fix: pin click>=8.1 to prevent Python 3.14/Homebrew env isolation crash (#1648)

* fix: pin click>=8.1 to prevent Python 3.14/Homebrew env isolation failures

Fixes #1631. When uv installs specify-cli on macOS with Homebrew Python
3.14, the virtual environment can fail to fully isolate from the system
site-packages, causing Homebrew's click to be loaded instead of the one
uv installed. If that system click is older than 8.1, it lacks the `ctx`
keyword argument in `ParamType.get_metavar()`, which typer 0.24.0 requires,
resulting in:

  TypeError: ParamType.get_metavar() got an unexpected keyword argument 'ctx'

Adding an explicit `click>=8.1` dependency gives uv a hard constraint so
the correct version is always resolved and installed.

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

* Update CHANGELOG.md

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

---------

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,22 @@
+## Description
+
+<!-- What does this PR do? Why is it needed? -->
+
+## Testing
+
+<!-- How did you test your changes? -->
+
+- [ ] Tested locally with `uv run specify --help`
+- [ ] Ran existing tests with `uv sync && uv run pytest`
+- [ ] Tested with a sample project (if applicable)
+
+## AI Disclosure
+
+<!-- Per our Contributing guidelines, AI assistance must be disclosed. -->
+<!-- See: https://github.com/github/spec-kit/blob/main/CONTRIBUTING.md#ai-contributions-in-spec-kit -->
+
+- [ ] I **did not** use AI assistance for this contribution
+- [ ] I **did** use AI assistance (describe below)
+
+<!-- If you used AI, briefly describe how (e.g., "Code generated by Copilot", "Consulted ChatGPT for approach"): -->
+

.github/workflows/codeql.yml

@@ -0,0 +1,32 @@
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      security-events: write
+      contents: read
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'actions', 'python' ]
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v4
+        with:
+          languages: ${{ matrix.language }}
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v4
+        with:
+          category: "/language:${{ matrix.language }}"

.github/workflows/release.yml

@@ -6,6 +6,7 @@ on:
     paths:
       - 'memory/**'
       - 'scripts/**'
+      - 'src/**'
       - 'templates/**'
       - '.github/workflows/**'
   workflow_dispatch:

.github/workflows/test.yml

@@ -0,0 +1,50 @@
+name: Test & Lint Python
+
+permissions:
+  contents: read
+
+on:
+  push:
+    branches: ["main"]
+  pull_request:
+
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.13"
+
+      - name: Run ruff check
+        run: uvx ruff check src/
+
+  pytest:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.11", "3.12", "3.13"]
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: uv sync --extra test
+
+      - name: Run tests
+        run: uv run pytest

CHANGELOG.md

@@ -2,11 +2,33 @@
 
 <!-- markdownlint-disable MD024 -->
 
+
 All notable changes to the Specify CLI and templates are documented here.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.1.2] - 2026-02-20
+
+### Fixed
+
+- **Python 3.14 / Homebrew compatibility**: Added explicit `click>=8.1` dependency so the resolver always selects a Click version compatible with Python 3.14 and avoids errors such as `TypeError: ParamType.get_metavar() got an unexpected keyword argument 'ctx'` when an older Click would otherwise be used. Note that broader uv/Homebrew environment isolation or `sys.path` bleed issues (see [#1631](https://github.com/github/spec-kit/issues/1631)) may still require environment-level workarounds.
+
+## [0.1.1] - 2026-02-13
+
+### Added
+
+- **Agent Skills Installation**: New `--ai-skills` CLI option to install Prompt.MD templates as agent skills following [agentskills.io specification](https://agentskills.io/specification)
+  - Skills are installed to agent-specific directories (e.g., `.claude/skills/`, `.gemini/skills/`, `.github/skills/`)
+  - Codex uses `.agents/skills/` following Codex agent directory conventions
+  - Default fallback directory is `.agents/skills/` for agents without a specific mapping
+  - Requires `--ai` flag to be specified
+  - Converts all 9 spec-kit command templates (specify, plan, tasks, implement, analyze, clarify, constitution, checklist, taskstoissues) to properly formatted SKILL.md files
+  - **New projects**: command files are not installed when `--ai-skills` is used (skills replace commands)
+  - **Existing repos** (`--here`): pre-existing command files are preserved — no breaking changes
+  - `pyyaml` dependency (already present) used for YAML frontmatter parsing
+- **Unit tests** for `install_ai_skills`, `_get_skills_dir`, and `--ai-skills` CLI validation (51 test cases covering all 18 supported agents)
+
 ## [0.1.0] - 2026-01-28
 
 ### Added

README.md

@@ -188,6 +188,7 @@ The `specify` command supports the following options:
 | `--skip-tls`           | Flag     | Skip SSL/TLS verification (not recommended)                                                                                                                                                  |
 | `--debug`              | Flag     | Enable detailed debug output for troubleshooting                                                                                                                                             |
 | `--github-token`       | Option   | GitHub token for API requests (or set GH_TOKEN/GITHUB_TOKEN env variable)                                                                                                                    |
+| `--ai-skills`          | Flag     | Install Prompt.MD templates as agent skills in agent-specific `skills/` directory (requires `--ai`)                                                                                          |
 
 ### Examples
 
@@ -238,6 +239,12 @@ specify init my-project --ai claude --debug
 # Use GitHub token for API requests (helpful for corporate environments)
 specify init my-project --ai claude --github-token ghp_your_token_here
 
