agileflow 3.4.3 → 4.0.0-alpha.1

package/src/core/commands/configure.md

@@ -1,1159 +0,0 @@
----
-description: Configure AgileFlow features, hooks, and project infrastructure (Visual E2E, CI, git)
-phase: pre-story
-argument-hint: "[--profile=<name>] [--save-profile=<name>] [--list-profiles] [--export-profile=<name>] [--import-profile=<file>] [--enable/--disable=features]"
-compact_context:
-  priority: critical
-  preserve_rules:
-    - "ACTIVE COMMAND: /agileflow:configure - Configuration manager for AgileFlow features"
-    - "CRITICAL: Max 4 options per AskUserQuestion - use hierarchical menus"
-    - "CRITICAL: Run --detect FIRST, handle issues, then show Main Menu"
-    - "Main Menu (5 categories): Profiles | Features | Sessions | Infrastructure | Maintenance"
-    - "Each category has its own sub-menu with max 4 options"
-    - "MUST show RED RESTART banner after ANY changes"
-  state_fields:
-    - detection_status
-    - has_format_issues
-    - has_outdated_scripts
-    - enabled_features
----
-
-<!-- COMPACT_SUMMARY_START -->
-
-## Compact Summary
-
-Configuration management with **hierarchical menus** (4 options max per question).
-
-### Workflow (MUST FOLLOW)
-
-1. **Run detection**: `node .agileflow/scripts/agileflow-configure.js --detect`
-2. **Handle issues**: If ⚠️ INVALID FORMAT → migrate. If 🔄 OUTDATED → upgrade.
-3. **Main menu** (5 categories): Profiles | Features | Sessions | Infrastructure | Maintenance
-4. **Sub-menu**: Based on selection, show category-specific options
-
-### Menu Flow
-
-```
-Main Menu → "What would you like to configure?"
-├─ Profiles       → Apply preset | Apply custom | Save current | Manage
-│                   ├─ Presets: Full | Basic | Minimal | None
-│                   └─ Custom: Save, Export, Import, Delete
-├─ Features       → Enable | Disable | Context Verbosity | View status
-│                   └─ Hooks (4) + Other Features (4) + Context Verbosity (full/lite/minimal)
-├─ Sessions       → Startup mode and Agent Teams configuration
-│                   ├─ Startup Mode: Normal | Skip permissions | Accept edits | No Claude
-│                   └─ Agent Teams: Enable/disable native multi-agent orchestration
-├─ Infrastructure → UI Testing | Damage Control | CI/CD | Quality Gates
-└─ Maintenance    → Fix format | Upgrade | Repair | Check status
-```
-
-### Quick Commands
-
-```bash
-node .agileflow/scripts/agileflow-configure.js --detect        # Check status
-node .agileflow/scripts/agileflow-configure.js --profile=full  # Enable all
-node .agileflow/scripts/agileflow-configure.js --migrate       # Fix format
-node .agileflow/scripts/agileflow-configure.js --upgrade       # Update scripts
-node .agileflow/scripts/agileflow-configure.js --repair        # Restore missing
-node .agileflow/scripts/agileflow-configure.js --new-options   # Check for new options
-```
-
-### Critical Rules
-
-- **Max 4 options per AskUserQuestion** - use hierarchical menus
-- **Run detection FIRST** - show current state before changes
-- **Restart required** - show red banner after any changes
-
-<!-- COMPACT_SUMMARY_END -->
-
-# configure
-
-Manage AgileFlow features with profiles, enable/disable, and format migration.
-
-## Prompt
-
-ROLE: Configuration Manager
-
-## STEP 1: Always Run Detection First
-
-```bash
-node .agileflow/scripts/agileflow-configure.js --detect
-```
-
-**CRITICAL**: Check the output for format issues (⚠️ INVALID FORMAT).
