proagents 1.0.18 → 1.2.0

package/README.md

@@ -149,15 +149,32 @@ Type these in any AI assistant (Claude, ChatGPT, Gemini, Cursor, etc.):
 | `pa:d` | `pa:doc` |
 | `pa:t` | `pa:test` |
 | `pa:q` | `pa:qa` |
+| `pa:a` | `pa:analyze` |
+| `pa:r` | `pa:requirements` |
+| `pa:p` | `pa:plan` |
+| `pa:i` | `pa:implement` |
 
 ### Core Commands
 | Command | Description |
 |---------|-------------|
-| `pa:feature "name"` | Start new feature workflow |
+| `pa:feature "name"` | Start new feature workflow (all phases) |
 | `pa:fix "description"` | Quick bug fix mode |
 | `pa:status` | Show current progress |
 | `pa:help` | Show all commands |
 
+### Workflow Phase Commands
+| Command | Phase | Description |
+|---------|-------|-------------|
+| `pa:analyze` | Analysis | Deep codebase analysis |
+| `pa:requirements` | Requirements | Gather feature requirements |
+| `pa:design` | Design | UI/Architecture design |
+| `pa:plan` | Planning | Create implementation plan |
+| `pa:implement` | Implementation | Execute code changes |
+| `pa:test` | Testing | Create and run tests |
+| `pa:review` | Review | Code review workflow |
+| `pa:doc` | Documentation | Generate documentation |
+| `pa:deploy` | Deployment | Deployment preparation |
+
 ### Documentation
 | Command | Description |
 |---------|-------------|
@@ -169,8 +186,7 @@ Type these in any AI assistant (Claude, ChatGPT, Gemini, Cursor, etc.):
 | Command | Description |
 |---------|-------------|
 | `pa:qa` | Run quality assurance checks |
-| `pa:test` | Run test workflow |
-| `pa:deploy` | Deployment preparation |
+| `pa:rollback` | Rollback procedures |
 
 ### Multi-AI Collaboration
 | Command | Description |
@@ -198,6 +214,96 @@ Type these in any AI assistant (Claude, ChatGPT, Gemini, Cursor, etc.):
 | `pa:ai-add` | Add more AI platforms |
 | `pa:ai-sync` | Sync config with files |
 
+### Navigation & Flow
+| Command | Description |
+|---------|-------------|
+| `pa:next` | Show next step in workflow |
+| `pa:resume` | Resume paused feature |
+| `pa:skip` | Skip current phase |
+| `pa:back` | Go to previous phase |
+| `pa:progress` | Show visual progress bar |
+
+### Context & History
+| Command | Description |
+|---------|-------------|
+| `pa:context` | View project context |
+| `pa:diff` | Show changes since last session |
+| `pa:history` | Show command history |
+| `pa:checkpoint` | Create restore point |
+| `pa:undo` | Undo last action |
+
+### Sprint & Estimation
+| Command | Description |
+|---------|-------------|
+| `pa:sprint-start` | Start new sprint |
+| `pa:sprint-end` | End sprint with summary |
+| `pa:estimate` | Estimate task complexity |
+| `pa:velocity` | Show velocity metrics |
+
+### Integration
+| Command | Description |
+|---------|-------------|
+| `pa:github` | GitHub integration |
+| `pa:github-pr` | Create pull request |
+| `pa:jira` | Sync with Jira |
+| `pa:notify` | Send notification |
+
+### Code Quality
+| Command | Description |
+|---------|-------------|
+| `pa:metrics` | Code quality metrics |
+| `pa:coverage` | Test coverage report |
+| `pa:deps` | Analyze dependencies |
+| `pa:deps-outdated` | Find outdated packages |
+| `pa:deps-security` | Security scan |
+
+### Code Generation
+| Command | Description |
+|---------|-------------|
+| `pa:generate` | Show generation options |
+| `pa:generate-component` | Generate component |
+| `pa:generate-api` | Generate API endpoint |
+| `pa:generate-test` | Generate test file |
+
+### Refactoring
+| Command | Description |
+|---------|-------------|
+| `pa:refactor` | Suggest refactoring |
+| `pa:rename` | Rename across codebase |
+| `pa:extract` | Extract function/component |
+| `pa:cleanup` | Remove dead code |
+
+### Time Tracking
+| Command | Description |
+|---------|-------------|
+| `pa:time-start` | Start time tracking |
+| `pa:time-stop` | Stop tracking |
+| `pa:time-report` | Show time report |
+
+### Environment & Database
+| Command | Description |
+|---------|-------------|
+| `pa:env-check` | Verify environment |
+| `pa:secrets-scan` | Scan for secrets |
+| `pa:db-migrate` | Run migrations |
+| `pa:db-seed` | Seed database |
+
+### Accessibility & Performance
+| Command | Description |
+|---------|-------------|
+| `pa:a11y` | Accessibility audit |
+| `pa:lighthouse` | Lighthouse audit |
+| `pa:perf` | Performance analysis |
+
+### Export & Learning
+| Command | Description |
+|---------|-------------|
+| `pa:export` | Export config/data |
+| `pa:import` | Import data |
+| `pa:backup` | Backup proagents |
+| `pa:learn` | Teach AI a pattern |
+| `pa:suggestions` | Show AI suggestions |
+
 ### Custom Commands
 | Command | Description |
 |---------|-------------|

package/lib/commands/init.js

@@ -784,6 +784,11 @@ function saveProjectConfig(projectConfig, configPath) {
     };
   }
 
