)",
       "id": "aide",
-      "description": "A structured 7-step workflow for building new projects from scratch with AI assistants — from vision through implementation.",
+      "description": "A structured 7-step workflow for building new projects from scratch with AI assistants \u2014 from vision through implementation.",
       "author": "mnriem",
       "version": "1.0.0",
       "download_url": "https://github.com/mnriem/spec-kit-extensions/releases/download/aide-v1.0.0/aide.zip",
@@ -170,7 +170,7 @@
     "cognitive-squad": {
       "name": "Cognitive Squad",
       "id": "cognitive-squad",
-      "description": "Multi-agent cognitive system with Triadic Model: understanding, internalization, application — with quality gates, backpropagation verification, and self-healing",
+      "description": "Multi-agent cognitive system with Triadic Model: understanding, internalization, application \u2014 with quality gates, backpropagation verification, and self-healing",
       "author": "Testimonial",
       "version": "0.1.0",
       "download_url": "https://github.com/Testimonial/cognitive-squad/archive/refs/tags/v0.1.0.zip",
@@ -379,7 +379,7 @@
     "iterate": {
       "name": "Iterate",
       "id": "iterate",
-      "description": "Iterate on spec documents with a two-phase define-and-apply workflow — refine specs mid-implementation and go straight back to building",
+      "description": "Iterate on spec documents with a two-phase define-and-apply workflow \u2014 refine specs mid-implementation and go straight back to building",
       "author": "Vianca Martinez",
       "version": "2.0.0",
       "download_url": "https://github.com/imviancagrace/spec-kit-iterate/archive/refs/tags/v2.0.0.zip",
@@ -437,6 +437,327 @@
       "created_at": "2026-03-05T00:00:00Z",
       "updated_at": "2026-03-05T00:00:00Z"
     },
+    "learn": {
+      "name": "Learning Extension",
+      "id": "learn",
+      "description": "Generate educational guides from implementations and enhance clarifications with mentoring context.",
+      "author": "Vianca Martinez",
+      "version": "1.0.0",
+      "download_url": "https://github.com/imviancagrace/spec-kit-learn/archive/refs/tags/v1.0.0.zip",
+      "repository": "https://github.com/imviancagrace/spec-kit-learn",
+      "homepage": "https://github.com/imviancagrace/spec-kit-learn",
+      "documentation": "https://github.com/imviancagrace/spec-kit-learn/blob/main/README.md",
+      "changelog": "https://github.com/imviancagrace/spec-kit-learn/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.1.0"
+      },
+      "provides": {
+        "commands": 2,
+        "hooks": 1
+      },
+      "tags": [
+        "learning",
+        "education",
+        "mentoring",
+        "knowledge-transfer"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-03-17T00:00:00Z",
+      "updated_at": "2026-03-17T00:00:00Z"
+    },
+    "maqa": {
+      "name": "MAQA \u2014 Multi-Agent & Quality Assurance",
+      "id": "maqa",
+      "description": "Coordinator \u2192 feature \u2192 QA agent workflow with parallel worktree-based implementation. Language-agnostic. Auto-detects installed board plugins (Trello, Linear, GitHub Projects, Jira, Azure DevOps). Optional CI gate.",
+      "author": "GenieRobot",
+      "version": "0.1.3",
+      "download_url": "https://github.com/GenieRobot/spec-kit-maqa-ext/releases/download/maqa-v0.1.3/maqa.zip",
+      "repository": "https://github.com/GenieRobot/spec-kit-maqa-ext",
+      "homepage": "https://github.com/GenieRobot/spec-kit-maqa-ext",
+      "documentation": "https://github.com/GenieRobot/spec-kit-maqa-ext/blob/main/README.md",
+      "changelog": "https://github.com/GenieRobot/spec-kit-maqa-ext/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.3.0"
+      },
+      "provides": {
+        "commands": 4,
+        "hooks": 1
+      },
+      "tags": [
+        "multi-agent",
+        "orchestration",
+        "quality-assurance",
+        "workflow",
+        "parallel",
+        "tdd"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-03-26T00:00:00Z",
+      "updated_at": "2026-03-27T00:00:00Z"
+    },
+    "maqa-azure-devops": {
+      "name": "MAQA Azure DevOps Integration",
+      "id": "maqa-azure-devops",
+      "description": "Azure DevOps Boards integration for the MAQA extension. Populates work items from specs, moves User Stories across columns as features progress, real-time Task child ticking.",
+      "author": "GenieRobot",
+      "version": "0.1.0",
+      "download_url": "https://github.com/GenieRobot/spec-kit-maqa-azure-devops/releases/download/maqa-azure-devops-v0.1.0/maqa-azure-devops.zip",
+      "repository": "https://github.com/GenieRobot/spec-kit-maqa-azure-devops",
+      "homepage": "https://github.com/GenieRobot/spec-kit-maqa-azure-devops",
+      "documentation": "https://github.com/GenieRobot/spec-kit-maqa-azure-devops/blob/main/README.md",
+      "changelog": "https://github.com/GenieRobot/spec-kit-maqa-azure-devops/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.3.0"
+      },
+      "provides": {
+        "commands": 2,
+        "hooks": 0
+      },
+      "tags": [
+        "azure-devops",
+        "project-management",
+        "multi-agent",
+        "maqa",
+        "kanban"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-03-27T00:00:00Z",
+      "updated_at": "2026-03-27T00:00:00Z"
+    },
+    "maqa-ci": {
+      "name": "MAQA CI/CD Gate",
+      "id": "maqa-ci",
+      "description": "CI/CD pipeline gate for the MAQA extension. Auto-detects GitHub Actions, CircleCI, GitLab CI, and Bitbucket Pipelines. Blocks QA handoff until pipeline is green.",
+      "author": "GenieRobot",
+      "version": "0.1.0",
+      "download_url": "https://github.com/GenieRobot/spec-kit-maqa-ci/releases/download/maqa-ci-v0.1.0/maqa-ci.zip",
+      "repository": "https://github.com/GenieRobot/spec-kit-maqa-ci",
+      "homepage": "https://github.com/GenieRobot/spec-kit-maqa-ci",
+      "documentation": "https://github.com/GenieRobot/spec-kit-maqa-ci/blob/main/README.md",
+      "changelog": "https://github.com/GenieRobot/spec-kit-maqa-ci/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.3.0"
+      },
+      "provides": {
+        "commands": 2,
+        "hooks": 0
+      },
+      "tags": [
+        "ci-cd",
+        "github-actions",
+        "circleci",
+        "gitlab-ci",
+        "quality-gate",
+        "maqa"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-03-27T00:00:00Z",
+      "updated_at": "2026-03-27T00:00:00Z"
+    },
+    "maqa-github-projects": {
+      "name": "MAQA GitHub Projects Integration",
+      "id": "maqa-github-projects",
+      "description": "GitHub Projects v2 integration for the MAQA extension. Populates draft issues from specs, moves items across Status columns as features progress, real-time task list ticking.",
+      "author": "GenieRobot",
+      "version": "0.1.0",
+      "download_url": "https://github.com/GenieRobot/spec-kit-maqa-github-projects/releases/download/maqa-github-projects-v0.1.0/maqa-github-projects.zip",
+      "repository": "https://github.com/GenieRobot/spec-kit-maqa-github-projects",
+      "homepage": "https://github.com/GenieRobot/spec-kit-maqa-github-projects",
+      "documentation": "https://github.com/GenieRobot/spec-kit-maqa-github-projects/blob/main/README.md",
+      "changelog": "https://github.com/GenieRobot/spec-kit-maqa-github-projects/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.3.0"
+      },
+      "provides": {
+        "commands": 2,
+        "hooks": 0
+      },
+      "tags": [
+        "github-projects",
+        "project-management",
+        "multi-agent",
+        "maqa",
+        "kanban"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-03-27T00:00:00Z",
+      "updated_at": "2026-03-27T00:00:00Z"
+    },
+    "maqa-jira": {
+      "name": "MAQA Jira Integration",
+      "id": "maqa-jira",
+      "description": "Jira integration for the MAQA extension. Populates Stories from specs, moves issues across board columns as features progress, real-time Subtask ticking.",
+      "author": "GenieRobot",
+      "version": "0.1.0",
+      "download_url": "https://github.com/GenieRobot/spec-kit-maqa-jira/releases/download/maqa-jira-v0.1.0/maqa-jira.zip",
+      "repository": "https://github.com/GenieRobot/spec-kit-maqa-jira",
+      "homepage": "https://github.com/GenieRobot/spec-kit-maqa-jira",
+      "documentation": "https://github.com/GenieRobot/spec-kit-maqa-jira/blob/main/README.md",
+      "changelog": "https://github.com/GenieRobot/spec-kit-maqa-jira/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.3.0"
+      },
+      "provides": {
+        "commands": 2,
+        "hooks": 0
+      },
+      "tags": [
+        "jira",
+        "project-management",