-
-## STEP 2: Handle Issues (Migration or Upgrade)
-
-### If ⚠️ INVALID FORMAT detected → Offer Migration
-```xml
-<invoke name="AskUserQuestion">
-<parameter name="questions">[{
-  "question": "Format issues detected in your settings! These will cause Claude Code errors. Fix them now?",
-  "header": "Fix Issues",
-  "multiSelect": false,
-  "options": [
-    {"label": "Yes, fix format issues (Recommended)", "description": "Migrate old formats to new Claude Code format. Creates backup first."},
-    {"label": "No, skip for now", "description": "Continue with configuration (issues will remain)"}
-  ]
-}]</parameter>
-</invoke>
-```
-
-If user says yes:
-```bash
-node .agileflow/scripts/agileflow-configure.js --migrate
-```
-
-### If 🔄 OUTDATED detected → Offer Upgrade
-```xml
-<invoke name="AskUserQuestion">
-<parameter name="questions">[{
-  "question": "Outdated scripts detected! Your features were configured with an older AgileFlow version. Update them?",
-  "header": "Upgrade",
-  "multiSelect": false,
-  "options": [
-    {"label": "Yes, upgrade scripts (Recommended)", "description": "Re-deploy all enabled features with latest scripts."},
-    {"label": "No, keep current versions", "description": "Continue with older scripts (may miss bug fixes)."}
-  ]
-}]</parameter>
-</invoke>
-```
-
-If user says yes:
-```bash
-node .agileflow/scripts/agileflow-configure.js --upgrade
-```
-
-## STEP 3: Main Menu
-
-After handling issues (or if none), present the main category menu:
-
-```xml
-<invoke name="AskUserQuestion">
-<parameter name="questions">[{
-  "question": "What would you like to configure?",
-  "header": "Configure",
-  "multiSelect": false,
-  "options": [
-    {"label": "Profiles", "description": "Quick setup with preset configurations (full, basic, minimal)"},
-    {"label": "Features", "description": "Enable or disable individual hooks and features"},
-    {"label": "Sessions", "description": "Configure default startup mode for new sessions"},
-    {"label": "Infrastructure", "description": "Set up UI Testing, Damage Control, or CI/CD"},
-    {"label": "Maintenance", "description": "Fix issues, repair scripts, or check status"}
-  ]
-}]</parameter>
-</invoke>
-```
-
----
-
-## STEP 4: Sub-menus
-
-### If "Profiles" selected
-
-```xml
-<invoke name="AskUserQuestion">
-<parameter name="questions">[{
-  "question": "What would you like to do with profiles?",
-  "header": "Profiles",
-  "multiSelect": false,
-  "options": [
-    {"label": "Apply preset profile", "description": "Full, Basic, Minimal, or None"},
-    {"label": "Apply custom profile", "description": "Use one of your saved profiles"},
-    {"label": "Save current as profile", "description": "Save current feature settings as reusable profile"},
-    {"label": "Manage profiles", "description": "View, export, import, or delete profiles"}
-  ]
-}]</parameter>
-</invoke>
-```
-
-#### If "Apply preset profile" selected
-
-```xml
-<invoke name="AskUserQuestion">
-<parameter name="questions">[{
-  "question": "Which preset?",
-  "header": "Preset",
-  "multiSelect": false,
-  "options": [
-    {"label": "Full (Recommended)", "description": "All features: hooks, archival, status line, AskUserQuestion, TmuxAutoSpawn"},
-    {"label": "Basic", "description": "SessionStart + PreCompact + Archival + AskUserQuestion + TmuxAutoSpawn"},
-    {"label": "Minimal", "description": "SessionStart + Archival only"},
-    {"label": "Experimental ⚠️", "description": "All features + full file injection during compact (CONTEXT HEAVY)"}
-  ]
-}]</parameter>
-</invoke>
-```
-
-**Note:** If user needs "None" (disable all), show as second page or via "Other" option.
-
-Then run:
-- "Full" → `node .agileflow/scripts/agileflow-configure.js --profile=full`
-- "Basic" → `node .agileflow/scripts/agileflow-configure.js --profile=basic`
-- "Minimal" → `node .agileflow/scripts/agileflow-configure.js --profile=minimal`
-- "Experimental" → `node .agileflow/scripts/agileflow-configure.js --profile=experimental`
-- "None" → `node .agileflow/scripts/agileflow-configure.js --profile=none`
-
-### Experimental Profile Details
-
-The **Experimental** profile enables all features like "Full", but changes how context is preserved during conversation compaction:
-
-| Aspect | Full Profile | Experimental Profile |
-|--------|--------------|---------------------|
-| Features | All enabled | All enabled |
-| PreCompact behavior | Extracts `COMPACT_SUMMARY` sections | Injects **entire command files** |
-| Context usage | ~200-500 tokens per command | ~2000-5000 tokens per command |
-| Reliability | Good for most cases | May improve instruction adherence |
-
-**When to use Experimental:**
-- Commands aren't being followed well after compaction
-- You have plenty of context budget
-- Working on long sessions with complex commands (babysit, mentor)
-
-**Trade-offs:**
-- ⚠️ Uses significantly more context tokens
-- ⚠️ May hit context limits faster
-- ✅ Full command instructions preserved
-- ✅ No loss of nuance from summarization
-
-#### If "Apply custom profile" selected
-
-First, check if custom profiles exist:
-```bash
-node .agileflow/scripts/agileflow-configure.js --list-profiles
-```
-
-If no profiles: "No custom profiles saved yet. Create one with 'Save current as profile'."
-
-If profiles exist, list them (max 4 at a time):
-```xml
-<invoke name="AskUserQuestion">
-<parameter name="questions">[{
-  "question": "Which custom profile?",
-  "header": "Custom",
-  "multiSelect": false,
-  "options": [
-    {"label": "my-backend-setup", "description": "Backend dev - no UI features"},
-    {"label": "ui-heavy", "description": "UI development with visual verification"},
-    {"label": "ci-mode", "description": "Minimal for CI/CD pipelines"}
-  ]
-}]</parameter>
-</invoke>
-```
-
-Then run: `node .agileflow/scripts/agileflow-configure.js --profile=<selected-name>`
-
-#### If "Save current as profile" selected
-
-Ask for profile name and description:
-```xml
-<invoke name="AskUserQuestion">
-<parameter name="questions">[{
-  "question": "What should we name this profile?",
-  "header": "Name",
-  "multiSelect": false,
-  "options": [
-    {"label": "my-setup", "description": "Generic name for personal setup"},
-    {"label": "backend-dev", "description": "For backend development work"},
-    {"label": "ui-dev", "description": "For UI/frontend development"},
-    {"label": "ci-mode", "description": "Minimal config for CI pipelines"}
-  ]
-}]</parameter>
-</invoke>
-```
-
-User can select or type custom name via "Other".