+  // Save platforms
+  if (projectConfig.platforms && projectConfig.platforms.length > 0) {
+    config.platforms = projectConfig.platforms;
+  }
+
   const yamlContent = yaml.dump(config, { indent: 2, lineWidth: 120 });
   writeFileSync(configPath, yamlContent);
 }
@@ -997,8 +1002,8 @@ For detailed commands, see \`./proagents/PROAGENTS.md\`
       console.log(chalk.green(`✓ Merged with existing: ${aiResults.merged.join(', ')}`));
     }
 
-    // Save project and platform config
-    const configPath = join(proagentsDir, 'proagents.config.yaml');
+    // Save project and platform config to ROOT config (not proagents/ folder)
+    const configPath = join(targetDir, 'proagents.config.yaml');
     saveProjectConfig(projectConfig, configPath);
     savePlatformConfig(selectedPlatforms, configPath);
 

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "proagents",
-  "version": "1.0.18",
+  "version": "1.2.0",
   "description": "AI-agnostic development workflow framework that automates the full software development lifecycle",
   "type": "module",
   "main": "lib/index.js",

package/proagents/AI_INSTRUCTIONS.md

@@ -237,6 +237,10 @@ When the user types commands starting with `pa:`, recognize and execute them.
 | `pa:d` | `pa:doc` |
 | `pa:t` | `pa:test` |
 | `pa:q` | `pa:qa` |
+| `pa:a` | `pa:analyze` |
+| `pa:r` | `pa:requirements` |
+| `pa:p` | `pa:plan` |
+| `pa:i` | `pa:implement` |
 
 ### Initialization
 | Command | Action |
@@ -255,6 +259,56 @@ When the user types commands starting with `pa:`, recognize and execute them.
 | `pa:feature-complete` | Mark feature complete |
 | `pa:fix "description"` | Quick bug fix mode |
 
+### Workflow Phase Commands
+Run individual phases of the development workflow:
+
+| Command | Phase | Action |
+|---------|-------|--------|
+| `pa:analyze` | Analysis | Deep codebase analysis - structure, patterns, dependencies |
+| `pa:analyze-full` | Analysis | Comprehensive analysis with full depth |
+| `pa:analyze-quick` | Analysis | Quick overview analysis |
+| `pa:requirements` | Requirements | Gather and document feature requirements |
+| `pa:requirements "feature"` | Requirements | Requirements for specific feature |
+| `pa:design` | Design | UI/UX and architecture design |
+| `pa:design-ui` | Design | Focus on UI/UX design |
+| `pa:design-arch` | Design | Focus on architecture design |
+| `pa:plan` | Planning | Create implementation plan |
+| `pa:plan "feature"` | Planning | Plan specific feature implementation |
+| `pa:implement` | Implementation | Execute implementation phase |
+| `pa:implement-continue` | Implementation | Continue paused implementation |
+
+**How to execute Workflow Phase commands:**
+
+For `pa:analyze`:
+1. Read `./proagents/prompts/01-analysis.md` for analysis workflow
+2. Scan project structure, dependencies, patterns
+3. Cache results in `./proagents/cache/`
+4. Output analysis report
+
+For `pa:requirements`:
+1. Read `./proagents/prompts/02-requirements.md`
+2. If feature name provided, create `./proagents/active-features/feature-{name}/requirements.md`
+3. Gather user stories, acceptance criteria, constraints
+4. Output requirements document
+
+For `pa:design`:
+1. Read `./proagents/prompts/03-ui-design.md`
+2. Check for design inputs (Figma, sketches, exports)
+3. Create component specifications
+4. Output design document
+
+For `pa:plan`:
+1. Read `./proagents/prompts/04-planning.md`
+2. Create implementation plan with task breakdown
+3. Identify dependencies and risks
+4. Save to `./proagents/active-features/feature-{name}/implementation-plan.md`
+
+For `pa:implement`:
+1. Read `./proagents/prompts/05-implementation.md`
+2. Follow existing project patterns
+3. Implement code changes
+4. Log progress to activity.log
+
 ### Documentation Commands
 | Command | Action |
 |---------|--------|
@@ -283,6 +337,580 @@ When the user types commands starting with `pa:`, recognize and execute them.
 | `pa:deploy` | Deployment preparation |
 | `pa:rollback` | Rollback procedures |
 