+        "multi-agent",
+        "maqa",
+        "kanban"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-03-27T00:00:00Z",
+      "updated_at": "2026-03-27T00:00:00Z"
+    },
+    "maqa-linear": {
+      "name": "MAQA Linear Integration",
+      "id": "maqa-linear",
+      "description": "Linear integration for the MAQA extension. Populates issues from specs, moves items across workflow states as features progress, real-time sub-issue ticking.",
+      "author": "GenieRobot",
+      "version": "0.1.0",
+      "download_url": "https://github.com/GenieRobot/spec-kit-maqa-linear/releases/download/maqa-linear-v0.1.0/maqa-linear.zip",
+      "repository": "https://github.com/GenieRobot/spec-kit-maqa-linear",
+      "homepage": "https://github.com/GenieRobot/spec-kit-maqa-linear",
+      "documentation": "https://github.com/GenieRobot/spec-kit-maqa-linear/blob/main/README.md",
+      "changelog": "https://github.com/GenieRobot/spec-kit-maqa-linear/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.3.0"
+      },
+      "provides": {
+        "commands": 2,
+        "hooks": 0
+      },
+      "tags": [
+        "linear",
+        "project-management",
+        "multi-agent",
+        "maqa",
+        "kanban"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-03-27T00:00:00Z",
+      "updated_at": "2026-03-27T00:00:00Z"
+    },
+    "maqa-trello": {
+      "name": "MAQA Trello Integration",
+      "id": "maqa-trello",
+      "description": "Trello board integration for the MAQA extension. Populates board from specs, moves cards between lists as features progress, real-time checklist ticking.",
+      "author": "GenieRobot",
+      "version": "0.1.1",
+      "download_url": "https://github.com/GenieRobot/spec-kit-maqa-trello/releases/download/maqa-trello-v0.1.1/maqa-trello.zip",
+      "repository": "https://github.com/GenieRobot/spec-kit-maqa-trello",
+      "homepage": "https://github.com/GenieRobot/spec-kit-maqa-trello",
+      "documentation": "https://github.com/GenieRobot/spec-kit-maqa-trello/blob/main/README.md",
+      "changelog": "https://github.com/GenieRobot/spec-kit-maqa-trello/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.3.0"
+      },
+      "provides": {
+        "commands": 2,
+        "hooks": 0
+      },
+      "tags": [
+        "trello",
+        "project-management",
+        "multi-agent",
+        "maqa",
+        "kanban"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-03-26T00:00:00Z",
+      "updated_at": "2026-03-26T00:00:00Z"
+    },
+    "onboard": {
+      "name": "Onboard",
+      "id": "onboard",
+      "description": "Contextual onboarding and progressive growth for developers new to spec-kit projects. Explains specs, maps dependencies, validates understanding, and guides the next step.",
+      "author": "Rafael Sales",
+      "version": "2.1.0",
+      "download_url": "https://github.com/dmux/spec-kit-onboard/archive/refs/tags/v2.1.0.zip",
+      "repository": "https://github.com/dmux/spec-kit-onboard",
+      "homepage": "https://github.com/dmux/spec-kit-onboard",
+      "documentation": "https://github.com/dmux/spec-kit-onboard/blob/main/README.md",
+      "changelog": "https://github.com/dmux/spec-kit-onboard/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.1.0"
+      },
+      "provides": {
+        "commands": 7,
+        "hooks": 3
+      },
+      "tags": [
+        "onboarding",
+        "learning",
+        "mentoring",
+        "developer-experience",
+        "gamification",
+        "knowledge-transfer"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-03-26T00:00:00Z",
+      "updated_at": "2026-03-26T00:00:00Z"
+    },
+    "plan-review-gate": {
+      "name": "Plan Review Gate",
+      "id": "plan-review-gate",
+      "description": "Require spec.md and plan.md to be merged via MR/PR before allowing task generation",
+      "author": "luno",
+      "version": "1.0.0",
+      "download_url": "https://github.com/luno/spec-kit-plan-review-gate/archive/refs/tags/v1.0.0.zip",
+      "repository": "https://github.com/luno/spec-kit-plan-review-gate",
+      "homepage": "https://github.com/luno/spec-kit-plan-review-gate",
+      "documentation": "https://github.com/luno/spec-kit-plan-review-gate/blob/main/README.md",
+      "changelog": "https://github.com/luno/spec-kit-plan-review-gate/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.1.0"
+      },
+      "provides": {
+        "commands": 1,
+        "hooks": 1
+      },
+      "tags": [
+        "review",
+        "quality",
+        "workflow",
+        "gate"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-03-27T08:22:30Z",
+      "updated_at": "2026-03-27T08:22:30Z"
+    },
     "presetify": {
       "name": "Presetify",
       "id": "presetify",
@@ -638,6 +959,38 @@
       "created_at": "2026-03-18T00:00:00Z",
       "updated_at": "2026-03-18T00:00:00Z"
     },
+    "status": {
+      "name": "Project Status",
+      "id": "status",
+      "description": "Show current SDD workflow progress \u2014 active feature, artifact status, task completion, workflow phase, and extensions summary.",
+      "author": "KhawarHabibKhan",
+      "version": "1.0.0",
+      "download_url": "https://github.com/KhawarHabibKhan/spec-kit-status/archive/refs/tags/v1.0.0.zip",
+      "repository": "https://github.com/KhawarHabibKhan/spec-kit-status",
+      "homepage": "https://github.com/KhawarHabibKhan/spec-kit-status",
+      "documentation": "https://github.com/KhawarHabibKhan/spec-kit-status/blob/main/README.md",
+      "changelog": "https://github.com/KhawarHabibKhan/spec-kit-status/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.1.0"
+      },
+      "provides": {
+        "commands": 1,
+        "hooks": 0
+      },
+      "tags": [
+        "status",
+        "workflow",
+        "progress",
+        "feature-tracking",
+        "task-progress"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-03-16T00:00:00Z",
+      "updated_at": "2026-03-16T00:00:00Z"
+    },
     "sync": {
       "name": "Spec Sync",
       "id": "sync",
@@ -711,38 +1064,6 @@
       "created_at": "2026-03-07T00:00:00Z",
       "updated_at": "2026-03-07T00:00:00Z"
     },
-    "status": {
-      "name": "Project Status",
-      "id": "status",
-      "description": "Show current SDD workflow progress — active feature, artifact status, task completion, workflow phase, and extensions summary.",
-      "author": "KhawarHabibKhan",
-      "version": "1.0.0",
-      "download_url": "https://github.com/KhawarHabibKhan/spec-kit-status/archive/refs/tags/v1.0.0.zip",
-      "repository": "https://github.com/KhawarHabibKhan/spec-kit-status",
-      "homepage": "https://github.com/KhawarHabibKhan/spec-kit-status",
-      "documentation": "https://github.com/KhawarHabibKhan/spec-kit-status/blob/main/README.md",
-      "changelog": "https://github.com/KhawarHabibKhan/spec-kit-status/blob/main/CHANGELOG.md",
-      "license": "MIT",
-      "requires": {
-        "speckit_version": ">=0.1.0"
-      },
-      "provides": {
-        "commands": 1,
-        "hooks": 0
-      },
-      "tags": [
-        "status",
-        "workflow",
-        "progress",
-        "feature-tracking",
-        "task-progress"
-      ],
-      "verified": false,
-      "downloads": 0,
-      "stars": 0,
-      "created_at": "2026-03-16T00:00:00Z",
-      "updated_at": "2026-03-16T00:00:00Z"
-    },
     "v-model": {
       "name": "V-Model Extension Pack",
       "id": "v-model",
@@ -775,37 +1096,6 @@
       "created_at": "2026-02-20T00:00:00Z",
       "updated_at": "2026-02-22T00:00:00Z"
     },
-    "learn": {
-      "name": "Learning Extension",
-      "id": "learn",
-      "description": "Generate educational guides from implementations and enhance clarifications with mentoring context.",
-      "author": "Vianca Martinez",
-      "version": "1.0.0",
-      "download_url": "https://github.com/imviancagrace/spec-kit-learn/archive/refs/tags/v1.0.0.zip",
-      "repository": "https://github.com/imviancagrace/spec-kit-learn",
-      "homepage": "https://github.com/imviancagrace/spec-kit-learn",
-      "documentation": "https://github.com/imviancagrace/spec-kit-learn/blob/main/README.md",
-      "changelog": "https://github.com/imviancagrace/spec-kit-learn/blob/main/CHANGELOG.md",
-      "license": "MIT",
-      "requires": {
-        "speckit_version": ">=0.1.0"
-      },
-      "provides": {
-        "commands": 2,
-        "hooks": 1
-      },
-      "tags": [
-        "learning",
-        "education",
-        "mentoring",
-        "knowledge-transfer"
-      ],
-      "verified": false,
-      "downloads": 0,
-      "stars": 0,
-      "created_at": "2026-03-17T00:00:00Z",
-      "updated_at": "2026-03-17T00:00:00Z"
-    },
     "verify": {
       "name": "Verify Extension",
       "id": "verify",