-
-Then run:
-```bash
-node .agileflow/scripts/agileflow-configure.js --save-profile=<name> --description="<description>"
-```
-
-#### If "Manage profiles" selected
-
-```xml
-<invoke name="AskUserQuestion">
-<parameter name="questions">[{
-  "question": "What would you like to do?",
-  "header": "Manage",
-  "multiSelect": false,
-  "options": [
-    {"label": "View all profiles", "description": "See details of all saved profiles"},
-    {"label": "Export profile", "description": "Export a profile to share with others"},
-    {"label": "Import profile", "description": "Import a profile from file"},
-    {"label": "Delete profile", "description": "Remove a saved custom profile"}
-  ]
-}]</parameter>
-</invoke>
-```
-
-Commands:
-- View: `node .agileflow/scripts/agileflow-configure.js --list-profiles --verbose`
-- Export: `node .agileflow/scripts/agileflow-configure.js --export-profile=<name> --output=profile.json`
-- Import: `node .agileflow/scripts/agileflow-configure.js --import-profile=profile.json`
-- Delete: `node .agileflow/scripts/agileflow-configure.js --delete-profile=<name>`
-
----
-
-### If "Features" selected
-
-```xml
-<invoke name="AskUserQuestion">
-<parameter name="questions">[{
-  "question": "What do you want to do?",
-  "header": "Features",
-  "multiSelect": false,
-  "options": [
-    {"label": "Enable features", "description": "Turn on specific hooks and features"},
-    {"label": "Disable features", "description": "Turn off specific hooks and features"},
-    {"label": "View current status", "description": "See what's currently enabled/disabled"}
-  ]
-}]</parameter>
-</invoke>
-```
-
-#### If "Enable features" or "Disable features" selected
-
-First, ask about hooks:
-
-```xml
-<invoke name="AskUserQuestion">
-<parameter name="questions">[{
-  "question": "Which hooks?",
-  "header": "Hooks",
-  "multiSelect": true,
-  "options": [
-    {"label": "SessionStart", "description": "Welcome display with project status on session start"},
-    {"label": "PreCompact", "description": "Context preservation when conversation compacts"},
-    {"label": "RalphLoop", "description": "Stop hook: autonomous story loop with tests"},
-    {"label": "SelfImprove", "description": "Stop hook: auto-update agent expertise from work"}
-  ]
-}]</parameter>
-</invoke>
-```
-
-Then ask about other features (page 1):
-
-```xml
-<invoke name="AskUserQuestion">
-<parameter name="questions">[{
-  "question": "Which other features? (Page 1/2)",
-  "header": "Features",
-  "multiSelect": true,
-  "options": [
-    {"label": "Archival", "description": "Auto-archive completed stories older than threshold"},
-    {"label": "Status Line", "description": "Custom status bar showing story/epic info"},
-    {"label": "Auto-Update", "description": "Automatically update AgileFlow on session start"},
-    {"label": "More options...", "description": "View additional features"}
-  ]
-}]</parameter>
-</invoke>
-```
-
-If "More options..." selected, show page 2:
-
-```xml
-<invoke name="AskUserQuestion">
-<parameter name="questions">[{
-  "question": "Which other features? (Page 2/2)",
-  "header": "Features",
-  "multiSelect": true,
-  "options": [
-    {"label": "AskUserQuestion Mode", "description": "End responses with guided options"},
-    {"label": "Tmux Auto-Spawn", "description": "Auto-start Claude in tmux session when using af/agileflow"},
-    {"label": "Shell Aliases", "description": "Add af/agileflow commands to ~/.bashrc and ~/.zshrc"},
-    {"label": "CLAUDE.md Rules", "description": "Add /babysit context preservation rules to CLAUDE.md"}
-  ]
-}]</parameter>
-</invoke>
-```
-
-Map selections to commands:
-- SessionStart → `sessionstart`
-- PreCompact → `precompact`
-- RalphLoop → `ralphloop`
-- SelfImprove → `selfimprove`
-- Archival → `archival`
-- Status Line → `statusline`
-- Auto-Update → `autoupdate`
-- AskUserQuestion Mode → `askuserquestion`
-- Tmux Auto-Spawn → `tmuxautospawn`
-- Shell Aliases → `shellaliases`
-- CLAUDE.md Rules → `claudemdreinforcement`
-
-Then run:
-```bash
-node .agileflow/scripts/agileflow-configure.js --enable=feature1,feature2
-# or
-node .agileflow/scripts/agileflow-configure.js --disable=feature1,feature2
-```
-
----
-
-### If "Sessions" selected
-
-Present the Sessions sub-menu:
-
-```xml
-<invoke name="AskUserQuestion">
-<parameter name="questions">[{
-  "question": "What session setting would you like to configure?",
-  "header": "Sessions",
-  "multiSelect": false,
-  "options": [
-    {"label": "Default startup mode", "description": "How Claude launches in new sessions (permissions, worktree-only)"},
-    {"label": "Agent Teams", "description": "Enable/disable native multi-agent orchestration (experimental)"}
-  ]
-}]</parameter>
-</invoke>
-```
-
-#### If "Default startup mode" selected
-
-Configure default startup mode for new sessions created with `/agileflow:session:new`.
-
-**How it works**: When skip-permissions is selected, `/configure` sets `permissions.defaultMode = "bypassPermissions"` in `.claude/settings.json`. Claude Code reads this on startup and skips all permission prompts automatically. No CLI flags needed.