+### Navigation & Flow
+| Command | Action |
+|---------|--------|
+| `pa:next` | Show next step in current workflow |
+| `pa:resume` | Resume paused feature from where left off |
+| `pa:skip` | Skip current phase, move to next |
+| `pa:back` | Go back to previous phase |
+| `pa:progress` | Show visual progress bar for current feature |
+
+**How to execute Navigation commands:**
+
+For `pa:next`:
+1. Read `./proagents/active-features/*/status.json` to find current feature
+2. Identify current phase from status
+3. Show what the next step/phase is
+4. Provide guidance for the next action
+
+For `pa:resume`:
+1. Read `./proagents/active-features/` to find paused features
+2. Read feature's `status.json` for last phase and progress
+3. Read `./proagents/handoff.md` for context
+4. Continue from where it was left off
+
+For `pa:skip`:
+1. Read current feature status
+2. Mark current phase as "skipped" in status.json
+3. Move to next phase
+4. Log skip reason to activity.log
+5. Warn if skipping critical phase (testing, review)
+
+For `pa:back`:
+1. Read current feature status
+2. Move to previous phase
+3. Update status.json
+4. Reload context from previous phase
+
+For `pa:progress`:
+1. Read `./proagents/active-features/*/status.json`
+2. Calculate percentage complete (current_phase / total_phases)
+3. Display visual progress bar:
+   ```
+   Feature: user-auth
+   Phase: 5/10 (Implementation)
+   Progress: [████████░░░░░░░░░░░░] 50%
+
+   ✓ Init → ✓ Analysis → ✓ Requirements → ✓ Design → ● Implementation → ○ Testing → ○ Review → ○ Docs → ○ Deploy
+   ```
+
+### Context & History
+| Command | Action |
+|---------|--------|
+| `pa:context` | Quick view/edit project context |
+| `pa:context-edit` | Edit project context interactively |
+| `pa:diff` | Show what changed since last session |
+| `pa:history` | Show command history with results |
+| `pa:checkpoint` | Create a snapshot/restore point |
+| `pa:checkpoint-restore` | Restore from a checkpoint |
+| `pa:undo` | Undo last AI action using git |
+
+**How to execute Context & History commands:**
+
+For `pa:context`:
+1. Read `./proagents/context.md`
+2. Display current project context summary
+3. Show last updated timestamp
+
+For `pa:diff`:
+1. Read `./proagents/activity.log` for last session timestamp
+2. Run `git diff` from that point
+3. Summarize changes by file/module
+4. Highlight significant changes
+
+For `pa:history`:
+1. Read `./proagents/history.log`
+2. Show recent commands with their results
+3. Format: `[timestamp] command → result`
+
+For `pa:checkpoint`:
+1. Create git commit with message "checkpoint: [description]"
+2. Save checkpoint info to `./proagents/checkpoints.json`:
+   ```json
+   {
+     "checkpoints": [
+       {
+         "id": "cp-001",
+         "timestamp": "2024-03-06T15:00:00Z",
+         "commit": "abc123",
+         "description": "Before auth refactor",
+         "feature": "user-auth",
+         "phase": "implementation"
+       }
+     ]
+   }
+   ```
+3. Log to activity.log
+
+For `pa:undo`:
+1. Read last action from `./proagents/activity.log`
+2. If file changes, run `git checkout` to revert
+3. If multiple files, offer selective undo
+4. Update activity.log with undo entry
+
+### Sprint & Project Management
+| Command | Action |
+|---------|--------|
+| `pa:sprint-start` | Start a new sprint |
+| `pa:sprint-end` | End sprint with summary |
+| `pa:sprint-status` | Show current sprint status |
+| `pa:estimate` | Estimate task complexity |
+| `pa:estimate "task"` | Estimate specific task |
+| `pa:velocity` | Show team velocity metrics |
+
+**How to execute Sprint commands:**
+
+For `pa:sprint-start`:
+1. Create `./proagents/sprints/sprint-{number}.json`:
+   ```json
+   {
+     "sprint_number": 1,
+     "start_date": "2024-03-06",
+     "end_date": "2024-03-20",
+     "goals": [],
+     "features": [],
+     "status": "active"
+   }
+   ```
+2. Ask for sprint goals
+3. Link active features to sprint
+
+For `pa:sprint-end`:
+1. Read current sprint file
+2. Calculate metrics (completed features, velocity)
+3. Generate sprint summary → `./proagents/sprints/sprint-{n}-summary.md`
+4. Archive sprint
+
+For `pa:estimate`:
+1. Analyze task/feature complexity
+2. Consider: code changes, files affected, dependencies, testing needs
+3. Provide estimate in story points or T-shirt sizes (S/M/L/XL)
+4. Save estimate to feature status.json
+
+For `pa:velocity`:
+1. Read completed sprints from `./proagents/sprints/`
+2. Calculate average story points per sprint
+3. Show velocity chart/trend
+
+### Integration Commands
+| Command | Action |
+|---------|--------|
+| `pa:github` | GitHub integration commands |
+| `pa:github-issue` | Create GitHub issue from current work |
+| `pa:github-pr` | Create pull request |
+| `pa:jira` | Jira integration commands |
+| `pa:jira-sync` | Sync with Jira ticket |
+| `pa:notify` | Send notification |
+| `pa:notify-slack` | Send Slack notification |
+| `pa:notify-email` | Send email notification |
+
+**How to execute Integration commands:**
+
+For `pa:github-issue`:
+1. Read current feature/bug context
+2. Generate issue title and body
+3. Show preview and ask for confirmation
+4. Provide `gh issue create` command or API call
+
+For `pa:github-pr`:
+1. Read current feature context
+2. Generate PR title and description
+3. Include: summary, changes, test plan
+4. Provide `gh pr create` command
+
+For `pa:jira-sync`:
+1. Read Jira config from `proagents.config.yaml`
+2. Find linked ticket (from feature name or config)