+# Install agent skills with the project
+specify init my-project --ai claude --ai-skills
+
+# Initialize in current directory with agent skills
+specify init --here --ai gemini --ai-skills
+
 # Check system requirements
 specify check
 ```

pyproject.toml

@@ -1,10 +1,11 @@
 [project]
 name = "specify-cli"
-version = "0.1.0"
+version = "0.1.2"
 description = "Specify CLI, part of GitHub Spec Kit. A tool to bootstrap your projects for Spec-Driven Development (SDD)."
 requires-python = ">=3.11"
 dependencies = [
     "typer",
+    "click>=8.1",
     "rich",
     "httpx[socks]",
     "platformdirs",

src/specify_cli/__init__.py

@@ -32,6 +32,7 @@ import tempfile
 import shutil
 import shlex
 import json
+import yaml
 from pathlib import Path
 from typing import Optional, Tuple
 
@@ -669,7 +670,7 @@ def download_template_from_github(ai_assistant: str, download_dir: Path, *, scri
         except ValueError as je:
             raise RuntimeError(f"Failed to parse release JSON: {je}\nRaw (truncated 400): {response.text[:400]}")
     except Exception as e:
-        console.print(f"[red]Error fetching release information[/red]")
+        console.print("[red]Error fetching release information[/red]")
         console.print(Panel(str(e), title="Fetch Error", border_style="red"))
         raise typer.Exit(1)
 
@@ -699,7 +700,7 @@ def download_template_from_github(ai_assistant: str, download_dir: Path, *, scri
 
     zip_path = download_dir / filename
     if verbose:
-        console.print(f"[cyan]Downloading template...[/cyan]")
+        console.print("[cyan]Downloading template...[/cyan]")
 
     try:
         with client.stream(
@@ -738,7 +739,7 @@ def download_template_from_github(ai_assistant: str, download_dir: Path, *, scri
                         for chunk in response.iter_bytes(chunk_size=8192):
                             f.write(chunk)
     except Exception as e:
-        console.print(f"[red]Error downloading template[/red]")
+        console.print("[red]Error downloading template[/red]")
         detail = str(e)
         if zip_path.exists():
             zip_path.unlink()
@@ -822,7 +823,7 @@ def download_and_extract_template(project_path: Path, ai_assistant: str, script_
                             tracker.add("flatten", "Flatten nested directory")
                             tracker.complete("flatten")
                         elif verbose:
-                            console.print(f"[cyan]Found nested directory structure[/cyan]")
+                            console.print("[cyan]Found nested directory structure[/cyan]")
 
                     for item in source_dir.iterdir():
                         dest_path = project_path / item.name
@@ -847,7 +848,7 @@ def download_and_extract_template(project_path: Path, ai_assistant: str, script_
                                 console.print(f"[yellow]Overwriting file:[/yellow] {item.name}")
                             shutil.copy2(item, dest_path)
                     if verbose and not tracker:
-                        console.print(f"[cyan]Template files merged into current directory[/cyan]")
+                        console.print("[cyan]Template files merged into current directory[/cyan]")
             else:
                 zip_ref.extractall(project_path)
 
@@ -873,7 +874,7 @@ def download_and_extract_template(project_path: Path, ai_assistant: str, script_
                         tracker.add("flatten", "Flatten nested directory")
                         tracker.complete("flatten")
                     elif verbose:
-                        console.print(f"[cyan]Flattened nested directory structure[/cyan]")
+                        console.print("[cyan]Flattened nested directory structure[/cyan]")
 
     except Exception as e:
         if tracker:
@@ -923,13 +924,17 @@ def ensure_executable_scripts(project_path: Path, tracker: StepTracker | None =
                         continue
             except Exception:
                 continue
-            st = script.stat(); mode = st.st_mode
+            st = script.stat()
+            mode = st.st_mode
             if mode & 0o111:
                 continue
             new_mode = mode
-            if mode & 0o400: new_mode |= 0o100
-            if mode & 0o040: new_mode |= 0o010
-            if mode & 0o004: new_mode |= 0o001
+            if mode & 0o400:
+                new_mode |= 0o100
+            if mode & 0o040:
+                new_mode |= 0o010
+            if mode & 0o004:
+                new_mode |= 0o001
             if not (new_mode & 0o100):
                 new_mode |= 0o100
             os.chmod(script, new_mode)
@@ -975,7 +980,7 @@ def ensure_constitution_from_template(project_path: Path, tracker: StepTracker |
             tracker.add("constitution", "Constitution setup")
             tracker.complete("constitution", "copied from template")
         else:
-            console.print(f"[cyan]Initialized constitution from template[/cyan]")
+            console.print("[cyan]Initialized constitution from template[/cyan]")
     except Exception as e:
         if tracker:
             tracker.add("constitution", "Constitution setup")
@@ -983,6 +988,203 @@ def ensure_constitution_from_template(project_path: Path, tracker: StepTracker |
         else:
             console.print(f"[yellow]Warning: Could not initialize constitution: {e}[/yellow]")
 
+# Agent-specific skill directory overrides for agents whose skills directory
+# doesn't follow the standard <agent_folder>/skills/ pattern
+AGENT_SKILLS_DIR_OVERRIDES = {
+    "codex": ".agents/skills",  # Codex agent layout override
+}
+
+# Default skills directory for agents not in AGENT_CONFIG
+DEFAULT_SKILLS_DIR = ".agents/skills"
+
+# Enhanced descriptions for each spec-kit command skill
+SKILL_DESCRIPTIONS = {
+    "specify": "Create or update feature specifications from natural language descriptions. Use when starting new features or refining requirements. Generates spec.md with user stories, functional requirements, and acceptance criteria following spec-driven development methodology.",
+    "plan": "Generate technical implementation plans from feature specifications. Use after creating a spec to define architecture, tech stack, and implementation phases. Creates plan.md with detailed technical design.",
+    "tasks": "Break down implementation plans into actionable task lists. Use after planning to create a structured task breakdown. Generates tasks.md with ordered, dependency-aware tasks.",
+    "implement": "Execute all tasks from the task breakdown to build the feature. Use after task generation to systematically implement the planned solution following TDD approach where applicable.",
+    "analyze": "Perform cross-artifact consistency analysis across spec.md, plan.md, and tasks.md. Use after task generation to identify gaps, duplications, and inconsistencies before implementation.",
+    "clarify": "Structured clarification workflow for underspecified requirements. Use before planning to resolve ambiguities through coverage-based questioning. Records answers in spec clarifications section.",