-
-First, read current setting:
-```bash
-cat docs/00-meta/agileflow-metadata.json | grep '"defaultStartupMode"' 2>/dev/null || echo "normal"
-```
-
-Then present options:
-```xml
-<invoke name="AskUserQuestion">
-<parameter name="questions">[{
-  "question": "What should be the default Claude startup mode for new sessions?",
-  "header": "Startup",
-  "multiSelect": false,
-  "options": [
-    {"label": "Normal (Recommended)", "description": "Standard Claude with permission prompts"},
-    {"label": "Skip permissions", "description": "claude --dangerously-skip-permissions (trusted mode)"},
-    {"label": "Accept edits only", "description": "claude --permission-mode acceptEdits"},
-    {"label": "Don't start Claude", "description": "Create worktree only, start Claude manually"}
-  ]
-}]</parameter>
-</invoke>
-```
-
-Map selection to value:
-| Selection | Mode value |
-|-----------|------------|
-| Normal | `normal` |
-| Skip permissions | `skip-permissions` |
-| Accept edits only | `accept-edits` |
-| Don't start Claude | `no-claude` |
-
-Run the configure script with `--startup-mode` to set BOTH metadata AND `.claude/settings.json` atomically:
-```bash
-node .agileflow/scripts/agileflow-configure.js --startup-mode={mode_value}
-```
-
-This single command handles everything:
-- Sets `permissions.defaultMode` in `.claude/settings.json` (for skip-permissions/accept-edits)
-- Removes `permissions.defaultMode` from `.claude/settings.json` (for normal/no-claude)
-- Updates `defaultStartupMode` in `docs/00-meta/agileflow-metadata.json`
-- Updates the `claudeFlags` feature metadata
-
-**IMPORTANT**: Do NOT manually edit metadata or settings.json for startup mode. Always use `--startup-mode=` to ensure both files stay in sync.
-
-**If user selected "Skip permissions" or "Accept edits only"**, offer shell alias:
-
-```xml
-<invoke name="AskUserQuestion">
-<parameter name="questions">[{
-  "question": "Also add a shell alias so 'claude' always uses this mode?",
-  "header": "Shell alias",
-  "multiSelect": false,
-  "options": [
-    {"label": "AgileFlow commands only (Recommended)", "description": "Only 'af' and /session:new use this mode. Direct 'claude' command unchanged."},
-    {"label": "Also add shell alias", "description": "Add 'alias claude=\"claude {flag}\"' to shell profile"},
-    {"label": "No thanks", "description": "Keep current setup"}
-  ]
-}]</parameter>
-</invoke>
-```
-
-**If "Also add shell alias" selected:**
-
-Determine the flag based on the selected mode:
-- `skip-permissions` → `--dangerously-skip-permissions`
-- `accept-edits` → `--permission-mode acceptEdits`
-
-```bash
-# Detect shell config file
-SHELL_RC="$HOME/.bashrc"
-[ -f "$HOME/.zshrc" ] && SHELL_RC="$HOME/.zshrc"
-
-# Check if alias already exists
-grep -q 'alias claude=' "$SHELL_RC" 2>/dev/null
-```
-
-If alias doesn't exist, add it using the Edit tool on the shell RC file:
-```bash
-# Append alias (idempotent - only if not already present)
-# For skip-permissions:
-echo 'alias claude="claude --dangerously-skip-permissions"' >> "$SHELL_RC"
-# For accept-edits:
-echo 'alias claude="claude --permission-mode acceptEdits"' >> "$SHELL_RC"
-```
-
-Display:
-```
-✅ Shell alias added to {SHELL_RC}
-Run `source {SHELL_RC}` or open a new terminal for the alias to take effect.
-
-To remove later: edit {SHELL_RC} and remove the 'alias claude=' line.
-```
-
-**If "AgileFlow commands only" or "No thanks" selected:**
-```
-AgileFlow commands (af, /session:new) will use the configured mode automatically.
-Direct 'claude' command remains unchanged.
-```
-
-#### If "Agent Teams" selected
-
-Configure Claude Code's native multi-agent orchestration (experimental feature).
-
-First, read current setting:
-```bash
-node -e "try{const m=JSON.parse(require('fs').readFileSync('docs/00-meta/agileflow-metadata.json','utf8'));console.log(JSON.stringify({enabled:m.features?.agentTeams?.enabled||false}))}catch(e){console.log(JSON.stringify({enabled:false}))}"
-```
-
-Then present options:
-```xml
-<invoke name="AskUserQuestion">
-<parameter name="questions">[{
-  "question": "Enable native Agent Teams? This uses Claude Code's experimental multi-agent orchestration (TeamCreate, SendMessage) for parallel agent coordination.",
-  "header": "Agent Teams",
-  "multiSelect": false,
-  "options": [
-    {"label": "Enable (Recommended)", "description": "Use native Agent Teams when available, subagent fallback when not"},
-    {"label": "Disable", "description": "Always use subagent mode (Task/TaskOutput) for multi-agent work"},
-    {"label": "What is this?", "description": "Learn more about Agent Teams before deciding"}
-  ]
-}]</parameter>
-</invoke>
-```
-
-**If "Enable" selected:**
-```bash
-node .agileflow/scripts/agileflow-configure.js --enable=agentteams
-```
-
-This sets `CLAUDE_CODE_EXPERIMENTAL_AGENT_TEAMS=1` in `.claude/settings.json` under the `env` key.