+3. Update ticket status based on feature phase
+4. Add comment with progress
+
+For `pa:notify`:
+1. Read notification config from `proagents.config.yaml`
+2. Generate notification message based on context
+3. Send via configured channel (Slack webhook, email, etc.)
+
+### Code Quality Commands
+| Command | Action |
+|---------|--------|
+| `pa:metrics` | Show code quality metrics |
+| `pa:metrics-history` | Show metrics over time |
+| `pa:coverage` | Show test coverage report |
+| `pa:coverage-diff` | Show coverage changes |
+| `pa:deps` | Analyze dependencies |
+| `pa:deps-outdated` | Find outdated dependencies |
+| `pa:deps-security` | Security scan dependencies |
+
+**How to execute Code Quality commands:**
+
+For `pa:metrics`:
+1. Analyze codebase for:
+   - Lines of code (by language)
+   - Cyclomatic complexity
+   - Code duplication
+   - Function/file sizes
+2. Save to `./proagents/metrics/latest.json`
+3. Display summary with warnings for issues
+
+For `pa:coverage`:
+1. Check for coverage reports (coverage/, .nyc_output/, etc.)
+2. Parse coverage data
+3. Display summary:
+   ```
+   Test Coverage Report
+   ═══════════════════
+   Overall: 82% ✓
+
+   By Module:
+   • src/auth/     95% ████████████████████ ✓
+   • src/api/      78% ███████████████░░░░░
+   • src/utils/    65% █████████████░░░░░░░ ⚠
+   ```
+
+For `pa:deps`:
+1. Read package.json / requirements.txt
+2. Analyze dependency tree
+3. Identify:
+   - Direct vs transitive deps
+   - Duplicate packages
+   - Large dependencies
+   - Outdated versions
+
+For `pa:deps-security`:
+1. Run `npm audit` or equivalent
+2. Parse security advisories
+3. Categorize by severity
+4. Suggest fixes
+
+### Code Generation
+| Command | Action |
+|---------|--------|
+| `pa:generate` | Show generation options |
+| `pa:generate-component "name"` | Generate React/Vue component |
+| `pa:generate-api "name"` | Generate API endpoint |
+| `pa:generate-test "file"` | Generate test file for module |
+| `pa:generate-hook "name"` | Generate custom hook |
+| `pa:generate-service "name"` | Generate service class |
+
+**How to execute Code Generation commands:**
+
+For `pa:generate-component`:
+1. Read project type and patterns from `./proagents/cache/patterns.json`
+2. Use template from `./proagents/scaffolding/` matching project type
+3. Apply project naming conventions
+4. Create component file with:
+   - Component code
+   - Types/interfaces
+   - Basic styles (if applicable)
+   - Test file (optional)
+5. Save to appropriate directory based on project structure
+
+For `pa:generate-api`:
+1. Detect API framework (Express, Next.js, NestJS, etc.)
+2. Use appropriate template
+3. Generate:
+   - Route handler
+   - Input validation
+   - Error handling
+   - Types
+4. Add to routes index if applicable
+
+For `pa:generate-test`:
+1. Read the source file
+2. Detect testing framework (Jest, Vitest, etc.)
+3. Generate test file with:
+   - Import statements
+   - Describe blocks
+   - Test cases for each function
+   - Mock setup
+4. Save alongside source or in tests/ folder
+
+### Refactoring
+| Command | Action |
+|---------|--------|
+| `pa:refactor` | Analyze and suggest refactoring |
+| `pa:refactor "file"` | Refactor specific file |
+| `pa:rename "old" "new"` | Rename symbol across codebase |
+| `pa:extract "name"` | Extract function/component |
+| `pa:cleanup` | Remove dead code, unused imports |
+| `pa:cleanup-imports` | Clean up imports only |
+
+**How to execute Refactoring commands:**
+
+For `pa:refactor`:
+1. Analyze codebase for:
+   - Long functions (>50 lines)
+   - Deep nesting (>3 levels)
+   - Duplicate code
+   - Complex conditionals
+   - God classes/components
+2. Prioritize by impact
+3. Suggest specific refactoring for each issue
+4. Offer to apply refactoring
+
+For `pa:rename`:
+1. Find all occurrences of symbol
+2. Check for naming conflicts
+3. Show preview of changes
+4. Apply rename across all files
+5. Update imports/exports
+
+For `pa:cleanup`:
+1. Find unused imports
+2. Find unused variables
+3. Find dead code (unreachable)
+4. Find unused exports
+5. Show list and offer to remove
+6. Log changes to activity.log
+
+### Time Tracking
+| Command | Action |
+|---------|--------|
+| `pa:time-start` | Start time tracking |
+| `pa:time-start "task"` | Start tracking specific task |
+| `pa:time-stop` | Stop current time tracking |
+| `pa:time-pause` | Pause time tracking |
+| `pa:time-report` | Show time report |
+| `pa:time-report "feature"` | Report for specific feature |
+
+**How to execute Time Tracking commands:**
+
+For `pa:time-start`:
+1. Create/update `./proagents/time-tracking.json`:
+   ```json
+   {
+     "current": {
+       "task": "feature-user-auth",
+       "started": "2024-03-06T15:00:00Z",
+       "status": "running"
+     },
+     "entries": []
+   }
+   ```
+2. Log to activity.log
+
+For `pa:time-stop`:
+1. Read current tracking
+2. Calculate duration
+3. Add to entries array:
+   ```json
+   {
+     "task": "feature-user-auth",
+     "started": "2024-03-06T15:00:00Z",
+     "ended": "2024-03-06T17:30:00Z",
+     "duration_minutes": 150,
+     "ai": "Claude:opus-4"
+   }
+   ```
+4. Clear current tracking
+
+For `pa:time-report`:
+1. Read all entries from time-tracking.json
+2. Group by task/feature
+3. Calculate totals
+4. Display report:
+   ```
+   Time Report
+   ═══════════
+   Feature: user-auth
+   Total: 5h 30m
+   Sessions: 3
+
+   Feature: dashboard
+   Total: 2h 15m
+   Sessions: 2
+   ```
+
+### Environment & Setup
+| Command | Action |