+    "constitution": "Create or update project governing principles and development guidelines. Use at project start to establish code quality, testing standards, and architectural constraints that guide all development.",
+    "checklist": "Generate custom quality checklists for validating requirements completeness and clarity. Use to create unit tests for English that ensure spec quality before implementation.",
+    "taskstoissues": "Convert tasks from tasks.md into GitHub issues. Use after task breakdown to track work items in GitHub project management.",
+}
+
+
+def _get_skills_dir(project_path: Path, selected_ai: str) -> Path:
+    """Resolve the agent-specific skills directory for the given AI assistant.
+
+    Uses ``AGENT_SKILLS_DIR_OVERRIDES`` first, then falls back to
+    ``AGENT_CONFIG[agent]["folder"] + "skills"``, and finally to
+    ``DEFAULT_SKILLS_DIR``.
+    """
+    if selected_ai in AGENT_SKILLS_DIR_OVERRIDES:
+        return project_path / AGENT_SKILLS_DIR_OVERRIDES[selected_ai]
+
+    agent_config = AGENT_CONFIG.get(selected_ai, {})
+    agent_folder = agent_config.get("folder", "")
+    if agent_folder:
+        return project_path / agent_folder.rstrip("/") / "skills"
+
+    return project_path / DEFAULT_SKILLS_DIR
+
+
+def install_ai_skills(project_path: Path, selected_ai: str, tracker: StepTracker | None = None) -> bool:
+    """Install Prompt.MD files from templates/commands/ as agent skills.
+
+    Skills are written to the agent-specific skills directory following the
+    `agentskills.io <https://agentskills.io/specification>`_ specification.
+    Installation is additive — existing files are never removed and prompt
+    command files in the agent's commands directory are left untouched.
+
+    Args:
+        project_path: Target project directory.
+        selected_ai: AI assistant key from ``AGENT_CONFIG``.
+        tracker: Optional progress tracker.
+
+    Returns:
+        ``True`` if at least one skill was installed or all skills were
+        already present (idempotent re-run), ``False`` otherwise.
+    """
+    # Locate command templates in the agent's extracted commands directory.
+    # download_and_extract_template() already placed the .md files here.
+    agent_config = AGENT_CONFIG.get(selected_ai, {})
+    agent_folder = agent_config.get("folder", "")
+    if agent_folder:
+        templates_dir = project_path / agent_folder.rstrip("/") / "commands"
+    else:
+        templates_dir = project_path / "commands"
+
+    if not templates_dir.exists() or not any(templates_dir.glob("*.md")):
+        # Fallback: try the repo-relative path (for running from source checkout)
+        # This also covers agents whose extracted commands are in a different
+        # format (e.g. gemini uses .toml, not .md).
+        script_dir = Path(__file__).parent.parent.parent  # up from src/specify_cli/
+        fallback_dir = script_dir / "templates" / "commands"
+        if fallback_dir.exists() and any(fallback_dir.glob("*.md")):
+            templates_dir = fallback_dir
+
+    if not templates_dir.exists() or not any(templates_dir.glob("*.md")):
+        if tracker:
+            tracker.error("ai-skills", "command templates not found")
+        else:
+            console.print("[yellow]Warning: command templates not found, skipping skills installation[/yellow]")
+        return False
+
+    command_files = sorted(templates_dir.glob("*.md"))
+    if not command_files:
+        if tracker:
+            tracker.skip("ai-skills", "no command templates found")
+        else:
+            console.print("[yellow]No command templates found to install[/yellow]")
+        return False
+
+    # Resolve the correct skills directory for this agent
+    skills_dir = _get_skills_dir(project_path, selected_ai)
+    skills_dir.mkdir(parents=True, exist_ok=True)
+
+    if tracker:
+        tracker.start("ai-skills")
+
+    installed_count = 0
+    skipped_count = 0
+    for command_file in command_files:
+        try:
+            content = command_file.read_text(encoding="utf-8")
+
+            # Parse YAML frontmatter
+            if content.startswith("---"):
+                parts = content.split("---", 2)
+                if len(parts) >= 3:
+                    frontmatter = yaml.safe_load(parts[1])
+                    if not isinstance(frontmatter, dict):
+                        frontmatter = {}
+                    body = parts[2].strip()
+                else:
+                    # File starts with --- but has no closing ---
+                    console.print(f"[yellow]Warning: {command_file.name} has malformed frontmatter (no closing ---), treating as plain content[/yellow]")
+                    frontmatter = {}
+                    body = content
+            else:
+                frontmatter = {}
+                body = content
+
+            command_name = command_file.stem
+            # Normalize: extracted commands may be named "speckit.<cmd>.md";
+            # strip the "speckit." prefix so skill names stay clean and
+            # SKILL_DESCRIPTIONS lookups work.
+            if command_name.startswith("speckit."):
+                command_name = command_name[len("speckit."):]
+            skill_name = f"speckit-{command_name}"
+
+            # Create skill directory (additive — never removes existing content)
+            skill_dir = skills_dir / skill_name
+            skill_dir.mkdir(parents=True, exist_ok=True)
+
+            # Select the best description available
+            original_desc = frontmatter.get("description", "")
+            enhanced_desc = SKILL_DESCRIPTIONS.get(command_name, original_desc or f"Spec-kit workflow command: {command_name}")
+
+            # Build SKILL.md following agentskills.io spec
+            # Use yaml.safe_dump to safely serialise the frontmatter and
+            # avoid YAML injection from descriptions containing colons,
+            # quotes, or newlines.
+            # Normalize source filename for metadata — strip speckit. prefix
+            # so it matches the canonical templates/commands/<cmd>.md path.
+            source_name = command_file.name
+            if source_name.startswith("speckit."):
+                source_name = source_name[len("speckit."):]
+
+            frontmatter_data = {
+                "name": skill_name,
+                "description": enhanced_desc,
+                "compatibility": "Requires spec-kit project structure with .specify/ directory",
+                "metadata": {
+                    "author": "github-spec-kit",
+                    "source": f"templates/commands/{source_name}",
+                },
+            }
+            frontmatter_text = yaml.safe_dump(frontmatter_data, sort_keys=False).strip()
+            skill_content = (
+                f"---\n"
+                f"{frontmatter_text}\n"
+                f"---\n\n"
+                f"# Speckit {command_name.title()} Skill\n\n"
+                f"{body}\n"
+            )
+
+            skill_file = skill_dir / "SKILL.md"
+            if skill_file.exists():
+                # Do not overwrite user-customized skills on re-runs
+                skipped_count += 1
+                continue
+            skill_file.write_text(skill_content, encoding="utf-8")