extensions/template/extension.yml

@@ -47,8 +47,8 @@ provides:
     - name: "speckit.my-extension.example"
       file: "commands/example.md"
       description: "Example command that demonstrates functionality"
-      # Optional: Add aliases for shorter command names
+      # Optional: Add aliases in the same namespaced format
-      aliases: ["speckit.example"]
+      aliases: ["speckit.my-extension.example-short"]
 
     # ADD MORE COMMANDS: Copy this block for each command
     # - name: "speckit.my-extension.another-command"

scripts/bash/create-new-feature.sh

@@ -3,6 +3,7 @@
 set -e
 
 JSON_MODE=false
+ALLOW_EXISTING=false
 SHORT_NAME=""
 BRANCH_NUMBER=""
 USE_TIMESTAMP=false
@@ -14,6 +15,9 @@ while [ $i -le $# ]; do
         --json)
             JSON_MODE=true
             ;;
+        --allow-existing-branch)
+            ALLOW_EXISTING=true
+            ;;
         --short-name)
             if [ $((i + 1)) -gt $# ]; then
                 echo 'Error: --short-name requires a value' >&2
@@ -45,10 +49,11 @@ while [ $i -le $# ]; do
             USE_TIMESTAMP=true
             ;;
         --help|-h)
-            echo "Usage: $0 [--json] [--short-name <name>] [--number N] [--timestamp] <feature_description>"
+            echo "Usage: $0 [--json] [--allow-existing-branch] [--short-name <name>] [--number N] [--timestamp] <feature_description>"
             echo ""
             echo "Options:"
             echo "  --json              Output in JSON format"
+            echo "  --allow-existing-branch  Switch to branch if it already exists instead of failing"
             echo "  --short-name <name> Provide a custom short name (2-4 words) for the branch"
             echo "  --number N          Specify branch number manually (overrides auto-detection)"
             echo "  --timestamp         Use timestamp prefix (YYYYMMDD-HHMMSS) instead of sequential numbering"
@@ -69,7 +74,7 @@ done
 
 FEATURE_DESCRIPTION="${ARGS[*]}"
 if [ -z "$FEATURE_DESCRIPTION" ]; then
-    echo "Usage: $0 [--json] [--short-name <name>] [--number N] [--timestamp] <feature_description>" >&2
+    echo "Usage: $0 [--json] [--allow-existing-branch] [--short-name <name>] [--number N] [--timestamp] <feature_description>" >&2
     exit 1
 fi
 
@@ -287,12 +292,19 @@ if [ "$HAS_GIT" = true ]; then
     if ! git checkout -b "$BRANCH_NAME" 2>/dev/null; then
         # Check if branch already exists
         if git branch --list "$BRANCH_NAME" | grep -q .; then
-            if [ "$USE_TIMESTAMP" = true ]; then
+            if [ "$ALLOW_EXISTING" = true ]; then
+                # Switch to the existing branch instead of failing
+                if ! git checkout "$BRANCH_NAME" 2>/dev/null; then
+                    >&2 echo "Error: Failed to switch to existing branch '$BRANCH_NAME'. Please resolve any local changes or conflicts and try again."
+                    exit 1
+                fi
+            elif [ "$USE_TIMESTAMP" = true ]; then
                 >&2 echo "Error: Branch '$BRANCH_NAME' already exists. Rerun to get a new timestamp or use a different --short-name."
+                exit 1
             else
                 >&2 echo "Error: Branch '$BRANCH_NAME' already exists. Please use a different feature name or specify a different number with --number."
+                exit 1
             fi
-            exit 1
         else
             >&2 echo "Error: Failed to create git branch '$BRANCH_NAME'. Please check your git configuration and try again."
             exit 1
@@ -305,13 +317,15 @@ fi
 FEATURE_DIR="$SPECS_DIR/$BRANCH_NAME"
 mkdir -p "$FEATURE_DIR"
 
-TEMPLATE=$(resolve_template "spec-template" "$REPO_ROOT") || true
 SPEC_FILE="$FEATURE_DIR/spec.md"
-if [ -n "$TEMPLATE" ] && [ -f "$TEMPLATE" ]; then
+if [ ! -f "$SPEC_FILE" ]; then
-    cp "$TEMPLATE" "$SPEC_FILE"
+    TEMPLATE=$(resolve_template "spec-template" "$REPO_ROOT") || true
-else
+    if [ -n "$TEMPLATE" ] && [ -f "$TEMPLATE" ]; then
-    echo "Warning: Spec template not found; created empty spec file" >&2
+        cp "$TEMPLATE" "$SPEC_FILE"
-    touch "$SPEC_FILE"
+    else
+        echo "Warning: Spec template not found; created empty spec file" >&2
+        touch "$SPEC_FILE"
+    fi
 fi
 
 # Inform the user how to persist the feature variable in their own shell

scripts/bash/update-agent-context.sh

@@ -63,7 +63,7 @@ AGENT_TYPE="${1:-}"
 # Agent-specific file paths  
 CLAUDE_FILE="$REPO_ROOT/CLAUDE.md"
 GEMINI_FILE="$REPO_ROOT/GEMINI.md"
-COPILOT_FILE="$REPO_ROOT/.github/agents/copilot-instructions.md"
+COPILOT_FILE="$REPO_ROOT/.github/copilot-instructions.md"
 CURSOR_FILE="$REPO_ROOT/.cursor/rules/specify-rules.mdc"
 QWEN_FILE="$REPO_ROOT/QWEN.md"
 AGENTS_FILE="$REPO_ROOT/AGENTS.md"

scripts/powershell/create-new-feature.ps1

@@ -3,6 +3,7 @@
 [CmdletBinding()]
 param(
     [switch]$Json,
+    [switch]$AllowExistingBranch,
     [string]$ShortName,
     [Parameter()]
     [long]$Number = 0,
@@ -15,10 +16,11 @@ $ErrorActionPreference = 'Stop'
 
 # Show help if requested
 if ($Help) {
-    Write-Host "Usage: ./create-new-feature.ps1 [-Json] [-ShortName <name>] [-Number N] [-Timestamp] <feature description>"
+    Write-Host "Usage: ./create-new-feature.ps1 [-Json] [-AllowExistingBranch] [-ShortName <name>] [-Number N] [-Timestamp] <feature description>"
     Write-Host ""
     Write-Host "Options:"
     Write-Host "  -Json               Output in JSON format"
+    Write-Host "  -AllowExistingBranch  Switch to branch if it already exists instead of failing"
     Write-Host "  -ShortName <name>   Provide a custom short name (2-4 words) for the branch"
     Write-Host "  -Number N           Specify branch number manually (overrides auto-detection)"
     Write-Host "  -Timestamp          Use timestamp prefix (YYYYMMDD-HHMMSS) instead of sequential numbering"
@@ -33,7 +35,7 @@ if ($Help) {
 
 # Check if feature description provided
 if (-not $FeatureDescription -or $FeatureDescription.Count -eq 0) {
-    Write-Error "Usage: ./create-new-feature.ps1 [-Json] [-ShortName <name>] [-Number N] [-Timestamp] <feature description>"
+    Write-Error "Usage: ./create-new-feature.ps1 [-Json] [-AllowExistingBranch] [-ShortName <name>] [-Number N] [-Timestamp] <feature description>"
     exit 1
 }
 