-Claude Code reads this automatically on startup - no manual env var setup needed.
-
-Display:
-```
-✅ Native Agent Teams enabled
-
-What was configured:
-  • Set CLAUDE_CODE_EXPERIMENTAL_AGENT_TEAMS=1 in .claude/settings.json
-  • Claude Code will use native TeamCreate/SendMessage tools
-  • Fallback: subagent mode (Task/TaskOutput) when native is unavailable
-
-⚠️  Restart Claude Code for the env var to take effect.
-```
-
-**If "Disable" selected:**
-```bash
-node .agileflow/scripts/agileflow-configure.js --disable=agentteams
-```
-
-This removes `CLAUDE_CODE_EXPERIMENTAL_AGENT_TEAMS` from `.claude/settings.json`.
-
-Display:
-```
-✅ Native Agent Teams disabled
-
-What was configured:
-  • Removed CLAUDE_CODE_EXPERIMENTAL_AGENT_TEAMS from .claude/settings.json
-  • AgileFlow will use subagent mode (Task/TaskOutput) for all multi-agent orchestration
-
-⚠️  Restart Claude Code for the change to take effect.
-```
-
-**If "What is this?" selected:**
-
-Display this explanation:
-```
-## Agent Teams (Experimental)
-
-Claude Code's native Agent Teams feature enables parallel multi-agent
-orchestration with explicit coordination tools:
-
-  • TeamCreate/TeamDelete - Spawn and manage agent teams
-  • SendMessage - Direct agent-to-agent communication (3ms vs 150ms JSONL)
-  • Enhanced TaskCreate/Update - Native task coordination
-
-How AgileFlow integrates:
-  1. When enabled, team-manager.js builds native TeamCreate payloads
-  2. messaging-bridge.js sends to BOTH native channel AND JSONL bus
-  3. damage-control-multi-agent.js validates Team/Task operations
-  4. Subagent mode remains available as automatic fallback
-
-Requirements:
-  • /configure sets CLAUDE_CODE_EXPERIMENTAL_AGENT_TEAMS=1 in .claude/settings.json automatically
-  • Feature is opt-in per project via this configuration
-  • CI/CD always uses subagent mode (safety gate)
-```
-
-Then re-ask the enable/disable question.
-
----
-
-### If "Infrastructure" selected
-
-```xml
-<invoke name="AskUserQuestion">
-<parameter name="questions">[{
-  "question": "What infrastructure to set up?",
-  "header": "Setup",
-  "multiSelect": false,
-  "options": [
-    {"label": "UI Testing (Bowser)", "description": "Agentic browser testing + visual verification with Playwright"},
-    {"label": "Damage Control", "description": "Block destructive commands, protect sensitive paths"},
-    {"label": "CI/CD Workflow", "description": "GitHub Actions for automated testing"},
-    {"label": "Quality Gates", "description": "Configure TeammateIdle and TaskCompleted gate thresholds"}
-  ]
-}]</parameter>
-</invoke>
-```
-
-Handle each selection directly:
-
-- **UI Testing (Bowser)**: `node .agileflow/scripts/agileflow-configure.js --enable=browserqa`
-- **Damage Control**: `node .agileflow/scripts/agileflow-configure.js --enable=damagecontrol`
-- **CI/CD**: `node .agileflow/scripts/agileflow-configure.js --enable=ci`
-- **Quality Gates**: Update `docs/00-meta/agileflow-metadata.json` under the `quality_gates` key with enable/disable for tests, lint, types gates per hook and coverage thresholds
-
----
-
-### If "Maintenance" selected
-
-```xml
-<invoke name="AskUserQuestion">
-<parameter name="questions">[{
-  "question": "What maintenance task?",
-  "header": "Maintenance",
-  "multiSelect": false,
-  "options": [
-    {"label": "Apply new options", "description": "Enable newly available configuration options"},
-    {"label": "Fix format issues", "description": "Migrate invalid settings to correct format"},
-    {"label": "Upgrade scripts", "description": "Update features to latest AgileFlow version"},
-    {"label": "Repair missing scripts", "description": "Restore accidentally deleted scripts"}
-  ]
-}]</parameter>
-</invoke>
-```
-
-Then run:
-- "Apply new options" → Show available new options and apply selected ones (see below)
-- "Fix format issues" → `node .agileflow/scripts/agileflow-configure.js --migrate`
-- "Upgrade scripts" → `node .agileflow/scripts/agileflow-configure.js --upgrade`
-- "Repair missing scripts" → `node .agileflow/scripts/agileflow-configure.js --repair`
-
-#### If "Apply new options" selected
-
-Check for unconfigured options:
-```bash
-node .agileflow/scripts/agileflow-configure.js --new-options
-```
-
-If new options found, present them:
-```xml
-<invoke name="AskUserQuestion">
-<parameter name="questions">[{
-  "question": "Which new options do you want to enable?",
-  "header": "New Options",
-  "multiSelect": true,
-  "options": [
-    {"label": "CLAUDE.md reinforcement", "description": "Add /babysit context preservation rules to CLAUDE.md"},
-    {"label": "Skip for now", "description": "Don't enable any new options"}
-  ]
-}]</parameter>
-</invoke>
-```
-
-Then apply selected options:
-```bash
-node .agileflow/scripts/agileflow-configure.js --apply-option=claudeMdReinforcement
-```
-
-If no new options: "✅ All configuration options are up to date!"