+            installed_count += 1
+
+        except Exception as e:
+            console.print(f"[yellow]Warning: Failed to install skill {command_file.stem}: {e}[/yellow]")
+            continue
+
+    if tracker:
+        if installed_count > 0 and skipped_count > 0:
+            tracker.complete("ai-skills", f"{installed_count} new + {skipped_count} existing skills in {skills_dir.relative_to(project_path)}")
+        elif installed_count > 0:
+            tracker.complete("ai-skills", f"{installed_count} skills → {skills_dir.relative_to(project_path)}")
+        elif skipped_count > 0:
+            tracker.complete("ai-skills", f"{skipped_count} skills already present")
+        else:
+            tracker.error("ai-skills", "no skills installed")
+    else:
+        if installed_count > 0:
+            console.print(f"[green]✓[/green] Installed {installed_count} agent skills to {skills_dir.relative_to(project_path)}/")
+        elif skipped_count > 0:
+            console.print(f"[green]✓[/green] {skipped_count} agent skills already present in {skills_dir.relative_to(project_path)}/")
+        else:
+            console.print("[yellow]No skills were installed[/yellow]")
+
+    return installed_count > 0 or skipped_count > 0
+
+
 @app.command()
 def init(
     project_name: str = typer.Argument(None, help="Name for your new project directory (optional if using --here, or use '.' for current directory)"),
@@ -995,6 +1197,7 @@ def init(
     skip_tls: bool = typer.Option(False, "--skip-tls", help="Skip SSL/TLS verification (not recommended)"),
     debug: bool = typer.Option(False, "--debug", help="Show verbose diagnostic output for network and extraction failures"),
     github_token: str = typer.Option(None, "--github-token", help="GitHub token to use for API requests (or set GH_TOKEN or GITHUB_TOKEN environment variable)"),
+    ai_skills: bool = typer.Option(False, "--ai-skills", help="Install Prompt.MD templates as agent skills (requires --ai)"),
 ):
     """
     Initialize a new Specify project from the latest template.
@@ -1019,6 +1222,8 @@ def init(
         specify init --here --ai codebuddy
         specify init --here
         specify init --here --force  # Skip confirmation when current directory not empty
+        specify init my-project --ai claude --ai-skills   # Install agent skills
+        specify init --here --ai gemini --ai-skills
     """
 
     show_banner()
@@ -1035,6 +1240,11 @@ def init(
         console.print("[red]Error:[/red] Must specify either a project name, use '.' for current directory, or use --here flag")
         raise typer.Exit(1)
 
+    if ai_skills and not ai_assistant:
+        console.print("[red]Error:[/red] --ai-skills requires --ai to be specified")
+        console.print("[yellow]Usage:[/yellow] specify init <project> --ai <agent> --ai-skills")
+        raise typer.Exit(1)
+
     if here:
         project_name = Path.cwd().name
         project_path = Path.cwd()
@@ -1150,6 +1360,11 @@ def init(
         ("extracted-summary", "Extraction summary"),
         ("chmod", "Ensure scripts executable"),
         ("constitution", "Constitution setup"),
+    ]:
+        tracker.add(key, label)
+    if ai_skills:
+        tracker.add("ai-skills", "Install agent skills")
+    for key, label in [
         ("cleanup", "Cleanup"),
         ("git", "Initialize git repository"),
         ("final", "Finalize")
@@ -1172,6 +1387,29 @@ def init(
 
             ensure_constitution_from_template(project_path, tracker=tracker)
 
+            if ai_skills:
+                skills_ok = install_ai_skills(project_path, selected_ai, tracker=tracker)
+
+                # When --ai-skills is used on a NEW project and skills were
+                # successfully installed, remove the command files that the
+                # template archive just created.  Skills replace commands, so
+                # keeping both would be confusing.  For --here on an existing
+                # repo we leave pre-existing commands untouched to avoid a
+                # breaking change.  We only delete AFTER skills succeed so the
+                # project always has at least one of {commands, skills}.
+                if skills_ok and not here:
+                    agent_cfg = AGENT_CONFIG.get(selected_ai, {})
+                    agent_folder = agent_cfg.get("folder", "")
+                    if agent_folder:
+                        cmds_dir = project_path / agent_folder.rstrip("/") / "commands"
+                        if cmds_dir.exists():
+                            try:
+                                shutil.rmtree(cmds_dir)
+                            except OSError:
+                                # Best-effort cleanup: skills are already installed,
+                                # so leaving stale commands is non-fatal.
+                                console.print("[yellow]Warning: could not remove extracted commands directory[/yellow]")
+
             if not no_git:
                 tracker.start("git")
                 if is_git_repo(project_path):
@@ -1276,9 +1514,9 @@ def init(
     enhancement_lines = [
         "Optional commands that you can use for your specs [bright_black](improve quality & confidence)[/bright_black]",
         "",
-        f"○ [cyan]/speckit.clarify[/] [bright_black](optional)[/bright_black] - Ask structured questions to de-risk ambiguous areas before planning (run before [cyan]/speckit.plan[/] if used)",
-        f"○ [cyan]/speckit.analyze[/] [bright_black](optional)[/bright_black] - Cross-artifact consistency & alignment report (after [cyan]/speckit.tasks[/], before [cyan]/speckit.implement[/])",
-        f"○ [cyan]/speckit.checklist[/] [bright_black](optional)[/bright_black] - Generate quality checklists to validate requirements completeness, clarity, and consistency (after [cyan]/speckit.plan[/])"
+        "○ [cyan]/speckit.clarify[/] [bright_black](optional)[/bright_black] - Ask structured questions to de-risk ambiguous areas before planning (run before [cyan]/speckit.plan[/] if used)",
+        "○ [cyan]/speckit.analyze[/] [bright_black](optional)[/bright_black] - Cross-artifact consistency & alignment report (after [cyan]/speckit.tasks[/], before [cyan]/speckit.implement[/])",
+        "○ [cyan]/speckit.checklist[/] [bright_black](optional)[/bright_black] - Generate quality checklists to validate requirements completeness, clarity, and consistency (after [cyan]/speckit.plan[/])"
     ]
     enhancements_panel = Panel("\n".join(enhancement_lines), title="Enhancement Commands", border_style="cyan", padding=(1,2))
     console.print()
@@ -1311,10 +1549,10 @@ def check():
 
     # Check VS Code variants (not in agent config)
     tracker.add("code", "Visual Studio Code")
-    code_ok = check_tool("code", tracker=tracker)
+    check_tool("code", tracker=tracker)
 
     tracker.add("code-insiders", "Visual Studio Code Insiders")
-    code_insiders_ok = check_tool("code-insiders", tracker=tracker)
+    check_tool("code-insiders", tracker=tracker)
 
     console.print(tracker.render())
 
@@ -1580,14 +1818,14 @@ def extension_add(
                     if zip_path.exists():
