Agent Skills: Disable unselected extensions (ignore errors if already in desired state)

You MUST complete ALL steps below. Do not stop after Step 1.

Step 1: Run init script

Run the command from <spex-init-command> in the <spex-context> system reminder. This is your first and only Bash call. Do not run anything else before it.

• If output contains NEED_INSTALL: show output, STOP.
• If output contains ERROR: show error, STOP.
• If the command was run with --refresh or --update and output contains RESTART_REQUIRED: SKIP Steps 2 and 3. Templates and extensions were refreshed but the existing configuration (enabled extensions, auto-commit, permissions) is preserved. Go directly to Step 4 and report that the refresh completed. Tell the user to restart Claude Code.
• If output contains READY or RESTART_REQUIRED: do not summarize yet, go to Step 2.

Step 2: Ask about extensions, auto-commit, and permissions

You MUST ask all 4 questions below in a SINGLE AskUserQuestion call. Do NOT split, merge, reword, or reorder them. Pass them exactly as specified:

1. (multiSelect: true, header: "Quality"): "Which quality & review extensions do you want to enable?"

   • "spex-gates": "Quality gates on speckit commands (review-spec, review-code, verification)"
   • "spex-deep-review": "Multi-perspective code review with autonomous fix loop (5 agents)"
   • "spex-teams": "Parallel implementation with spec guardian review via Agent Teams (experimental, requires: spex-gates)"

2. (multiSelect: true, header: "Workflow"): "Which workflow extensions do you want to enable?"

   • "spex-worktrees": "Git worktree isolation after speckit-specify (creates sibling worktree)"
   • "spex-collab": "Phase-split collaboration with REVIEWERS.md for team PRs"

3. (multiSelect: true, header: "Auto-commit"): "When should spec-kit auto-commit? Select all that apply."

   • "After spec": "Auto-commit after specify completes"
   • "After plan+tasks": "Auto-commit after plan and tasks complete"
   • "After implement": "Auto-commit after implement completes"

4. (multiSelect: false, header: "Permissions"): "How should spex commands handle permission prompts?"

   • "Standard (Recommended)": "Auto-approve spex plugin scripts (spex-init.sh, specify CLI)"
   • "YOLO": "Auto-approve everything + enable auto mode for unattended workflows (requires Max/Team/Enterprise)"
   • "None": "Confirm every spex command before execution"

Then apply the selections:

Dependency resolution: If the user selected spex-teams but NOT spex-gates, auto-enable spex-gates and warn:

Note: spex-gates was auto-enabled because spex-teams depends on it for spec guardian review.

Extensions: Extensions are already installed and enabled by the init script. For any extensions the user did NOT select (after dependency resolution), disable them:

# Disable unselected extensions (ignore errors if already in desired state)
specify extension disable <extension-name> 2>/dev/null || true

If the user selected all extensions, no action needed (all are enabled by default after init).

Auto-commit: Update .specify/extensions/git/git-config.yml based on the user's selections. Only modify if the file exists (git extension is installed by spec-kit core). Enable each selected option with yq. If the user selected nothing, no changes needed (default is already false).

• After spec: yq -i '.auto_commit.after_specify.enabled = true' .specify/extensions/git/git-config.yml
• After plan+tasks: yq -i '.auto_commit.after_plan.enabled = true | .auto_commit.after_tasks.enabled = true' .specify/extensions/git/git-config.yml
• After implement: yq -i '.auto_commit.after_implement.enabled = true' .specify/extensions/git/git-config.yml

Combine all selected options into a single yq call when multiple are chosen.

Permissions: The specify CLI does not manage permissions. Instead, write permission allowlists directly to .claude/settings.json based on the user's choice. Use the EXACT allow arrays below (copy verbatim, do not modify or rephrase the permission strings):

• Standard:

  {"permissions": {"allow": ["Skill", "Bash(specify *)", "Bash(*spex-init.sh*)", "Bash(*spex-ship-statusline.sh*)"]}}
  

• YOLO:

  {"permissions": {"defaultMode": "auto", "allow": ["Bash(*)", "Read(*)", "Edit(*)", "Write(*)", "WebFetch", "WebSearch", "Skill", "Bash(specify *)", "Bash(*spex-init.sh*)", "Bash(*spex-ship-statusline.sh*)"]}}
  

  Note: defaultMode: "auto" enables the classifier-based auto mode that replaces bypassPermissions. Auto mode auto-approves routine operations (file edits, skill invocations, local commands) while blocking genuinely dangerous actions. It requires Max, Team, Enterprise, or API plan. The broad allow rules serve as fallback for environments where auto mode is unavailable.

  MCP tools: Claude Code does not support wildcard MCP server names in allow rules (e.g., mcp__*__* is invalid). To allow MCP tools, add server-specific entries like mcp__playwright__* or mcp__slack__* for each MCP server the project uses. Since available MCP servers vary by project, do NOT add MCP allow rules by default. The user can add them manually if needed.

• None: Do not modify permissions (leave defaults)

Use the existing project .claude/settings.json (create if missing). Merge permission entries without overwriting existing settings.

Step 3: Detect companion plugins and seed memory

Scan the available skills list from the system reminder for companion plugins:

3a: Superpowers plugin

Check for any of these upstream superpowers skills: test-driven-development, systematic-debugging, brainstorming, writing-plans. These are skills from obra/superpowers that complement spex but are NOT bundled with it.

• If found: record "superpowers" as a detected companion plugin in the Step 4 report. No further action needed.
• If not found and the user enabled the spex-gates extension in Step 2: show a recommendation in the Step 4 report (see below). Do NOT block init or make it an error.

Step 4: Report

Summarize: extensions enabled, auto-commit level, permission level, and companion plugins detected. If Step 1 said RESTART_REQUIRED or Step 2 permissions said CHANGED, tell user to restart Claude Code.

If superpowers companion plugin was NOT detected (Step 3b), append this to the report:

Recommended companion: The Superpowers plugin by Jesse Vincent adds TDD discipline and systematic debugging skills that complement spex's spec-first workflow. spex absorbs superpowers' quality gates and anti-rationalization patterns, but does not bundle these standalone skills:

• test-driven-development: strict RED-GREEN-REFACTOR, no production code without failing test
• systematic-debugging: 4-phase root cause analysis with defense-in-depth

Install with: /plugin install superpowers@claude-plugins-official (or claude plugin install superpowers@claude-plugins-official from the terminal)