+|---------|--------|
+| `pa:env-check` | Verify environment setup |
+| `pa:env-setup` | Setup development environment |
+| `pa:env-diff` | Compare environments |
+| `pa:secrets-scan` | Scan for exposed secrets |
+| `pa:secrets-check` | Verify required secrets exist |
+
+**How to execute Environment commands:**
+
+For `pa:env-check`:
+1. Check for required files (.env, .env.local, etc.)
+2. Verify Node/Python/etc. version matches
+3. Check for required dependencies
+4. Verify database connection (if applicable)
+5. Check for required environment variables
+6. Report status:
+   ```
+   Environment Check
+   ═════════════════
+   ✓ Node.js v18.17.0 (required: >=18)
+   ✓ npm v9.6.0
+   ✓ .env.local exists
+   ⚠ DATABASE_URL not set
+   ✗ Redis not running
+   ```
+
+For `pa:secrets-scan`:
+1. Scan codebase for patterns:
+   - API keys (sk_, pk_, api_key, etc.)
+   - Passwords in code
+   - Private keys
+   - Connection strings
+2. Check .gitignore for sensitive files
+3. Report findings with file locations
+4. Suggest fixes (move to .env, etc.)
+
+### Database Commands
+| Command | Action |
+|---------|--------|
+| `pa:db-migrate` | Run database migrations |
+| `pa:db-migrate-create "name"` | Create new migration |
+| `pa:db-seed` | Seed database with test data |
+| `pa:db-reset` | Reset database |
+| `pa:db-status` | Show migration status |
+
+**How to execute Database commands:**
+
+For `pa:db-migrate`:
+1. Detect ORM (Prisma, TypeORM, Sequelize, Drizzle, etc.)
+2. Run appropriate migrate command:
+   - Prisma: `npx prisma migrate dev`
+   - TypeORM: `npm run typeorm migration:run`
+3. Report results
+
+For `pa:db-seed`:
+1. Find seed files (prisma/seed.ts, seeds/, etc.)
+2. Run seed command
+3. Report inserted records
+
+For `pa:db-reset`:
+1. Warn user about data loss
+2. Require confirmation
+3. Drop and recreate database
+4. Run migrations
+5. Optionally run seeds
+
+### Accessibility & Performance
+| Command | Action |
+|---------|--------|
+| `pa:a11y` | Run accessibility audit |
+| `pa:a11y "url"` | Audit specific page |
+| `pa:lighthouse` | Run Lighthouse audit |
+| `pa:lighthouse "url"` | Audit specific URL |
+| `pa:perf` | Performance analysis |
+| `pa:perf-bundle` | Bundle size analysis |
+
+**How to execute A11y & Performance commands:**
+
+For `pa:a11y`:
+1. Check for a11y tools (axe, pa11y, etc.)
+2. Run audit on pages/components
+3. Report issues by severity:
+   ```
+   Accessibility Audit
+   ═══════════════════
+   Critical: 2
+   Serious: 5
+   Moderate: 12
+   Minor: 8
+
+   Top Issues:
+   • Missing alt text on images (5 instances)
+   • Low color contrast (3 instances)
+   • Missing form labels (2 instances)
+   ```
+4. Link to WCAG guidelines for each issue
+
+For `pa:lighthouse`:
+1. Check if Lighthouse is available
+2. Run audit (provide command or use API)
+3. Parse results
+4. Display scores:
+   ```
+   Lighthouse Scores
+   ═════════════════
+   Performance:    85 ████████░░
+   Accessibility:  92 █████████░
+   Best Practices: 100 ██████████
+   SEO:            90 █████████░
+   ```
+
+For `pa:perf`:
+1. Analyze:
+   - Bundle sizes
+   - Load times
+   - Render performance
+   - Memory usage patterns
+2. Identify bottlenecks
+3. Suggest optimizations
+
+### Export & Backup
+| Command | Action |
+|---------|--------|
+| `pa:export` | Export ProAgents config and data |
+| `pa:export-config` | Export only configuration |
+| `pa:import` | Import from export file |
+| `pa:backup` | Create full backup |
+| `pa:backup-restore` | Restore from backup |
+
+**How to execute Export & Backup commands:**
+
+For `pa:export`:
+1. Gather all ProAgents data:
+   - proagents.config.yaml
+   - context.md
+   - decisions.md
+   - feedback.md
+   - active-features/
+   - learned patterns
+2. Create export file: `proagents-export-YYYY-MM-DD.json`
+3. Optionally encrypt sensitive data
+
+For `pa:import`:
+1. Read export file
+2. Validate format
+3. Merge or replace existing data
+4. Report what was imported
+
+For `pa:backup`:
+1. Create timestamped backup of entire proagents/ folder
+2. Save to `./proagents/backups/` or specified location
+3. Compress if large
+4. Maintain rolling backups (keep last N)
+
+### Learning & AI
+| Command | Action |
+|---------|--------|
+| `pa:learn "pattern"` | Teach AI a new pattern |
+| `pa:learn-from "file"` | Learn patterns from file |
+| `pa:forget "pattern"` | Remove learned pattern |
+| `pa:suggestions` | Show AI suggestions for project |
+| `pa:suggestions-apply` | Apply a suggestion |
+
+**How to execute Learning commands:**
+
+For `pa:learn`:
+1. Parse the pattern description
+2. Add to `./proagents/.learning/`:
+   ```json
+   {
+     "pattern": "Always use React Query for API calls",
+     "type": "preference",
+     "added": "2024-03-06",
+     "added_by": "user",
+     "applies_to": ["api", "data-fetching"]
+   }
+   ```
+3. Confirm pattern learned
+
+For `pa:forget`:
+1. Find matching pattern
+2. Remove from learning data
+3. Confirm removal
+
+For `pa:suggestions`:
+1. Analyze project state
+2. Check learned patterns
+3. Generate suggestions:
+   ```
+   AI Suggestions
+   ══════════════
+   1. [Code Quality] Consider adding error boundaries to page components
+   2. [Performance] Bundle size increased 15% - review new dependencies
+   3. [Testing] Test coverage dropped below 80% in src/utils/
+   4. [Security] 2 dependencies have known vulnerabilities
+   ```
+4. Offer to apply each suggestion
+
 ### AI Platform Management
 | Command | Action |
 |---------|--------|