                         zip_path.unlink()
 
-        console.print(f"\n[green]✓[/green] Extension installed successfully!")
+        console.print("\n[green]✓[/green] Extension installed successfully!")
         console.print(f"\n[bold]{manifest.name}[/bold] (v{manifest.version})")
         console.print(f"  {manifest.description}")
-        console.print(f"\n[bold cyan]Provided commands:[/bold cyan]")
+        console.print("\n[bold cyan]Provided commands:[/bold cyan]")
         for cmd in manifest.commands:
             console.print(f"  • {cmd['name']} - {cmd.get('description', '')}")
 
-        console.print(f"\n[yellow]⚠[/yellow]  Configuration may be required")
+        console.print("\n[yellow]⚠[/yellow]  Configuration may be required")
         console.print(f"   Check: .specify/extensions/{manifest.id}/")
 
     except ValidationError as e:
@@ -1637,11 +1875,11 @@ def extension_remove(
 
     # Confirm removal
     if not force:
-        console.print(f"\n[yellow]⚠  This will remove:[/yellow]")
+        console.print("\n[yellow]⚠  This will remove:[/yellow]")
         console.print(f"   • {cmd_count} commands from AI agent")
         console.print(f"   • Extension directory: .specify/extensions/{extension}/")
         if not keep_config:
-            console.print(f"   • Config files (will be backed up)")
+            console.print("   • Config files (will be backed up)")
         console.print()
 
         confirm = typer.confirm("Continue?")
@@ -1660,7 +1898,7 @@ def extension_remove(
             console.print(f"\nConfig files backed up to .specify/extensions/.backup/{extension}/")
         console.print(f"\nTo reinstall: specify extension add {extension}")
     else:
-        console.print(f"[red]Error:[/red] Failed to remove extension")
+        console.print("[red]Error:[/red] Failed to remove extension")
         raise typer.Exit(1)
 
 
@@ -1935,8 +2173,8 @@ def extension_update(
             # TODO: Implement download and reinstall from URL
             # For now, just show  message
             console.print(
-                f"[yellow]Note:[/yellow] Automatic update not yet implemented. "
-                f"Please update manually:"
+                "[yellow]Note:[/yellow] Automatic update not yet implemented. "
+                "Please update manually:"
             )
             console.print(f"  specify extension remove {ext_id} --keep-config")
             console.print(f"  specify extension add {ext_id}")
@@ -2036,7 +2274,7 @@ def extension_disable(
         hook_executor.save_project_config(config)
 
     console.print(f"[green]✓[/green] Extension '{extension}' disabled")
-    console.print(f"\nCommands will no longer be available. Hooks will not execute.")
+    console.print("\nCommands will no longer be available. Hooks will not execute.")
     console.print(f"To re-enable: specify extension enable {extension}")
 
 

tests/test_ai_skills.py

@@ -0,0 +1,632 @@
+"""
+Unit tests for AI agent skills installation.
+
+Tests cover:
+- Skills directory resolution for different agents (_get_skills_dir)
+- YAML frontmatter parsing and SKILL.md generation (install_ai_skills)
+- Cleanup of duplicate command files when --ai-skills is used
+- Missing templates directory handling
+- Malformed template error handling
+- CLI validation: --ai-skills requires --ai
+"""
+
+import re
+import pytest
+import tempfile
+import shutil
+import yaml
+from pathlib import Path
+from unittest.mock import patch
+
+import specify_cli
+
+from specify_cli import (
+    _get_skills_dir,
+    install_ai_skills,
+    AGENT_SKILLS_DIR_OVERRIDES,
+    DEFAULT_SKILLS_DIR,
+    SKILL_DESCRIPTIONS,
+    AGENT_CONFIG,
+    app,
+)
+
+
+# ===== Fixtures =====
+
+@pytest.fixture
+def temp_dir():
+    """Create a temporary directory for tests."""
+    tmpdir = tempfile.mkdtemp()
+    yield Path(tmpdir)
+    shutil.rmtree(tmpdir)
+
+
+@pytest.fixture
+def project_dir(temp_dir):
+    """Create a mock project directory."""
+    proj_dir = temp_dir / "test-project"
+    proj_dir.mkdir()
+    return proj_dir
+
+
+@pytest.fixture
+def templates_dir(project_dir):
+    """Create mock command templates in the project's agent commands directory.
+
+    This simulates what download_and_extract_template() does: it places
+    command .md files into project_path/<agent_folder>/commands/.
+    install_ai_skills() now reads from here instead of from the repo
+    source tree.
+    """
+    tpl_root = project_dir / ".claude" / "commands"
+    tpl_root.mkdir(parents=True, exist_ok=True)
+
+    # Template with valid YAML frontmatter
+    (tpl_root / "specify.md").write_text(
+        "---\n"
+        "description: Create or update the feature specification.\n"
+        "handoffs:\n"
+        "  - label: Build Plan\n"
+        "    agent: speckit.plan\n"
+        "scripts:\n"
+        "  sh: scripts/bash/create-new-feature.sh\n"
+        "---\n"
+        "\n"
+        "# Specify Command\n"
+        "\n"
+        "Run this to create a spec.\n",
+        encoding="utf-8",
+    )
+
+    # Template with minimal frontmatter
+    (tpl_root / "plan.md").write_text(
+        "---\n"
+        "description: Generate implementation plan.\n"
+        "---\n"
+        "\n"
+        "# Plan Command\n"
+        "\n"
+        "Plan body content.\n",
+        encoding="utf-8",
+    )
+
+    # Template with no frontmatter
+    (tpl_root / "tasks.md").write_text(
+        "# Tasks Command\n"
+        "\n"
+        "Body without frontmatter.\n",
+        encoding="utf-8",
+    )
+
+    # Template with empty YAML frontmatter (yaml.safe_load returns None)
+    (tpl_root / "empty_fm.md").write_text(
+        "---\n"
+        "---\n"
+        "\n"
+        "# Empty Frontmatter Command\n"
+        "\n"
+        "Body with empty frontmatter.\n",
+        encoding="utf-8",
+    )
+
+    return tpl_root
+
+
+@pytest.fixture
+def commands_dir_claude(project_dir):
+    """Create a populated .claude/commands directory simulating template extraction."""
+    cmd_dir = project_dir / ".claude" / "commands"
+    cmd_dir.mkdir(parents=True, exist_ok=True)
+    for name in ["speckit.specify.md", "speckit.plan.md", "speckit.tasks.md"]:
+        (cmd_dir / name).write_text(f"# {name}\nContent here\n")
+    return cmd_dir
+
+
+@pytest.fixture
+def commands_dir_gemini(project_dir):
+    """Create a populated .gemini/commands directory (TOML format)."""
+    cmd_dir = project_dir / ".gemini" / "commands"
+    cmd_dir.mkdir(parents=True)
+    for name in ["speckit.specify.toml", "speckit.plan.toml", "speckit.tasks.toml"]:
+        (cmd_dir / name).write_text(f'[command]\nname = "{name}"\n')
+    return cmd_dir
+
+
+# ===== _get_skills_dir Tests =====
+
+class TestGetSkillsDir:
+    """Test the _get_skills_dir() helper function."""
+
+    def test_claude_skills_dir(self, project_dir):
+        """Claude should use .claude/skills/."""
+        result = _get_skills_dir(project_dir, "claude")
+        assert result == project_dir / ".claude" / "skills"
+
+    def test_gemini_skills_dir(self, project_dir):
+        """Gemini should use .gemini/skills/."""
+        result = _get_skills_dir(project_dir, "gemini")
+        assert result == project_dir / ".gemini" / "skills"