@@ -251,12 +253,20 @@ if ($hasGit) {
         # Check if branch already exists
         $existingBranch = git branch --list $branchName 2>$null
         if ($existingBranch) {
-            if ($Timestamp) {
+            if ($AllowExistingBranch) {
+                # Switch to the existing branch instead of failing
+                git checkout -q $branchName 2>$null | Out-Null
+                if ($LASTEXITCODE -ne 0) {
+                    Write-Error "Error: Branch '$branchName' exists but could not be checked out. Resolve any uncommitted changes or conflicts and try again."
+                    exit 1
+                }
+            } elseif ($Timestamp) {
                 Write-Error "Error: Branch '$branchName' already exists. Rerun to get a new timestamp or use a different -ShortName."
+                exit 1
             } else {
                 Write-Error "Error: Branch '$branchName' already exists. Please use a different feature name or specify a different number with -Number."
+                exit 1
             }
-            exit 1
         } else {
             Write-Error "Error: Failed to create git branch '$branchName'. Please check your git configuration and try again."
             exit 1
@@ -269,12 +279,14 @@ if ($hasGit) {
 $featureDir = Join-Path $specsDir $branchName
 New-Item -ItemType Directory -Path $featureDir -Force | Out-Null
 
-$template = Resolve-Template -TemplateName 'spec-template' -RepoRoot $repoRoot
 $specFile = Join-Path $featureDir 'spec.md'
-if ($template -and (Test-Path $template)) { 
+if (-not (Test-Path -PathType Leaf $specFile)) {
-    Copy-Item $template $specFile -Force 
+    $template = Resolve-Template -TemplateName 'spec-template' -RepoRoot $repoRoot
-} else { 
+    if ($template -and (Test-Path $template)) {
-    New-Item -ItemType File -Path $specFile | Out-Null 
+        Copy-Item $template $specFile -Force
+    } else {
+        New-Item -ItemType File -Path $specFile | Out-Null
+    }
 }
 
 # Set the SPECIFY_FEATURE environment variable for the current session

scripts/powershell/update-agent-context.ps1

@@ -46,7 +46,7 @@ $NEW_PLAN = $IMPL_PLAN
 # Agent file paths
 $CLAUDE_FILE   = Join-Path $REPO_ROOT 'CLAUDE.md'
 $GEMINI_FILE   = Join-Path $REPO_ROOT 'GEMINI.md'
-$COPILOT_FILE  = Join-Path $REPO_ROOT '.github/agents/copilot-instructions.md'
+$COPILOT_FILE  = Join-Path $REPO_ROOT '.github/copilot-instructions.md'
 $CURSOR_FILE   = Join-Path $REPO_ROOT '.cursor/rules/specify-rules.mdc'
 $QWEN_FILE     = Join-Path $REPO_ROOT 'QWEN.md'
 $AGENTS_FILE   = Join-Path $REPO_ROOT 'AGENTS.md'

src/specify_cli/__init__.py

@@ -345,6 +345,7 @@ AI_ASSISTANT_HELP = _build_ai_assistant_help()
 SCRIPT_TYPE_CHOICES = {"sh": "POSIX Shell (bash/zsh)", "ps": "PowerShell"}
 
 CLAUDE_LOCAL_PATH = Path.home() / ".claude" / "local" / "claude"
+CLAUDE_NPM_LOCAL_PATH = Path.home() / ".claude" / "local" / "node_modules" / ".bin" / "claude"
 
 BANNER = """
 ███████╗██████╗ ███████╗ ██████╗██╗███████╗██╗   ██╗
@@ -605,13 +606,15 @@ def check_tool(tool: str, tracker: StepTracker = None) -> bool:
     Returns:
         True if tool is found, False otherwise
     """
-    # Special handling for Claude CLI after `claude migrate-installer`
+    # Special handling for Claude CLI local installs
     # See: https://github.com/github/spec-kit/issues/123
-    # The migrate-installer command REMOVES the original executable from PATH
+    # See: https://github.com/github/spec-kit/issues/550
-    # and creates an alias at ~/.claude/local/claude instead
+    # Claude Code can be installed in two local paths:
-    # This path should be prioritized over other claude executables in PATH
+    #   1. ~/.claude/local/claude          (after `claude migrate-installer`)
+    #   2. ~/.claude/local/node_modules/.bin/claude  (npm-local install, e.g. via nvm)
+    # Neither path may be on the system PATH, so we check them explicitly.
     if tool == "claude":
-        if CLAUDE_LOCAL_PATH.exists() and CLAUDE_LOCAL_PATH.is_file():
+        if CLAUDE_LOCAL_PATH.is_file() or CLAUDE_NPM_LOCAL_PATH.is_file():
             if tracker:
                 tracker.complete(tool, "available")
             return True

src/specify_cli/extensions.py

@@ -25,6 +25,49 @@ import yaml
 from packaging import version as pkg_version
 from packaging.specifiers import SpecifierSet, InvalidSpecifier
 
+_FALLBACK_CORE_COMMAND_NAMES = frozenset({
+    "analyze",
+    "checklist",
+    "clarify",
+    "constitution",
+    "implement",
+    "plan",
+    "specify",
+    "tasks",
+    "taskstoissues",
+})
+EXTENSION_COMMAND_NAME_PATTERN = re.compile(r"^speckit\.([a-z0-9-]+)\.([a-z0-9-]+)$")
+
+
+def _load_core_command_names() -> frozenset[str]:
+    """Discover bundled core command names from the packaged templates.
+
+    Prefer the wheel-time ``core_pack`` bundle when present, and fall back to
+    the source checkout when running from the repository. If neither is
+    available, use the baked-in fallback set so validation still works.
+    """
+    candidate_dirs = [
+        Path(__file__).parent / "core_pack" / "commands",
+        Path(__file__).resolve().parent.parent.parent / "templates" / "commands",
+    ]
+
+    for commands_dir in candidate_dirs:
+        if not commands_dir.is_dir():
+            continue
+
+        command_names = {
+            command_file.stem
+            for command_file in commands_dir.iterdir()
+            if command_file.is_file() and command_file.suffix == ".md"
+        }
+        if command_names:
+            return frozenset(command_names)
+
+    return _FALLBACK_CORE_COMMAND_NAMES
+
+
+CORE_COMMAND_NAMES = _load_core_command_names()
+
 
 class ExtensionError(Exception):
     """Base exception for extension-related errors."""
@@ -149,7 +192,7 @@ class ExtensionManifest:
                 raise ValidationError("Command missing 'name' or 'file'")
 
             # Validate command name format
-            if not re.match(r'^speckit\.[a-z0-9-]+\.[a-z0-9-]+$', cmd["name"]):
+            if EXTENSION_COMMAND_NAME_PATTERN.match(cmd["name"]) is None:
                 raise ValidationError(
                     f"Invalid command name '{cmd['name']}': "
                     "must follow pattern 'speckit.{extension}.{command}'"
@@ -446,6 +489,126 @@ class ExtensionManager:
         self.extensions_dir = project_root / ".specify" / "extensions"
         self.registry = ExtensionRegistry(self.extensions_dir)
 