package/proagents/PROAGENTS.md

@@ -3,7 +3,7 @@
 Execute these commands when user types them (prefix: `pa:`):
 
 ## Quick Aliases
-`pa:f` → feature | `pa:s` → status | `pa:h` → help | `pa:d` → doc | `pa:t` → test | `pa:q` → qa
+`pa:f` → feature | `pa:s` → status | `pa:h` → help | `pa:d` → doc | `pa:t` → test | `pa:q` → qa | `pa:a` → analyze | `pa:r` → requirements | `pa:p` → plan | `pa:i` → implement
 
 > **Multi-AI Note:** Multiple AIs may work on this project. Always read `./proagents/activity.log` before executing commands, and log your actions after completing them.
 
@@ -14,6 +14,11 @@ Execute these commands when user types them (prefix: `pa:`):
 | `pa:help` | Show this command table |
 | `pa:feature "name"` | Create `./proagents/active-features/feature-[name]/`, analyze codebase, implement feature |
 | `pa:fix "description"` | Find bug, fix it, update `./CHANGELOG.md` |
+| `pa:analyze` | Deep codebase analysis → `./proagents/cache/` |
+| `pa:requirements` | Gather requirements → `./proagents/active-features/` |
+| `pa:design` | UI/Architecture design phase |
+| `pa:plan` | Create implementation plan |
+| `pa:implement` | Execute implementation phase |
 | `pa:status` | Read `./proagents/active-features/*/status.json`, show progress |
 | `pa:qa` | Check code quality, run tests, report issues |
 | `pa:test` | Create/run tests for current work |
@@ -36,6 +41,120 @@ Execute these commands when user types them (prefix: `pa:`):
 | `pa:standup` | Generate daily standup summary |
 | `pa:tech-debt` | Scan for technical debt |
 