+
+    def test_copilot_skills_dir(self, project_dir):
+        """Copilot should use .github/skills/."""
+        result = _get_skills_dir(project_dir, "copilot")
+        assert result == project_dir / ".github" / "skills"
+
+    def test_codex_uses_override(self, project_dir):
+        """Codex should use the AGENT_SKILLS_DIR_OVERRIDES value."""
+        result = _get_skills_dir(project_dir, "codex")
+        assert result == project_dir / ".agents" / "skills"
+
+    def test_cursor_agent_skills_dir(self, project_dir):
+        """Cursor should use .cursor/skills/."""
+        result = _get_skills_dir(project_dir, "cursor-agent")
+        assert result == project_dir / ".cursor" / "skills"
+
+    def test_unknown_agent_uses_default(self, project_dir):
+        """Unknown agents should fall back to DEFAULT_SKILLS_DIR."""
+        result = _get_skills_dir(project_dir, "nonexistent-agent")
+        assert result == project_dir / DEFAULT_SKILLS_DIR
+
+    def test_all_configured_agents_resolve(self, project_dir):
+        """Every agent in AGENT_CONFIG should resolve to a valid path."""
+        for agent_key in AGENT_CONFIG:
+            result = _get_skills_dir(project_dir, agent_key)
+            assert result is not None
+            assert str(result).startswith(str(project_dir))
+            # Should always end with "skills"
+            assert result.name == "skills"
+
+    def test_override_takes_precedence_over_config(self, project_dir):
+        """AGENT_SKILLS_DIR_OVERRIDES should take precedence over AGENT_CONFIG."""
+        for agent_key in AGENT_SKILLS_DIR_OVERRIDES:
+            result = _get_skills_dir(project_dir, agent_key)
+            expected = project_dir / AGENT_SKILLS_DIR_OVERRIDES[agent_key]
+            assert result == expected
+
+
+# ===== install_ai_skills Tests =====
+
+class TestInstallAiSkills:
+    """Test SKILL.md generation and installation logic."""
+
+    def test_skills_installed_with_correct_structure(self, project_dir, templates_dir):
+        """Verify SKILL.md files have correct agentskills.io structure."""
+        result = install_ai_skills(project_dir, "claude")
+
+        assert result is True
+
+        skills_dir = project_dir / ".claude" / "skills"
+        assert skills_dir.exists()
+
+        # Check that skill directories were created
+        skill_dirs = sorted([d.name for d in skills_dir.iterdir() if d.is_dir()])
+        assert "speckit-plan" in skill_dirs
+        assert "speckit-specify" in skill_dirs
+        assert "speckit-tasks" in skill_dirs
+        assert "speckit-empty_fm" in skill_dirs
+
+        # Verify SKILL.md content for speckit-specify
+        skill_file = skills_dir / "speckit-specify" / "SKILL.md"
+        assert skill_file.exists()
+        content = skill_file.read_text()
+
+        # Check agentskills.io frontmatter
+        assert content.startswith("---\n")
+        assert "name: speckit-specify" in content
+        assert "description:" in content
+        assert "compatibility:" in content
+        assert "metadata:" in content
+        assert "author: github-spec-kit" in content
+        assert "source: templates/commands/specify.md" in content
+
+        # Check body content is included
+        assert "# Speckit Specify Skill" in content
+        assert "Run this to create a spec." in content
+
+    def test_generated_skill_has_parseable_yaml(self, project_dir, templates_dir):
+        """Generated SKILL.md should contain valid, parseable YAML frontmatter."""
+        install_ai_skills(project_dir, "claude")
+
+        skill_file = project_dir / ".claude" / "skills" / "speckit-specify" / "SKILL.md"
+        content = skill_file.read_text()
+
+        # Extract and parse frontmatter
+        assert content.startswith("---\n")
+        parts = content.split("---", 2)
+        assert len(parts) >= 3
+        parsed = yaml.safe_load(parts[1])
+        assert isinstance(parsed, dict)
+        assert "name" in parsed
+        assert parsed["name"] == "speckit-specify"
+        assert "description" in parsed
+
+    def test_empty_yaml_frontmatter(self, project_dir, templates_dir):
+        """Templates with empty YAML frontmatter (---\\n---) should not crash."""
+        result = install_ai_skills(project_dir, "claude")
+
+        assert result is True
+
+        skill_file = project_dir / ".claude" / "skills" / "speckit-empty_fm" / "SKILL.md"
+        assert skill_file.exists()
+        content = skill_file.read_text()
+        assert "name: speckit-empty_fm" in content
+        assert "Body with empty frontmatter." in content
+
+    def test_enhanced_descriptions_used_when_available(self, project_dir, templates_dir):
+        """SKILL_DESCRIPTIONS take precedence over template frontmatter descriptions."""
+        install_ai_skills(project_dir, "claude")
+
+        skill_file = project_dir / ".claude" / "skills" / "speckit-specify" / "SKILL.md"
+        content = skill_file.read_text()
+
+        # Parse the generated YAML to compare the description value
+        # (yaml.safe_dump may wrap long strings across multiple lines)
+        parts = content.split("---", 2)
+        parsed = yaml.safe_load(parts[1])
+
+        if "specify" in SKILL_DESCRIPTIONS:
+            assert parsed["description"] == SKILL_DESCRIPTIONS["specify"]
+
+    def test_template_without_frontmatter(self, project_dir, templates_dir):
+        """Templates without YAML frontmatter should still produce valid skills."""
+        install_ai_skills(project_dir, "claude")
+
+        skill_file = project_dir / ".claude" / "skills" / "speckit-tasks" / "SKILL.md"
+        assert skill_file.exists()
+        content = skill_file.read_text()
+
+        # Should still have valid SKILL.md structure
+        assert "name: speckit-tasks" in content
+        assert "Body without frontmatter." in content
+
+    def test_missing_templates_directory(self, project_dir):
+        """Returns False when no command templates exist anywhere."""
+        # No .claude/commands/ exists, and __file__ fallback won't find anything
+        fake_init = project_dir / "nonexistent" / "src" / "specify_cli" / "__init__.py"
+        fake_init.parent.mkdir(parents=True, exist_ok=True)
+        fake_init.touch()
+
+        with patch.object(specify_cli, "__file__", str(fake_init)):
+            result = install_ai_skills(project_dir, "claude")
+
+        assert result is False
+
+        # Skills directory should not exist
+        skills_dir = project_dir / ".claude" / "skills"
+        assert not skills_dir.exists()
+
+    def test_empty_templates_directory(self, project_dir):
+        """Returns False when commands directory has no .md files."""
+        # Create empty .claude/commands/
+        empty_cmds = project_dir / ".claude" / "commands"
+        empty_cmds.mkdir(parents=True)
+
+        # Block the __file__ fallback so it can't find real templates
+        fake_init = project_dir / "nowhere" / "src" / "specify_cli" / "__init__.py"
+        fake_init.parent.mkdir(parents=True, exist_ok=True)
+        fake_init.touch()
+
+        with patch.object(specify_cli, "__file__", str(fake_init)):