+    @staticmethod
+    def _collect_manifest_command_names(manifest: ExtensionManifest) -> Dict[str, str]:
+        """Collect command and alias names declared by a manifest.
+
+        Performs install-time validation for extension-specific constraints:
+        - commands and aliases must use the canonical `speckit.{extension}.{command}` shape
+        - commands and aliases must use this extension's namespace
+        - command namespaces must not shadow core commands
+        - duplicate command/alias names inside one manifest are rejected
+
+        Args:
+            manifest: Parsed extension manifest
+
+        Returns:
+            Mapping of declared command/alias name -> kind ("command"/"alias")
+
+        Raises:
+            ValidationError: If any declared name is invalid
+        """
+        if manifest.id in CORE_COMMAND_NAMES:
+            raise ValidationError(
+                f"Extension ID '{manifest.id}' conflicts with core command namespace '{manifest.id}'"
+            )
+
+        declared_names: Dict[str, str] = {}
+
+        for cmd in manifest.commands:
+            primary_name = cmd["name"]
+            aliases = cmd.get("aliases", [])
+
+            if aliases is None:
+                aliases = []
+            if not isinstance(aliases, list):
+                raise ValidationError(
+                    f"Aliases for command '{primary_name}' must be a list"
+                )
+
+            for kind, name in [("command", primary_name)] + [
+                ("alias", alias) for alias in aliases
+            ]:
+                if not isinstance(name, str):
+                    raise ValidationError(
+                        f"{kind.capitalize()} for command '{primary_name}' must be a string"
+                    )
+
+                match = EXTENSION_COMMAND_NAME_PATTERN.match(name)
+                if match is None:
+                    raise ValidationError(
+                        f"Invalid {kind} '{name}': "
+                        "must follow pattern 'speckit.{extension}.{command}'"
+                    )
+
+                namespace = match.group(1)
+                if namespace != manifest.id:
+                    raise ValidationError(
+                        f"{kind.capitalize()} '{name}' must use extension namespace '{manifest.id}'"
+                    )
+
+                if namespace in CORE_COMMAND_NAMES:
+                    raise ValidationError(
+                        f"{kind.capitalize()} '{name}' conflicts with core command namespace '{namespace}'"
+                    )
+
+                if name in declared_names:
+                    raise ValidationError(
+                        f"Duplicate command or alias '{name}' in extension manifest"
+                    )
+
+                declared_names[name] = kind
+
+        return declared_names
+
+    def _get_installed_command_name_map(
+        self,
+        exclude_extension_id: Optional[str] = None,
+    ) -> Dict[str, str]:
+        """Return registered command and alias names for installed extensions."""
+        installed_names: Dict[str, str] = {}
+
+        for ext_id in self.registry.keys():
+            if ext_id == exclude_extension_id:
+                continue
+
+            manifest = self.get_extension(ext_id)
+            if manifest is None:
+                continue
+
+            for cmd in manifest.commands:
+                cmd_name = cmd.get("name")
+                if isinstance(cmd_name, str):
+                    installed_names.setdefault(cmd_name, ext_id)
+
+                aliases = cmd.get("aliases", [])
+                if not isinstance(aliases, list):
+                    continue
+
+                for alias in aliases:
+                    if isinstance(alias, str):
+                        installed_names.setdefault(alias, ext_id)
+
+        return installed_names
+
+    def _validate_install_conflicts(self, manifest: ExtensionManifest) -> None:
+        """Reject installs that would shadow core or installed extension commands."""
+        declared_names = self._collect_manifest_command_names(manifest)
+        installed_names = self._get_installed_command_name_map(
+            exclude_extension_id=manifest.id
+        )
+
+        collisions = [
+            f"{name} (already provided by extension '{installed_names[name]}')"
+            for name in sorted(declared_names)
+            if name in installed_names
+        ]
+        if collisions:
+            raise ValidationError(
+                "Extension commands conflict with installed extensions:\n- "
+                + "\n- ".join(collisions)
+            )
+
     @staticmethod
     def _load_extensionignore(source_dir: Path) -> Optional[Callable[[str, List[str]], Set[str]]]:
         """Load .extensionignore and return an ignore function for shutil.copytree.
@@ -861,6 +1024,9 @@ class ExtensionManager:
                 f"Use 'specify extension remove {manifest.id}' first."
             )
 
+        # Reject manifests that would shadow core commands or installed extensions.
+        self._validate_install_conflicts(manifest)
+
         # Install extension
         dest_dir = self.extensions_dir / manifest.id
         if dest_dir.exists():

tests/test_check_tool.py

@@ -0,0 +1,96 @@
+"""Tests for check_tool() — Claude Code CLI detection across install methods.
+
+Covers issue https://github.com/github/spec-kit/issues/550:
+  `specify check` reports "Claude Code CLI (not found)" even when claude is
+  installed via npm-local (the default `claude` installer path).
+"""
+
+from unittest.mock import patch, MagicMock
+
+from specify_cli import check_tool
+
+
+class TestCheckToolClaude:
+    """Claude CLI detection must work for all install methods."""
+
+    def test_detected_via_migrate_installer_path(self, tmp_path):
+        """claude migrate-installer puts binary at ~/.claude/local/claude."""
+        fake_claude = tmp_path / "claude"
+        fake_claude.touch()
+
+        # Ensure npm-local path is missing so we only exercise migrate-installer path
+        fake_missing = tmp_path / "nonexistent" / "claude"
+
+        with patch("specify_cli.CLAUDE_LOCAL_PATH", fake_claude), \
+             patch("specify_cli.CLAUDE_NPM_LOCAL_PATH", fake_missing), \
+             patch("shutil.which", return_value=None):
+            assert check_tool("claude") is True
+
+    def test_detected_via_npm_local_path(self, tmp_path):
+        """npm-local install puts binary at ~/.claude/local/node_modules/.bin/claude."""
+        fake_npm_claude = tmp_path / "node_modules" / ".bin" / "claude"
+        fake_npm_claude.parent.mkdir(parents=True)
+        fake_npm_claude.touch()
+
+        # Neither the migrate-installer path nor PATH has claude
+        fake_migrate = tmp_path / "nonexistent" / "claude"
+
+        with patch("specify_cli.CLAUDE_LOCAL_PATH", fake_migrate), \
+             patch("specify_cli.CLAUDE_NPM_LOCAL_PATH", fake_npm_claude), \
+             patch("shutil.which", return_value=None):
+            assert check_tool("claude") is True
+
+    def test_detected_via_path(self, tmp_path):
+        """claude on PATH (global npm install) should still work."""
+        fake_missing = tmp_path / "nonexistent" / "claude"
+
+        with patch("specify_cli.CLAUDE_LOCAL_PATH", fake_missing), \
+             patch("specify_cli.CLAUDE_NPM_LOCAL_PATH", fake_missing), \
+             patch("shutil.which", return_value="/usr/local/bin/claude"):
+            assert check_tool("claude") is True
+
+    def test_not_found_when_nowhere(self, tmp_path):
+        """Should return False when claude is genuinely not installed."""
+        fake_missing = tmp_path / "nonexistent" / "claude"
+
+        with patch("specify_cli.CLAUDE_LOCAL_PATH", fake_missing), \
+             patch("specify_cli.CLAUDE_NPM_LOCAL_PATH", fake_missing), \
+             patch("shutil.which", return_value=None):
+            assert check_tool("claude") is False
+
+    def test_tracker_updated_on_npm_local_detection(self, tmp_path):
+        """StepTracker should be marked 'available' for npm-local installs."""
+        fake_npm_claude = tmp_path / "node_modules" / ".bin" / "claude"
+        fake_npm_claude.parent.mkdir(parents=True)
+        fake_npm_claude.touch()
+
+        fake_missing = tmp_path / "nonexistent" / "claude"
+        tracker = MagicMock()
+
+        with patch("specify_cli.CLAUDE_LOCAL_PATH", fake_missing), \
+             patch("specify_cli.CLAUDE_NPM_LOCAL_PATH", fake_npm_claude), \
+             patch("shutil.which", return_value=None):
+            result = check_tool("claude", tracker=tracker)
+
+        assert result is True
+        tracker.complete.assert_called_once_with("claude", "available")
+
+
+class TestCheckToolOther:
+    """Non-Claude tools should be unaffected by the fix."""
+
+    def test_git_detected_via_path(self):
+        with patch("shutil.which", return_value="/usr/bin/git"):
+            assert check_tool("git") is True
+
+    def test_missing_tool(self):
+        with patch("shutil.which", return_value=None):
+            assert check_tool("nonexistent-tool") is False
+
+    def test_kiro_fallback(self):
+        """kiro-cli detection should try both kiro-cli and kiro."""
+        def fake_which(name):
+            return "/usr/bin/kiro" if name == "kiro" else None
+
+        with patch("shutil.which", side_effect=fake_which):
+            assert check_tool("kiro-cli") is True

tests/test_extensions.py

@@ -18,6 +18,7 @@ from datetime import datetime, timezone
 
 from specify_cli.extensions import (
     CatalogEntry,
+    CORE_COMMAND_NAMES,
     ExtensionManifest,
     ExtensionRegistry,
     ExtensionManager,
@@ -63,7 +64,7 @@ def valid_manifest_data():
         "provides": {
             "commands": [
                 {
-                    "name": "speckit.test.hello",
+                    "name": "speckit.test-ext.hello",
                     "file": "commands/hello.md",
                     "description": "Test command",
                 }
@@ -71,7 +72,7 @@ def valid_manifest_data():
         },
         "hooks": {
             "after_tasks": {
-                "command": "speckit.test.hello",
+                "command": "speckit.test-ext.hello",
                 "optional": True,
                 "prompt": "Run test?",
             }
@@ -189,7 +190,18 @@ class TestExtensionManifest:
         assert manifest.version == "1.0.0"
         assert manifest.description == "A test extension"
         assert len(manifest.commands) == 1
-        assert manifest.commands[0]["name"] == "speckit.test.hello"
+        assert manifest.commands[0]["name"] == "speckit.test-ext.hello"
+
+    def test_core_command_names_match_bundled_templates(self):
+        """Core command reservations should stay aligned with bundled templates."""
+        commands_dir = Path(__file__).resolve().parent.parent / "templates" / "commands"
+        expected = {
+            command_file.stem
+            for command_file in commands_dir.iterdir()
+            if command_file.is_file() and command_file.suffix == ".md"
+        }
+
+        assert CORE_COMMAND_NAMES == expected
 
     def test_missing_required_field(self, temp_dir):
         """Test manifest missing required field."""
@@ -589,6 +601,172 @@ class TestExtensionManager:
         with pytest.raises(ExtensionError, match="already installed"):
             manager.install_from_directory(extension_dir, "0.1.0", register_commands=False)
 