-
----
-
-## Profile Details
-
-| Profile | SessionStart | PreCompact | RalphLoop | SelfImprove | Archival | StatusLine | AskUserQuestion | Full File Injection |
-|---------|-------------|------------|-----------|-------------|----------|------------|-----------------|---------------------|
-| `full` | ✅ | ✅ | ✅ | ✅ | ✅ 30 days | ✅ | ✅ | ❌ |
-| `basic` | ✅ | ✅ | ❌ | ❌ | ✅ 30 days | ❌ | ✅ | ❌ |
-| `minimal` | ✅ | ❌ | ❌ | ❌ | ✅ 30 days | ❌ | ❌ | ❌ |
-| `experimental` | ✅ | ✅ | ✅ | ✅ | ✅ 30 days | ✅ | ✅ | ⚠️ **YES** |
-| `none` | ❌ | ❌ | ❌ | ❌ | ❌ | ❌ | ❌ | ❌ |
-
-**⚠️ Experimental Profile Warning:**
-The `experimental` profile enables **Full File Injection** during context compaction. Instead of injecting compact summaries (~200-500 tokens), it injects the **entire command file** (~2000-5000+ tokens per command). This is very context-heavy but may improve instruction adherence for complex commands like `/babysit`.
-
-**Note:** Shell Aliases and CLAUDE.md Rules are **not** included in any profile. These are per-user preferences that must be explicitly enabled:
-- `--enable=shellaliases` - Adds `af` and `agileflow` commands to ~/.bashrc and ~/.zshrc
-- `--enable=claudemdreinforcement` - Adds /babysit context preservation rules to CLAUDE.md
-
-## CLI Commands Reference
-
-```bash
-# Preset Profiles
-node .agileflow/scripts/agileflow-configure.js --profile=full
-node .agileflow/scripts/agileflow-configure.js --profile=basic
-node .agileflow/scripts/agileflow-configure.js --profile=minimal
-node .agileflow/scripts/agileflow-configure.js --profile=experimental
-node .agileflow/scripts/agileflow-configure.js --profile=none
-
-# Custom Profiles
-node .agileflow/scripts/agileflow-configure.js --profile=my-custom-profile    # Apply custom
-node .agileflow/scripts/agileflow-configure.js --save-profile=my-setup        # Save current
-node .agileflow/scripts/agileflow-configure.js --list-profiles                # List all
-node .agileflow/scripts/agileflow-configure.js --list-profiles --verbose      # With details
-node .agileflow/scripts/agileflow-configure.js --delete-profile=my-setup      # Delete
-
-# Export/Import Profiles (for sharing)
-node .agileflow/scripts/agileflow-configure.js --export-profile=my-setup --output=my-setup.json
-node .agileflow/scripts/agileflow-configure.js --import-profile=my-setup.json
-
-# Enable/disable features
-node .agileflow/scripts/agileflow-configure.js --enable=sessionstart,precompact
-node .agileflow/scripts/agileflow-configure.js --disable=statusline
-node .agileflow/scripts/agileflow-configure.js --enable=archival --archival-days=14
-node .agileflow/scripts/agileflow-configure.js --enable=shellaliases
-node .agileflow/scripts/agileflow-configure.js --enable=claudemdreinforcement
-node .agileflow/scripts/agileflow-configure.js --enable=agentteams
-node .agileflow/scripts/agileflow-configure.js --disable=agentteams
-
-# Maintenance
-node .agileflow/scripts/agileflow-configure.js --detect
-node .agileflow/scripts/agileflow-configure.js --migrate
-node .agileflow/scripts/agileflow-configure.js --upgrade
-node .agileflow/scripts/agileflow-configure.js --repair
-node .agileflow/scripts/agileflow-configure.js --list-scripts
-node .agileflow/scripts/agileflow-configure.js --version
-
-# New config options
-node .agileflow/scripts/agileflow-configure.js --new-options                  # List unconfigured options
-node .agileflow/scripts/agileflow-configure.js --apply-option=optionName      # Apply specific option
-```
-
-## Custom Profiles
-
-Custom profiles let you save and reuse your preferred feature combinations.
-
-### Data Model
-
-Profiles are stored in `docs/00-meta/agileflow-metadata.json`:
-
-```json
-{
-  "version": "2.78.0",
-  "profiles": {
-    "my-backend-setup": {
-      "description": "Backend development - no UI features",
-      "created": "2026-01-09T10:00:00.000Z",
-      "features": {
-        "sessionstart": true,
-        "precompact": true,
-        "ralphloop": true,
-        "selfimprove": false,
-        "archival": true,
-        "statusline": false,
-        "autoupdate": true,
-        "askuserquestion": false
-      }
-    },
-    "ui-heavy": {
-      "description": "UI development with visual verification",
-      "created": "2026-01-09T10:00:00.000Z",
-      "features": {
-        "sessionstart": true,
-        "precompact": true,
-        "ralphloop": true,
-        "selfimprove": false,
-        "archival": true,
-        "statusline": true,
-        "autoupdate": false,
-        "askuserquestion": true
-      }
-    }
-  },
-  "features": { ... }
-}
-```
-
-### Export Format
-
-Exported profiles use this format (for sharing):
-
-```json
-{
-  "name": "my-backend-setup",
-  "description": "Backend development - no UI features",
-  "agileflow_version": "2.78.0",
-  "exported": "2026-01-09T10:00:00.000Z",
-  "features": {
-    "sessionstart": true,
-    "precompact": true,
-    "ralphloop": true,
-    "selfimprove": false,
-    "archival": true,
-    "statusline": false,
-    "autoupdate": true,
-    "askuserquestion": false
-  }
-}
-```
-
-### Sharing Profiles
-
-1. **Export**: `--export-profile=my-setup --output=my-setup.json`
-2. **Share**: Send the JSON file to teammate
-3. **Import**: `--import-profile=my-setup.json`
-
-Imported profiles are added to the local metadata with the same name.