+            result = install_ai_skills(project_dir, "claude")
+
+        assert result is False
+
+    def test_malformed_yaml_frontmatter(self, project_dir):
+        """Malformed YAML in a template should be handled gracefully, not crash."""
+        # Create .claude/commands/ with a broken template
+        cmds_dir = project_dir / ".claude" / "commands"
+        cmds_dir.mkdir(parents=True)
+
+        (cmds_dir / "broken.md").write_text(
+            "---\n"
+            "description: [unclosed bracket\n"
+            "  invalid: yaml: content: here\n"
+            "---\n"
+            "\n"
+            "# Broken\n",
+            encoding="utf-8",
+        )
+
+        # Should not raise — errors are caught per-file
+        result = install_ai_skills(project_dir, "claude")
+
+        # The broken template should be skipped but not crash the process
+        assert result is False
+
+    def test_additive_does_not_overwrite_other_files(self, project_dir, templates_dir):
+        """Installing skills should not remove non-speckit files in the skills dir."""
+        # Pre-create a custom skill
+        custom_dir = project_dir / ".claude" / "skills" / "my-custom-skill"
+        custom_dir.mkdir(parents=True)
+        custom_file = custom_dir / "SKILL.md"
+        custom_file.write_text("# My Custom Skill\n")
+
+        install_ai_skills(project_dir, "claude")
+
+        # Custom skill should still exist
+        assert custom_file.exists()
+        assert custom_file.read_text() == "# My Custom Skill\n"
+
+    def test_return_value(self, project_dir, templates_dir):
+        """install_ai_skills returns True when skills installed, False otherwise."""
+        assert install_ai_skills(project_dir, "claude") is True
+
+    def test_return_false_when_no_templates(self, project_dir):
+        """install_ai_skills returns False when no templates found."""
+        fake_init = project_dir / "missing" / "src" / "specify_cli" / "__init__.py"
+        fake_init.parent.mkdir(parents=True, exist_ok=True)
+        fake_init.touch()
+
+        with patch.object(specify_cli, "__file__", str(fake_init)):
+            assert install_ai_skills(project_dir, "claude") is False
+
+    def test_non_md_commands_dir_falls_back(self, project_dir):
+        """When extracted commands are .toml (e.g. gemini), fall back to repo templates."""
+        # Simulate gemini template extraction: .gemini/commands/ with .toml files only
+        cmds_dir = project_dir / ".gemini" / "commands"
+        cmds_dir.mkdir(parents=True)
+        (cmds_dir / "speckit.specify.toml").write_text('[command]\nname = "specify"\n')
+        (cmds_dir / "speckit.plan.toml").write_text('[command]\nname = "plan"\n')
+
+        # The __file__ fallback should find the real repo templates/commands/*.md
+        result = install_ai_skills(project_dir, "gemini")
+
+        assert result is True
+        skills_dir = project_dir / ".gemini" / "skills"
+        assert skills_dir.exists()
+        # Should have installed skills from the fallback .md templates
+        skill_dirs = [d.name for d in skills_dir.iterdir() if d.is_dir()]
+        assert len(skill_dirs) >= 1
+        # .toml commands should be untouched
+        assert (cmds_dir / "speckit.specify.toml").exists()
+
+    @pytest.mark.parametrize("agent_key", list(AGENT_CONFIG.keys()))
+    def test_skills_install_for_all_agents(self, temp_dir, agent_key):
+        """install_ai_skills should produce skills for every configured agent."""
+        proj = temp_dir / f"proj-{agent_key}"
+        proj.mkdir()
+
+        # Place .md templates in the agent's commands directory
+        agent_folder = AGENT_CONFIG[agent_key]["folder"]
+        cmds_dir = proj / agent_folder.rstrip("/") / "commands"
+        cmds_dir.mkdir(parents=True)
+        (cmds_dir / "specify.md").write_text(
+            "---\ndescription: Test command\n---\n\n# Test\n\nBody.\n"
+        )
+
+        result = install_ai_skills(proj, agent_key)
+
+        assert result is True
+        skills_dir = _get_skills_dir(proj, agent_key)
+        assert skills_dir.exists()
+        skill_dirs = [d.name for d in skills_dir.iterdir() if d.is_dir()]
+        assert "speckit-specify" in skill_dirs
+        assert (skills_dir / "speckit-specify" / "SKILL.md").exists()
+
+
+
+class TestCommandCoexistence:
+    """Verify install_ai_skills never touches command files.
+
+    Cleanup of freshly-extracted commands for NEW projects is handled
+    in init(), not in install_ai_skills().  These tests confirm that
+    install_ai_skills leaves existing commands intact.
+    """
+
+    def test_existing_commands_preserved_claude(self, project_dir, templates_dir, commands_dir_claude):
+        """install_ai_skills must NOT remove pre-existing .claude/commands files."""
+        # Verify commands exist before
+        assert len(list(commands_dir_claude.glob("speckit.*"))) == 3
+
+        install_ai_skills(project_dir, "claude")
+
+        # Commands must still be there — install_ai_skills never touches them
+        remaining = list(commands_dir_claude.glob("speckit.*"))
+        assert len(remaining) == 3
+
+    def test_existing_commands_preserved_gemini(self, project_dir, templates_dir, commands_dir_gemini):
+        """install_ai_skills must NOT remove pre-existing .gemini/commands files."""
+        assert len(list(commands_dir_gemini.glob("speckit.*"))) == 3
+
+        install_ai_skills(project_dir, "gemini")
+
+        remaining = list(commands_dir_gemini.glob("speckit.*"))
+        assert len(remaining) == 3
+
+    def test_commands_dir_not_removed(self, project_dir, templates_dir, commands_dir_claude):
+        """install_ai_skills must not remove the commands directory."""
+        install_ai_skills(project_dir, "claude")
+
+        assert commands_dir_claude.exists()
+
+    def test_no_commands_dir_no_error(self, project_dir, templates_dir):
+        """No error when installing skills — commands dir has templates and is preserved."""
+        result = install_ai_skills(project_dir, "claude")
+
+        # Should succeed since templates are in .claude/commands/ via fixture
+        assert result is True
+
+
+# ===== New-Project Command Skip Tests =====
+
+class TestNewProjectCommandSkip:
+    """Test that init() removes extracted commands for new projects only.
+
+    These tests run init() end-to-end via CliRunner with
+    download_and_extract_template patched to create local fixtures.
+    """
+
+    def _fake_extract(self, agent, project_path, **_kwargs):
+        """Simulate template extraction: create agent commands dir."""
+        agent_cfg = AGENT_CONFIG.get(agent, {})
+        agent_folder = agent_cfg.get("folder", "")
+        if agent_folder:
+            cmds_dir = project_path / agent_folder.rstrip("/") / "commands"
+            cmds_dir.mkdir(parents=True, exist_ok=True)
+            (cmds_dir / "speckit.specify.md").write_text("# spec")
+
+    def test_new_project_commands_removed_after_skills_succeed(self, tmp_path):
+        """For new projects, commands should be removed when skills succeed."""
+        from typer.testing import CliRunner
+
+        runner = CliRunner()