+    def test_install_rejects_extension_id_in_core_namespace(self, temp_dir, project_dir):
+        """Install should reject extension IDs that shadow core commands."""
+        import yaml
+
+        ext_dir = temp_dir / "analyze-ext"
+        ext_dir.mkdir()
+        (ext_dir / "commands").mkdir()
+
+        manifest_data = {
+            "schema_version": "1.0",
+            "extension": {
+                "id": "analyze",
+                "name": "Analyze Extension",
+                "version": "1.0.0",
+                "description": "Test",
+            },
+            "requires": {"speckit_version": ">=0.1.0"},
+            "provides": {
+                "commands": [
+                    {
+                        "name": "speckit.analyze.extra",
+                        "file": "commands/cmd.md",
+                    }
+                ]
+            },
+        }
+
+        (ext_dir / "extension.yml").write_text(yaml.dump(manifest_data))
+        (ext_dir / "commands" / "cmd.md").write_text("---\ndescription: Test\n---\n\nBody")
+
+        manager = ExtensionManager(project_dir)
+        with pytest.raises(ValidationError, match="conflicts with core command namespace"):
+            manager.install_from_directory(ext_dir, "0.1.0", register_commands=False)
+
+    def test_install_rejects_alias_without_extension_namespace(self, temp_dir, project_dir):
+        """Install should reject legacy short aliases that can shadow core commands."""
+        import yaml
+
+        ext_dir = temp_dir / "alias-shortcut"
+        ext_dir.mkdir()
+        (ext_dir / "commands").mkdir()
+
+        manifest_data = {
+            "schema_version": "1.0",
+            "extension": {
+                "id": "alias-shortcut",
+                "name": "Alias Shortcut",
+                "version": "1.0.0",
+                "description": "Test",
+            },
+            "requires": {"speckit_version": ">=0.1.0"},
+            "provides": {
+                "commands": [
+                    {
+                        "name": "speckit.alias-shortcut.cmd",
+                        "file": "commands/cmd.md",
+                        "aliases": ["speckit.shortcut"],
+                    }
+                ]
+            },
+        }
+
+        (ext_dir / "extension.yml").write_text(yaml.dump(manifest_data))
+        (ext_dir / "commands" / "cmd.md").write_text("---\ndescription: Test\n---\n\nBody")
+
+        manager = ExtensionManager(project_dir)
+        with pytest.raises(ValidationError, match="Invalid alias 'speckit.shortcut'"):
+            manager.install_from_directory(ext_dir, "0.1.0", register_commands=False)
+
+    def test_install_rejects_namespace_squatting(self, temp_dir, project_dir):
+        """Install should reject commands and aliases outside the extension namespace."""
+        import yaml
+
+        ext_dir = temp_dir / "squat-ext"
+        ext_dir.mkdir()
+        (ext_dir / "commands").mkdir()
+
+        manifest_data = {
+            "schema_version": "1.0",
+            "extension": {
+                "id": "squat-ext",
+                "name": "Squat Extension",
+                "version": "1.0.0",
+                "description": "Test",
+            },
+            "requires": {"speckit_version": ">=0.1.0"},
+            "provides": {
+                "commands": [
+                    {
+                        "name": "speckit.other-ext.cmd",
+                        "file": "commands/cmd.md",
+                        "aliases": ["speckit.squat-ext.ok"],
+                    }
+                ]
+            },
+        }
+
+        (ext_dir / "extension.yml").write_text(yaml.dump(manifest_data))
+        (ext_dir / "commands" / "cmd.md").write_text("---\ndescription: Test\n---\n\nBody")
+
+        manager = ExtensionManager(project_dir)
+        with pytest.raises(ValidationError, match="must use extension namespace 'squat-ext'"):
+            manager.install_from_directory(ext_dir, "0.1.0", register_commands=False)
+
+    def test_install_rejects_command_collision_with_installed_extension(self, temp_dir, project_dir):
+        """Install should reject names already claimed by an installed legacy extension."""
+        import yaml
+
+        first_dir = temp_dir / "ext-one"
+        first_dir.mkdir()
+        (first_dir / "commands").mkdir()
+        first_manifest = {
+            "schema_version": "1.0",
+            "extension": {
+                "id": "ext-one",
+                "name": "Extension One",
+                "version": "1.0.0",
+                "description": "Test",
+            },
+            "requires": {"speckit_version": ">=0.1.0"},
+            "provides": {
+                "commands": [
+                    {
+                        "name": "speckit.ext-one.sync",
+                        "file": "commands/cmd.md",
+                        "aliases": ["speckit.shared.sync"],
+                    }
+                ]
+            },
+        }
+        (first_dir / "extension.yml").write_text(yaml.dump(first_manifest))
+        (first_dir / "commands" / "cmd.md").write_text("---\ndescription: Test\n---\n\nBody")
+        installed_ext_dir = project_dir / ".specify" / "extensions" / "ext-one"
+        installed_ext_dir.parent.mkdir(parents=True, exist_ok=True)
+        shutil.copytree(first_dir, installed_ext_dir)
+
+        second_dir = temp_dir / "ext-two"
+        second_dir.mkdir()
+        (second_dir / "commands").mkdir()
+        second_manifest = {
+            "schema_version": "1.0",
+            "extension": {
+                "id": "shared",
+                "name": "Shared Extension",
+                "version": "1.0.0",
+                "description": "Test",
+            },
+            "requires": {"speckit_version": ">=0.1.0"},
+            "provides": {
+                "commands": [
+                    {
+                        "name": "speckit.shared.sync",
+                        "file": "commands/cmd.md",
+                    }
+                ]
+            },
+        }
+        (second_dir / "extension.yml").write_text(yaml.dump(second_manifest))
+        (second_dir / "commands" / "cmd.md").write_text("---\ndescription: Test\n---\n\nBody")
+
+        manager = ExtensionManager(project_dir)
+        manager.registry.add("ext-one", {"version": "1.0.0", "source": "local"})
+
+        with pytest.raises(ValidationError, match="already provided by extension 'ext-one'"):
+            manager.install_from_directory(second_dir, "0.1.0", register_commands=False)
+
     def test_remove_extension(self, extension_dir, project_dir):
         """Test removing an installed extension."""
         manager = ExtensionManager(project_dir)
@@ -852,10 +1030,10 @@ $ARGUMENTS
         )
 
         assert len(registered) == 1
-        assert "speckit.test.hello" in registered
+        assert "speckit.test-ext.hello" in registered
 
         # Check command file was created
-        cmd_file = claude_dir / "speckit.test.hello.md"
+        cmd_file = claude_dir / "speckit.test-ext.hello.md"
         assert cmd_file.exists()
 
         content = cmd_file.read_text()
@@ -885,9 +1063,9 @@ $ARGUMENTS
             "provides": {
                 "commands": [
                     {
-                        "name": "speckit.alias.cmd",
+                        "name": "speckit.ext-alias.cmd",
                         "file": "commands/cmd.md",
-                        "aliases": ["speckit.shortcut"],
+                        "aliases": ["speckit.ext-alias.shortcut"],
                     }
                 ]
             },
@@ -907,10 +1085,10 @@ $ARGUMENTS
         registered = registrar.register_commands_for_claude(manifest, ext_dir, project_dir)
 
         assert len(registered) == 2
-        assert "speckit.alias.cmd" in registered
+        assert "speckit.ext-alias.cmd" in registered
-        assert "speckit.shortcut" in registered
+        assert "speckit.ext-alias.shortcut" in registered
-        assert (claude_dir / "speckit.alias.cmd.md").exists()
+        assert (claude_dir / "speckit.ext-alias.cmd.md").exists()
-        assert (claude_dir / "speckit.shortcut.md").exists()
+        assert (claude_dir / "speckit.ext-alias.shortcut.md").exists()
 
     def test_unregister_commands_for_codex_skills_uses_mapped_names(self, project_dir):
         """Codex skill cleanup should use the same mapped names as registration."""
@@ -951,11 +1129,11 @@ $ARGUMENTS
         registrar = CommandRegistrar()
         registrar.register_commands_for_agent("codex", manifest, extension_dir, project_dir)
 