-
-## Auto-Update Configuration
-
-Enable auto-update to automatically update AgileFlow when a new version is available:
-
-```bash
-# Enable auto-update
-node .agileflow/scripts/agileflow-configure.js --enable=autoupdate
-
-# Or manually edit docs/00-meta/agileflow-metadata.json:
-```
-
-```json
-{
-  "updates": {
-    "autoUpdate": true,
-    "checkFrequency": "daily"
-  }
-}
-```
-
-**Check frequencies:** `hourly`, `daily`, `weekly`, `never`
-
-## AskUserQuestion Mode
-
-Enable AskUserQuestion to have all commands end with guided options:
-
-```bash
-# Enable AskUserQuestion mode
-node .agileflow/scripts/agileflow-configure.js --enable=askuserquestion
-
-# Disable AskUserQuestion mode
-node .agileflow/scripts/agileflow-configure.js --disable=askuserquestion
-```
-
-**What it does:**
-- When enabled: All commands end with AskUserQuestion tool call (guided options)
-- When disabled: Commands can end with natural text questions
-
-**Storage in metadata:**
-```json
-{
-  "features": {
-    "askUserQuestion": {
-      "enabled": true,
-      "mode": "all"
-    }
-  }
-}
-```
-
-**Modes:**
-- `all`: All commands use AskUserQuestion (default)
-- `interactive`: Only interactive commands (babysit, mentor, configure, epic-planner)
-- `none`: Disabled
-
-The guidance is injected via `obtain-context.js` when commands run.
-
-## Stop Hook Features
-
-Stop hooks run when Claude completes a task or pauses for user input. These enable autonomous workflows.
-
-### RalphLoop (`ralphloop`)
-
-Autonomous story processing loop (named after the "Ralph Wiggum" pattern):
-- Runs tests automatically when Claude stops
-- If tests pass → marks story as completed, loads next story in epic
-- If tests fail → shows failures for Claude to fix
-- Tracks iterations with configurable limits (default: 20)
-- Enable: `--enable=ralphloop`
-
-**How to use:**
-1. Enable: `node .agileflow/scripts/agileflow-configure.js --enable=ralphloop`
-2. Start a loop: `node .agileflow/scripts/ralph-loop.js --init --epic=EP-XXXX`
-3. Work on stories - tests run automatically when Claude stops
-4. Check status: `node .agileflow/scripts/ralph-loop.js --status`
-5. Stop loop: `node .agileflow/scripts/ralph-loop.js --stop`
-
-### SelfImprove (`selfimprove`)
-
-Automatic agent expertise learning:
-- Analyzes git changes when Claude stops
-- Detects which domain (database, api, ui, etc.) was modified
-- Appends learnings to the relevant agent's expertise.yaml
-- Helps agents improve over time based on actual work
-- Enable: `--enable=selfimprove`
-
-**What it learns:**
-- Files modified per domain
-- New patterns discovered
-- Test file changes
-- Configuration updates
-
-Both Stop hooks use error suppression (`2>/dev/null || true`) to avoid blocking Claude if they fail.
-
-## Format Migration Details
-
-The script handles these migrations automatically:
-
-**Hook string format:**
-```json
-// OLD (invalid)
-"PreCompact": "./.agileflow/scripts/precompact-context.sh"
-
-// NEW (valid)
-"PreCompact": [{"matcher": "", "hooks": [{"type": "command", "command": "bash ./.agileflow/scripts/precompact-context.sh"}]}]
-```
-
-**StatusLine missing type:**
-```json
-// OLD (invalid)
-"statusLine": {"command": "./.agileflow/scripts/statusline.sh", "refreshInterval": 5000}
-
-// NEW (valid)
-"statusLine": {"type": "command", "command": "./.agileflow/scripts/statusline.sh", "padding": 0}
-```
-
-## Metadata Tracking
-
-The script updates `docs/00-meta/agileflow-metadata.json`:
-
-```json
-{
-  "version": "2.71.0",
-  "updated": "2025-12-29T...",
-  "archival": {
-    "enabled": true,
-    "threshold_days": 7
-  },
-  "features": {
-    "sessionstart": {"enabled": true, "version": "2.71.0", "at": "..."},
-    "precompact": {"enabled": true, "version": "2.71.0", "at": "..."},
-    "archival": {"enabled": true, "version": "2.71.0", "at": "..."},
-    "statusline": {"enabled": true, "version": "2.71.0", "at": "..."}
-  }
-}
-```
-
-## Rules
-
-1. **Always show detection first** - User sees current state before changes
-2. **Auto-migrate on enable** - Script fixes format issues automatically when enabling features
-3. **Backup on migrate** - Creates `.claude/settings.json.backup`
-4. **Restart reminder** - Always show red banner after changes
-
-## Output Format
-
-After configuration:
-
-```
-✅ Configuration Complete!