+## Navigation & Flow
+
+| Command | What to Do |
+|---------|------------|
+| `pa:next` | Show next step in current workflow |
+| `pa:resume` | Resume paused feature from last checkpoint |
+| `pa:skip` | Skip current phase, move to next |
+| `pa:back` | Go back to previous phase |
+| `pa:progress` | Show visual progress bar |
+
+## Context & History
+
+| Command | What to Do |
+|---------|------------|
+| `pa:context` | View project context |
+| `pa:diff` | Show changes since last session |
+| `pa:history` | Show command history with results |
+| `pa:checkpoint` | Create snapshot/restore point |
+| `pa:undo` | Undo last AI action (git revert) |
+
+## Sprint & Estimation
+
+| Command | What to Do |
+|---------|------------|
+| `pa:sprint-start` | Start new sprint → `./proagents/sprints/` |
+| `pa:sprint-end` | End sprint with summary |
+| `pa:estimate` | Estimate task complexity (S/M/L/XL) |
+| `pa:velocity` | Show velocity metrics |
+
+## Integration
+
+| Command | What to Do |
+|---------|------------|
+| `pa:github` | GitHub commands (issue, PR) |
+| `pa:github-pr` | Create pull request |
+| `pa:jira` | Sync with Jira ticket |
+| `pa:notify` | Send notification (Slack/email) |
+
+## Code Quality
+
+| Command | What to Do |
+|---------|------------|
+| `pa:metrics` | Show code quality metrics |
+| `pa:coverage` | Show test coverage report |
+| `pa:deps` | Analyze dependencies |
+| `pa:deps-outdated` | Find outdated packages |
+| `pa:deps-security` | Security scan dependencies |
+
+## Code Generation
+
+| Command | What to Do |
+|---------|------------|
+| `pa:generate` | Show generation options |
+| `pa:generate-component "name"` | Generate component from template |
+| `pa:generate-api "name"` | Generate API endpoint |
+| `pa:generate-test "file"` | Generate test file |
+
+## Refactoring
+
+| Command | What to Do |
+|---------|------------|
+| `pa:refactor` | Suggest refactoring opportunities |
+| `pa:rename "old" "new"` | Rename across codebase |
+| `pa:extract "name"` | Extract function/component |
+| `pa:cleanup` | Remove dead code, unused imports |
+
+## Time Tracking
+
+| Command | What to Do |
+|---------|------------|
+| `pa:time-start` | Start tracking → `./proagents/time-tracking.json` |
+| `pa:time-stop` | Stop tracking, save duration |
+| `pa:time-report` | Show time report by feature |
+
+## Environment & Setup
+
+| Command | What to Do |
+|---------|------------|
+| `pa:env-check` | Verify environment setup |
+| `pa:env-setup` | Setup dev environment |
+| `pa:secrets-scan` | Scan for exposed secrets |
+
+## Database
+
+| Command | What to Do |
+|---------|------------|
+| `pa:db-migrate` | Run database migrations |
+| `pa:db-seed` | Seed with test data |
+| `pa:db-reset` | Reset database (caution!) |
+
+## Accessibility & Performance
+
+| Command | What to Do |
+|---------|------------|
+| `pa:a11y` | Run accessibility audit |
+| `pa:lighthouse` | Run Lighthouse audit |
+| `pa:perf` | Performance analysis |
+
+## Export & Backup
+
+| Command | What to Do |
+|---------|------------|
+| `pa:export` | Export config/data → JSON file |
+| `pa:import` | Import from export file |
+| `pa:backup` | Backup proagents folder |
+
+## Learning & AI
+
+| Command | What to Do |
+|---------|------------|
+| `pa:learn "pattern"` | Teach AI a pattern |
+| `pa:forget "pattern"` | Remove learned pattern |
+| `pa:suggestions` | Show AI suggestions |
+
 ## Key Files to Read
 
 | File | Purpose |
@@ -48,16 +167,20 @@ Execute these commands when user types them (prefix: `pa:`):
 
 ## Feature Workflow
 
-`pa:feature` follows these phases:
-1. **Init** → Create tracking files
-2. **Analysis** → Understand existing code
-3. **Requirements** → Define what to build
-4. **Design** → Plan architecture
-5. **Implementation** → Write code
-6. **Testing** → Create tests
-7. **Review** → Quality check
-8. **Documentation** → Update docs
-9. **Deploy** → Prepare release
+`pa:feature` runs all phases, or run individually:
+
+| Phase | Command | Action |
+|-------|---------|--------|
+| 1. Init | `pa:feature "name"` | Create tracking files |
+| 2. Analysis | `pa:analyze` | Understand existing code |
+| 3. Requirements | `pa:requirements` | Define what to build |
+| 4. Design | `pa:design` | Plan UI/architecture |
+| 5. Planning | `pa:plan` | Create implementation plan |
+| 6. Implementation | `pa:implement` | Write code |
+| 7. Testing | `pa:test` | Create/run tests |
+| 8. Review | `pa:review` | Quality check |
+| 9. Documentation | `pa:doc` | Update docs |
+| 10. Deployment | `pa:deploy` | Prepare release |
 
 ## Save Locations
 

package/proagents/backups/README.md

@@ -0,0 +1,34 @@
+# Backups
+
+This folder contains ProAgents backups created with `pa:backup`.
+
+## Commands
+
+- `pa:backup` - Create full backup
+- `pa:backup-restore` - Restore from backup
+
+## Backup Format
+
+Backups are stored as timestamped folders or compressed archives:
+
+```
+backups/
+├── 2024-03-06-150000/
+│   ├── proagents.config.yaml
+│   ├── context.md
+│   ├── decisions.md
+│   ├── feedback.md
+│   ├── active-features/
+│   └── ...
+└── 2024-03-05-100000.tar.gz
+```
+
+## Retention
+
+By default, the last 5 backups are kept. Configure in proagents.config.yaml:
+
+```yaml
+backup:
+  retention: 5
+  compress: true
+```

package/proagents/checkpoints.json

@@ -0,0 +1,13 @@
+{
+  "checkpoints": [],
+  "_comment": "Checkpoints are created with pa:checkpoint command",
+  "_format": {
+    "id": "cp-001",
+    "timestamp": "2024-03-06T15:00:00Z",
+    "commit": "abc123def",
+    "description": "Before major refactor",
+    "feature": "feature-name",
+    "phase": "implementation",
+    "created_by": "Claude:opus-4"
+  }
+}

package/proagents/metrics/README.md

@@ -1,174 +1,69 @@
-# Metrics & KPIs
+# Code Metrics
 
-Track development productivity, code quality, and workflow effectiveness.
+This folder contains code quality metrics and reports.
 