-        skill_file = skills_dir / "speckit-test-hello" / "SKILL.md"
+        skill_file = skills_dir / "speckit-test-ext-hello" / "SKILL.md"
         assert skill_file.exists()
 
         content = skill_file.read_text()
-        assert "name: speckit-test-hello" in content
+        assert "name: speckit-test-ext-hello" in content
         assert "description: Test hello command" in content
         assert "compatibility:" in content
         assert "metadata:" in content
@@ -982,7 +1160,7 @@ $ARGUMENTS
             "provides": {
                 "commands": [
                     {
-                        "name": "speckit.test.plan",
+                        "name": "speckit.ext-scripted.plan",
                         "file": "commands/plan.md",
                         "description": "Scripted command",
                     }
@@ -1020,7 +1198,7 @@ Agent __AGENT__
         registrar = CommandRegistrar()
         registrar.register_commands_for_agent("codex", manifest, ext_dir, project_dir)
 
-        skill_file = skills_dir / "speckit-test-plan" / "SKILL.md"
+        skill_file = skills_dir / "speckit-ext-scripted-plan" / "SKILL.md"
         assert skill_file.exists()
 
         content = skill_file.read_text()
@@ -1051,9 +1229,9 @@ Agent __AGENT__
             "provides": {
                 "commands": [
                     {
-                        "name": "speckit.alias.cmd",
+                        "name": "speckit.ext-alias-skill.cmd",
                         "file": "commands/cmd.md",
-                        "aliases": ["speckit.shortcut"],
+                        "aliases": ["speckit.ext-alias-skill.shortcut"],
                     }
                 ]
             },
@@ -1070,13 +1248,13 @@ Agent __AGENT__
         registrar = CommandRegistrar()
         registrar.register_commands_for_agent("codex", manifest, ext_dir, project_dir)
 
-        primary = skills_dir / "speckit-alias-cmd" / "SKILL.md"
+        primary = skills_dir / "speckit-ext-alias-skill-cmd" / "SKILL.md"
-        alias = skills_dir / "speckit-shortcut" / "SKILL.md"
+        alias = skills_dir / "speckit-ext-alias-skill-shortcut" / "SKILL.md"
 
         assert primary.exists()
         assert alias.exists()
-        assert "name: speckit-alias-cmd" in primary.read_text()
+        assert "name: speckit-ext-alias-skill-cmd" in primary.read_text()
-        assert "name: speckit-shortcut" in alias.read_text()
+        assert "name: speckit-ext-alias-skill-shortcut" in alias.read_text()
 
     def test_codex_skill_registration_uses_fallback_script_variant_without_init_options(
         self, project_dir, temp_dir
@@ -1100,7 +1278,7 @@ Agent __AGENT__
             "provides": {
                 "commands": [
                     {
-                        "name": "speckit.fallback.plan",
+                        "name": "speckit.ext-script-fallback.plan",
                         "file": "commands/plan.md",
                     }
                 ]
@@ -1132,7 +1310,7 @@ Then {AGENT_SCRIPT}
         registrar = CommandRegistrar()
         registrar.register_commands_for_agent("codex", manifest, ext_dir, project_dir)
 
-        skill_file = skills_dir / "speckit-fallback-plan" / "SKILL.md"
+        skill_file = skills_dir / "speckit-ext-script-fallback-plan" / "SKILL.md"
         assert skill_file.exists()
 
         content = skill_file.read_text()
@@ -1163,7 +1341,7 @@ Then {AGENT_SCRIPT}
             "provides": {
                 "commands": [
                     {
-                        "name": "speckit.list.plan",
+                        "name": "speckit.ext-script-list-init.plan",
                         "file": "commands/plan.md",
                     }
                 ]
@@ -1194,7 +1372,7 @@ Run {SCRIPT}
         registrar = CommandRegistrar()
         registrar.register_commands_for_agent("codex", manifest, ext_dir, project_dir)
 
-        content = (skills_dir / "speckit-list-plan" / "SKILL.md").read_text()
+        content = (skills_dir / "speckit-ext-script-list-init-plan" / "SKILL.md").read_text()
         assert '.specify/scripts/bash/setup-plan.sh --json "$ARGUMENTS"' in content
 
     def test_codex_skill_registration_fallback_prefers_powershell_on_windows(
@@ -1221,7 +1399,7 @@ Run {SCRIPT}
             "provides": {
                 "commands": [
                     {
-                        "name": "speckit.windows.plan",
+                        "name": "speckit.ext-script-windows-fallback.plan",
                         "file": "commands/plan.md",
                     }
                 ]
@@ -1253,7 +1431,7 @@ Then {AGENT_SCRIPT}
         registrar = CommandRegistrar()
         registrar.register_commands_for_agent("codex", manifest, ext_dir, project_dir)
 
-        skill_file = skills_dir / "speckit-windows-plan" / "SKILL.md"
+        skill_file = skills_dir / "speckit-ext-script-windows-fallback-plan" / "SKILL.md"
         assert skill_file.exists()
 
         content = skill_file.read_text()
@@ -1275,14 +1453,14 @@ Then {AGENT_SCRIPT}
         )
 
         assert len(registered) == 1
-        assert "speckit.test.hello" in registered
+        assert "speckit.test-ext.hello" in registered
 
         # Verify command file uses .agent.md extension
-        cmd_file = agents_dir / "speckit.test.hello.agent.md"
+        cmd_file = agents_dir / "speckit.test-ext.hello.agent.md"
         assert cmd_file.exists()
 
         # Verify NO plain .md file was created
-        plain_md_file = agents_dir / "speckit.test.hello.md"
+        plain_md_file = agents_dir / "speckit.test-ext.hello.md"
         assert not plain_md_file.exists()
 
         content = cmd_file.read_text()
@@ -1302,12 +1480,12 @@ Then {AGENT_SCRIPT}
         )
 
         # Verify companion .prompt.md file exists
-        prompt_file = project_dir / ".github" / "prompts" / "speckit.test.hello.prompt.md"
+        prompt_file = project_dir / ".github" / "prompts" / "speckit.test-ext.hello.prompt.md"
         assert prompt_file.exists()
 
         # Verify content has correct agent frontmatter
         content = prompt_file.read_text()
-        assert content == "---\nagent: speckit.test.hello\n---\n"
+        assert content == "---\nagent: speckit.test-ext.hello\n---\n"
 
     def test_copilot_aliases_get_companion_prompts(self, project_dir, temp_dir):
         """Test that aliases also get companion .prompt.md files for Copilot."""
@@ -1328,9 +1506,9 @@ Then {AGENT_SCRIPT}
             "provides": {
                 "commands": [
                     {
-                        "name": "speckit.alias-copilot.cmd",
+                        "name": "speckit.ext-alias-copilot.cmd",
                         "file": "commands/cmd.md",
-                        "aliases": ["speckit.shortcut-copilot"],
+                        "aliases": ["speckit.ext-alias-copilot.shortcut"],
                     }
                 ]
             },
@@ -1357,8 +1535,8 @@ Then {AGENT_SCRIPT}
 
         # Both primary and alias get companion .prompt.md
         prompts_dir = project_dir / ".github" / "prompts"
-        assert (prompts_dir / "speckit.alias-copilot.cmd.prompt.md").exists()
+        assert (prompts_dir / "speckit.ext-alias-copilot.cmd.prompt.md").exists()
-        assert (prompts_dir / "speckit.shortcut-copilot.prompt.md").exists()
+        assert (prompts_dir / "speckit.ext-alias-copilot.shortcut.prompt.md").exists()
 
     def test_non_copilot_agent_no_companion_file(self, extension_dir, project_dir):
         """Test that non-copilot agents do NOT create .prompt.md files."""
@@ -1431,7 +1609,7 @@ class TestIntegration:
         assert installed[0]["id"] == "test-ext"
 
         # Verify command registered
-        cmd_file = project_dir / ".claude" / "commands" / "speckit.test.hello.md"
+        cmd_file = project_dir / ".claude" / "commands" / "speckit.test-ext.hello.md"
         assert cmd_file.exists()
 
         # Verify registry has registered commands (now a dict keyed by agent)
@@ -1439,7 +1617,7 @@ class TestIntegration:
         registered_commands = metadata["registered_commands"]
         # Check that the command is registered for at least one agent
         assert any(
-            "speckit.test.hello" in cmds
+            "speckit.test-ext.hello" in cmds
             for cmds in registered_commands.values()
         )
 
@@ -1465,8 +1643,8 @@ class TestIntegration:
         assert "copilot" in metadata["registered_commands"]
 