-
-Enabled:
-  ✅ sessionstart
-  ✅ precompact
-  ✅ archival
-
-Disabled:
-  ❌ statusline
-
-═══════════════════════════════════════════════════════
-🔴 RESTART CLAUDE CODE NOW!
-   Quit completely, wait 5 seconds, restart
-═══════════════════════════════════════════════════════
-```
-
-After upgrade:
-
-```
-🔄 Upgrading Outdated Features...
-
-Upgrading sessionstart...
-✅ Deployed agileflow-welcome.js
-✅ SessionStart hook enabled
-
-Upgrading precompact...
-✅ Deployed precompact-context.sh
-✅ PreCompact hook enabled
-
-✅ Upgraded 2 feature(s) to v2.71.0
-```
-
-## Repair & Diagnostics
-
-When scripts are accidentally deleted or corrupted, use these commands:
-
-### List Scripts Status
-
-```bash
-node .agileflow/scripts/agileflow-configure.js --list-scripts
-```
-
-Shows all scripts with their status (present/missing/modified):
-
-```
-📋 Installed Scripts
-  ✅ agileflow-welcome.js: present
-  ✅ precompact-context.sh: present
-  ❌ agileflow-statusline.sh: MISSING
-     └─ Feature: statusline
-  ⚠️  obtain-context.js: modified (local changes)
-
-Summary: 15 present, 1 modified, 1 missing
-
-💡 Run with --repair to restore missing scripts
-```
-
-### Show Version Info
-
-```bash
-node .agileflow/scripts/agileflow-configure.js --version
-```
-
-Shows installed vs latest versions:
-
-```
-📊 Version Information
-Installed:  v2.71.0
-CLI:        v2.73.0
-Latest:     v2.73.0
-
-🔄 Update available! Run: npx agileflow update
-
-Feature Versions:
-  ✅ sessionstart: v2.73.0
-  🔄 precompact: v2.68.0 → v2.73.0
-  ✅ archival: v2.73.0
-  ❌ statusline: disabled
-```
-
-### Repair Missing Scripts
-
-```bash
-# Repair all missing scripts
-node .agileflow/scripts/agileflow-configure.js --repair
-
-# Repair scripts for a specific feature only
-node .agileflow/scripts/agileflow-configure.js --repair=statusline
-```
-
-Output:
-
-```
-🔧 Repairing Scripts...
-✅ Restored agileflow-statusline.sh
-
-Repaired: 1, Errors: 0, Skipped: 18
-
-═══════════════════════════════════════════════════════
-🔴 RESTART CLAUDE CODE NOW!
-   Quit completely, wait 5 seconds, restart
-═══════════════════════════════════════════════════════
-```
-
-### When to Use Each Command
-
-| Scenario | Command |
-|----------|---------|
-| Accidentally deleted a script | `--repair` |
-| Want to see what's installed | `--list-scripts` |
-| Check if update is available | `--version` |
-| Scripts outdated (feature version differs) | `--upgrade` |
-| Settings format broken | `--migrate` |
-| Major corruption/reinstall needed | `npx agileflow update --force`
-
----
-
-## Expected Output
-
-### Success - Feature Enabled
-
-```
-🔧 AgileFlow Configuration
-══════════════════════════════════════════════════════════════
-
-Enabling feature: damage-control
-
-✓ Created .claude/hooks/PreToolUse/damage-control-bash.js
-✓ Created .claude/hooks/PreToolUse/damage-control-edit.js
-✓ Created .claude/hooks/patterns.yaml
-✓ Updated settings.json
-
-━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
-✅ damage-control enabled
-━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
-
-31 protection patterns active.
-Test: Try running a blocked command to verify.
-```
-
-### Success - List Features
-
-```
-🔧 AgileFlow Configuration
-══════════════════════════════════════════════════════════════
-
-Installed Features:
-✅ damage-control (v2.94.1) - 31 patterns
-✅ precompact (v2.94.1) - context preservation
-✅ status-line (v2.94.1) - story tracking
-⚪ browserqa (not installed)
-⚪ hooks (not installed)
-
-Scripts:
-✅ obtain-context.js (v2.94.1)
-✅ archive-completed-stories.sh (v2.94.1)
-
-Run /agileflow:configure FEATURE=<name> to install features.
-```
-
-### Error - Unknown Feature
-
-```
-❌ Error: Unknown feature: super-ai
-
-Available features:
-- damage-control: Protect against destructive commands
-- precompact: Context preservation during compaction
-- status-line: Story status in Claude Code UI
-- browserqa: Agentic browser testing + visual verification
-- hooks: Event-driven automation
-- ci: CI/CD workflow setup
-
-Usage: /agileflow:configure FEATURE=damage-control
-```
-
----
-
-## Related Commands
-
-- `/agileflow:ci` - Bootstrap CI/CD workflow
-- `/agileflow:deploy` - Set up deployment pipeline
-- `/agileflow:tests` - Set up testing infrastructure
-- `/agileflow:template` - Manage custom templates
-- `/agileflow:diagnose` - System health diagnostics
-- `/agileflow:help` - Display AgileFlow overview