+        target = tmp_path / "new-proj"
+
+        def fake_download(project_path, *args, **kwargs):
+            self._fake_extract("claude", project_path)
+
+        with patch("specify_cli.download_and_extract_template", side_effect=fake_download), \
+             patch("specify_cli.ensure_executable_scripts"), \
+             patch("specify_cli.ensure_constitution_from_template"), \
+             patch("specify_cli.install_ai_skills", return_value=True) as mock_skills, \
+             patch("specify_cli.is_git_repo", return_value=False), \
+             patch("specify_cli.shutil.which", return_value="/usr/bin/git"):
+            result = runner.invoke(app, ["init", str(target), "--ai", "claude", "--ai-skills", "--script", "sh", "--no-git"])
+
+        # Skills should have been called
+        mock_skills.assert_called_once()
+
+        # Commands dir should have been removed after skills succeeded
+        cmds_dir = target / ".claude" / "commands"
+        assert not cmds_dir.exists()
+
+    def test_commands_preserved_when_skills_fail(self, tmp_path):
+        """If skills fail, commands should NOT be removed (safety net)."""
+        from typer.testing import CliRunner
+
+        runner = CliRunner()
+        target = tmp_path / "fail-proj"
+
+        def fake_download(project_path, *args, **kwargs):
+            self._fake_extract("claude", project_path)
+
+        with patch("specify_cli.download_and_extract_template", side_effect=fake_download), \
+             patch("specify_cli.ensure_executable_scripts"), \
+             patch("specify_cli.ensure_constitution_from_template"), \
+             patch("specify_cli.install_ai_skills", return_value=False), \
+             patch("specify_cli.is_git_repo", return_value=False), \
+             patch("specify_cli.shutil.which", return_value="/usr/bin/git"):
+            result = runner.invoke(app, ["init", str(target), "--ai", "claude", "--ai-skills", "--script", "sh", "--no-git"])
+
+        # Commands should still exist since skills failed
+        cmds_dir = target / ".claude" / "commands"
+        assert cmds_dir.exists()
+        assert (cmds_dir / "speckit.specify.md").exists()
+
+    def test_here_mode_commands_preserved(self, tmp_path, monkeypatch):
+        """For --here on existing repos, commands must NOT be removed."""
+        from typer.testing import CliRunner
+
+        runner = CliRunner()
+        # Create a mock existing project with commands already present
+        target = tmp_path / "existing"
+        target.mkdir()
+        agent_folder = AGENT_CONFIG["claude"]["folder"]
+        cmds_dir = target / agent_folder.rstrip("/") / "commands"
+        cmds_dir.mkdir(parents=True)
+        (cmds_dir / "speckit.specify.md").write_text("# spec")
+
+        # --here uses CWD, so chdir into the target
+        monkeypatch.chdir(target)
+
+        def fake_download(project_path, *args, **kwargs):
+            pass  # commands already exist, no need to re-create
+
+        with patch("specify_cli.download_and_extract_template", side_effect=fake_download), \
+             patch("specify_cli.ensure_executable_scripts"), \
+             patch("specify_cli.ensure_constitution_from_template"), \
+             patch("specify_cli.install_ai_skills", return_value=True), \
+             patch("specify_cli.is_git_repo", return_value=True), \
+             patch("specify_cli.shutil.which", return_value="/usr/bin/git"):
+            result = runner.invoke(app, ["init", "--here", "--ai", "claude", "--ai-skills", "--script", "sh", "--no-git"])
+
+        # Commands must remain for --here
+        assert cmds_dir.exists()
+        assert (cmds_dir / "speckit.specify.md").exists()
+
+
+# ===== Skip-If-Exists Tests =====
+
+class TestSkipIfExists:
+    """Test that install_ai_skills does not overwrite existing SKILL.md files."""
+
+    def test_existing_skill_not_overwritten(self, project_dir, templates_dir):
+        """Pre-existing SKILL.md should not be replaced on re-run."""
+        # Pre-create a custom SKILL.md for speckit-specify
+        skill_dir = project_dir / ".claude" / "skills" / "speckit-specify"
+        skill_dir.mkdir(parents=True)
+        custom_content = "# My Custom Specify Skill\nUser-modified content\n"
+        (skill_dir / "SKILL.md").write_text(custom_content)
+
+        result = install_ai_skills(project_dir, "claude")
+
+        # The custom SKILL.md should be untouched
+        assert (skill_dir / "SKILL.md").read_text() == custom_content
+
+        # But other skills should still be installed
+        assert result is True
+        assert (project_dir / ".claude" / "skills" / "speckit-plan" / "SKILL.md").exists()
+        assert (project_dir / ".claude" / "skills" / "speckit-tasks" / "SKILL.md").exists()
+
+    def test_fresh_install_writes_all_skills(self, project_dir, templates_dir):
+        """On first install (no pre-existing skills), all should be written."""
+        result = install_ai_skills(project_dir, "claude")
+
+        assert result is True
+        skills_dir = project_dir / ".claude" / "skills"
+        skill_dirs = [d.name for d in skills_dir.iterdir() if d.is_dir()]
+        # All 4 templates should produce skills (specify, plan, tasks, empty_fm)
+        assert len(skill_dirs) == 4
+
+
+# ===== SKILL_DESCRIPTIONS Coverage Tests =====
+
+class TestSkillDescriptions:
+    """Test SKILL_DESCRIPTIONS constants."""
+
+    def test_all_known_commands_have_descriptions(self):
+        """All standard spec-kit commands should have enhanced descriptions."""
+        expected_commands = [
+            "specify", "plan", "tasks", "implement", "analyze",
+            "clarify", "constitution", "checklist", "taskstoissues",
+        ]
+        for cmd in expected_commands:
+            assert cmd in SKILL_DESCRIPTIONS, f"Missing description for '{cmd}'"
+            assert len(SKILL_DESCRIPTIONS[cmd]) > 20, f"Description for '{cmd}' is too short"
+
+
+# ===== CLI Validation Tests =====
+
+class TestCliValidation:
+    """Test --ai-skills CLI flag validation."""
+
+    def test_ai_skills_without_ai_fails(self):
+        """--ai-skills without --ai should fail with exit code 1."""
+        from typer.testing import CliRunner
+
+        runner = CliRunner()
+        result = runner.invoke(app, ["init", "test-proj", "--ai-skills"])
+
+        assert result.exit_code == 1
+        assert "--ai-skills requires --ai" in result.output
+
+    def test_ai_skills_without_ai_shows_usage(self):
+        """Error message should include usage hint."""
+        from typer.testing import CliRunner
+
+        runner = CliRunner()
+        result = runner.invoke(app, ["init", "test-proj", "--ai-skills"])
+
+        assert "Usage:" in result.output
+        assert "--ai" in result.output
+
+    def test_ai_skills_flag_appears_in_help(self):
+        """--ai-skills should appear in init --help output."""
+        from typer.testing import CliRunner
+
+        runner = CliRunner()
+        result = runner.invoke(app, ["init", "--help"])
+
+        plain = re.sub(r'\x1b\[[0-9;]*m', '', result.output)
+        assert "--ai-skills" in plain
+        assert "agent skills" in plain.lower()