         # Verify files exist before cleanup
-        agent_file = agents_dir / "speckit.test.hello.agent.md"
+        agent_file = agents_dir / "speckit.test-ext.hello.agent.md"
-        prompt_file = project_dir / ".github" / "prompts" / "speckit.test.hello.prompt.md"
+        prompt_file = project_dir / ".github" / "prompts" / "speckit.test-ext.hello.prompt.md"
         assert agent_file.exists()
         assert prompt_file.exists()
 
@@ -2776,7 +2954,7 @@ class TestExtensionUpdateCLI:
             "provides": {
                 "commands": [
                     {
-                        "name": "speckit.test.hello",
+                        "name": "speckit.test-ext.hello",
                         "file": "commands/hello.md",
                         "description": "Test command",
                     }
@@ -2784,7 +2962,7 @@ class TestExtensionUpdateCLI:
             },
             "hooks": {
                 "after_tasks": {
-                    "command": "speckit.test.hello",
+                    "command": "speckit.test-ext.hello",
                     "optional": True,
                 }
             },
@@ -2813,7 +2991,7 @@ class TestExtensionUpdateCLI:
                 "description": "A test extension",
             },
             "requires": {"speckit_version": ">=0.1.0"},
-            "provides": {"commands": [{"name": "speckit.test.hello", "file": "commands/hello.md"}]},
+            "provides": {"commands": [{"name": "speckit.test-ext.hello", "file": "commands/hello.md"}]},
         }
 
         with zipfile.ZipFile(zip_path, "w") as zf:
@@ -3442,15 +3620,15 @@ class TestHookInvocationRendering:
             [
                 {
                     "extension": "test-ext",
-                    "command": "speckit.test.hello",
+                    "command": "speckit.test-ext.hello",
                     "optional": False,
                 }
             ],
         )
 
-        assert "Executing: `/skill:speckit-test-hello`" in message
+        assert "Executing: `/skill:speckit-test-ext-hello`" in message
-        assert "EXECUTE_COMMAND: speckit.test.hello" in message
+        assert "EXECUTE_COMMAND: speckit.test-ext.hello" in message
-        assert "EXECUTE_COMMAND_INVOCATION: /skill:speckit-test-hello" in message
+        assert "EXECUTE_COMMAND_INVOCATION: /skill:speckit-test-ext-hello" in message
 
     def test_hook_executor_caches_init_options_lookup(self, project_dir, monkeypatch):
         """Init options should be loaded once per executor instance."""

tests/test_timestamp_branches.py

@@ -269,3 +269,146 @@ class TestE2EFlow:
         assert (git_repo / "specs" / branch).is_dir()
         val = source_and_call(f'check_feature_branch "{branch}" "true"')
         assert val.returncode == 0
+
+
+# ── Allow Existing Branch Tests ──────────────────────────────────────────────
+
+
+class TestAllowExistingBranch:
+    def test_allow_existing_switches_to_branch(self, git_repo: Path):
+        """T006: Pre-create branch, verify script switches to it."""
+        subprocess.run(
+            ["git", "checkout", "-b", "004-pre-exist"],
+            cwd=git_repo, check=True, capture_output=True,
+        )
+        subprocess.run(
+            ["git", "checkout", "-"],
+            cwd=git_repo, check=True, capture_output=True,
+        )
+        result = run_script(
+            git_repo, "--allow-existing-branch", "--short-name", "pre-exist",
+            "--number", "4", "Pre-existing feature",
+        )
+        assert result.returncode == 0, result.stderr
+        current = subprocess.run(
+            ["git", "rev-parse", "--abbrev-ref", "HEAD"],
+            cwd=git_repo, capture_output=True, text=True,
+        ).stdout.strip()
+        assert current == "004-pre-exist", f"expected 004-pre-exist, got {current}"
+
+    def test_allow_existing_already_on_branch(self, git_repo: Path):
+        """T007: Verify success when already on the target branch."""
+        subprocess.run(
+            ["git", "checkout", "-b", "005-already-on"],
+            cwd=git_repo, check=True, capture_output=True,
+        )
+        result = run_script(
+            git_repo, "--allow-existing-branch", "--short-name", "already-on",
+            "--number", "5", "Already on branch",
+        )
+        assert result.returncode == 0, result.stderr
+
+    def test_allow_existing_creates_spec_dir(self, git_repo: Path):
+        """T008: Verify spec directory created on existing branch."""
+        subprocess.run(
+            ["git", "checkout", "-b", "006-spec-dir"],
+            cwd=git_repo, check=True, capture_output=True,
+        )
+        subprocess.run(
+            ["git", "checkout", "-"],
+            cwd=git_repo, check=True, capture_output=True,
+        )
+        result = run_script(
+            git_repo, "--allow-existing-branch", "--short-name", "spec-dir",
+            "--number", "6", "Spec dir feature",
+        )
+        assert result.returncode == 0, result.stderr
+        assert (git_repo / "specs" / "006-spec-dir").is_dir()
+        assert (git_repo / "specs" / "006-spec-dir" / "spec.md").exists()
+
+    def test_without_flag_still_errors(self, git_repo: Path):
+        """T009: Verify backwards compatibility (error without flag)."""
+        subprocess.run(
+            ["git", "checkout", "-b", "007-no-flag"],
+            cwd=git_repo, check=True, capture_output=True,
+        )
+        subprocess.run(
+            ["git", "checkout", "-"],
+            cwd=git_repo, check=True, capture_output=True,
+        )
+        result = run_script(
+            git_repo, "--short-name", "no-flag", "--number", "7", "No flag feature",
+        )
+        assert result.returncode != 0, "should fail without --allow-existing-branch"
+        assert "already exists" in result.stderr
+
+    def test_allow_existing_no_overwrite_spec(self, git_repo: Path):
+        """T010: Pre-create spec.md with content, verify it is preserved."""
+        subprocess.run(
+            ["git", "checkout", "-b", "008-no-overwrite"],
+            cwd=git_repo, check=True, capture_output=True,
+        )
+        spec_dir = git_repo / "specs" / "008-no-overwrite"
+        spec_dir.mkdir(parents=True)
+        spec_file = spec_dir / "spec.md"
+        spec_file.write_text("# My custom spec content\n")
+        subprocess.run(
+            ["git", "checkout", "-"],
+            cwd=git_repo, check=True, capture_output=True,
+        )
+        result = run_script(
+            git_repo, "--allow-existing-branch", "--short-name", "no-overwrite",
+            "--number", "8", "No overwrite feature",
+        )
+        assert result.returncode == 0, result.stderr
+        assert spec_file.read_text() == "# My custom spec content\n"
+
+    def test_allow_existing_creates_branch_if_not_exists(self, git_repo: Path):
+        """T011: Verify normal creation when branch doesn't exist."""
+        result = run_script(
+            git_repo, "--allow-existing-branch", "--short-name", "new-branch",
+            "New branch feature",
+        )
+        assert result.returncode == 0, result.stderr
+        current = subprocess.run(
+            ["git", "rev-parse", "--abbrev-ref", "HEAD"],
+            cwd=git_repo, capture_output=True, text=True,
+        ).stdout.strip()
+        assert "new-branch" in current
+
+    def test_allow_existing_with_json(self, git_repo: Path):
+        """T012: Verify JSON output is correct."""
+        import json
+
+        subprocess.run(
+            ["git", "checkout", "-b", "009-json-test"],
+            cwd=git_repo, check=True, capture_output=True,
+        )
+        subprocess.run(
+            ["git", "checkout", "-"],
+            cwd=git_repo, check=True, capture_output=True,
+        )
+        result = run_script(
+            git_repo, "--allow-existing-branch", "--json", "--short-name", "json-test",
+            "--number", "9", "JSON test",
+        )
+        assert result.returncode == 0, result.stderr
+        data = json.loads(result.stdout)
+        assert data["BRANCH_NAME"] == "009-json-test"
+
+    def test_allow_existing_no_git(self, no_git_dir: Path):
+        """T013: Verify flag is silently ignored in non-git repos."""
+        result = run_script(
+            no_git_dir, "--allow-existing-branch", "--short-name", "no-git",
+            "No git feature",
+        )
+        assert result.returncode == 0, result.stderr
+
+
+class TestAllowExistingBranchPowerShell:
+    def test_powershell_supports_allow_existing_branch_flag(self):
+        """Static guard: PS script exposes and uses -AllowExistingBranch."""
+        contents = CREATE_FEATURE_PS.read_text(encoding="utf-8")
+        assert "-AllowExistingBranch" in contents
+        # Ensure the flag is referenced in script logic, not just declared
+        assert "AllowExistingBranch" in contents.replace("-AllowExistingBranch", "")