----
+## Commands
 
-## Overview
+- `pa:metrics` - Show current code quality metrics
+- `pa:metrics-history` - Show metrics over time
+- `pa:coverage` - Show test coverage report
+- `pa:coverage-diff` - Show coverage changes
 
-ProAgents provides comprehensive metrics collection and KPI tracking to help teams understand their development velocity, code quality, and workflow effectiveness.
+## Files
 
----
-
-## Available Metrics
-
-| Category | Document | Description |
-|----------|----------|-------------|
-| [Developer Productivity](./developer-productivity.md) | Velocity, cycle time, throughput | Track team and individual efficiency |
-| [Code Quality KPIs](./code-quality-kpis.md) | Coverage, complexity, debt | Measure code health over time |
-| [Deployment Metrics](./deployment-metrics.md) | DORA, frequency, stability | Track delivery performance |
-| [Learning Effectiveness](./learning-effectiveness.md) | Adoption, improvement rates | Measure workflow optimization |
-
----
-
-## Quick Start
-
-### Enable Metrics Collection
-
-```yaml
-# proagents.config.yaml
-metrics:
-  enabled: true
-
-  collection:
-    developer_productivity: true
-    code_quality: true
-    deployment: true
-    learning: true
-
-  storage:
-    type: "local"  # local, database, api
-    path: ".proagents/metrics/"
-    retention_days: 90
-
-  reporting:
-    schedule: "weekly"  # daily, weekly, monthly
-    format: "markdown"  # markdown, json, html
-    output: "./reports/"
 ```
-
----
-
-## Dashboard Commands
-
-```bash
-# View current metrics dashboard
-pa:metrics dashboard
-
-# Generate weekly report
-pa:metrics report --period weekly
-
-# View specific category
-pa:metrics productivity
-pa:metrics quality
-pa:metrics deployment
-
-# Export metrics
-pa:metrics export --format json --output ./metrics.json
+metrics/
+├── latest.json         # Most recent metrics snapshot
+├── history/            # Historical metrics
+│   ├── 2024-03-01.json
+│   └── 2024-03-15.json
+└── README.md
 ```
 
----
-
-## Metric Categories
-
-### Developer Productivity Metrics
-
-| Metric | Description | Target |
-|--------|-------------|--------|
-| Cycle Time | Time from start to completion | < 3 days |
-| Throughput | Features completed per sprint | Consistent |
-| Lead Time | Time from request to delivery | < 1 week |
-| WIP | Work in progress count | < 3 per dev |
-
-### Code Quality Metrics
-
-| Metric | Description | Target |
-|--------|-------------|--------|
-| Test Coverage | Percentage of code tested | > 80% |
-| Code Complexity | Cyclomatic complexity | < 10 |
-| Tech Debt Ratio | Debt vs development time | < 5% |
-| Duplication | Duplicated code percentage | < 3% |
-
-### Deployment Metrics (DORA)
-
-| Metric | Description | Elite Target |
-|--------|-------------|--------------|
-| Deployment Frequency | How often you deploy | Multiple/day |
-| Lead Time for Changes | Commit to production | < 1 hour |
-| Change Failure Rate | Deployments causing failure | < 5% |
-| MTTR | Mean time to recovery | < 1 hour |
-
----
-
-## Integration
-
-### With CI/CD
-
-```yaml
-# .github/workflows/metrics.yml
-- name: Collect ProAgents Metrics
-  run: |
-    proagents metrics collect \
-      --coverage ./coverage/lcov.info \
-      --tests ./test-results.xml \
-      --commit ${{ github.sha }}
-```
-
-### With Dashboards
-
-```yaml
-# Export to external dashboards
-metrics:
-  export:
-    grafana:
-      enabled: true
-      endpoint: "${GRAFANA_URL}"
-    datadog:
-      enabled: true
-      api_key: "${DD_API_KEY}"
-```
-
----
-
-## Reports
-
-### Weekly Summary Template
-
-```markdown
-## Development Metrics - Week {{week}}
-
-### Productivity
-- Features Completed: {{features_completed}}
-- Average Cycle Time: {{avg_cycle_time}}
-- Throughput Trend: {{throughput_trend}}
-
-### Code Quality
-- Test Coverage: {{coverage}}% ({{coverage_trend}})
-- New Technical Debt: {{new_debt}}
-- Debt Resolved: {{resolved_debt}}
-
-### Deployment
-- Deployments: {{deployment_count}}
-- Success Rate: {{success_rate}}%
-- Average Lead Time: {{avg_lead_time}}
-
-### Highlights
-{{#each highlights}}
-- {{this}}
-{{/each}}
-
-### Action Items
-{{#each actions}}
-- [ ] {{this}}
-{{/each}}
+## Metrics Format
+
+```json
+{
+  "timestamp": "2024-03-06T15:00:00Z",
+  "generated_by": "Claude:opus-4",
+  "summary": {
+    "total_files": 45,
+    "total_lines": 12500,
+    "languages": {
+      "typescript": 10200,
+      "javascript": 1500,
+      "css": 800
+    }
+  },
+  "quality": {
+    "complexity": {
+      "average": 4.2,
+      "max": 15,
+      "high_complexity_files": ["src/utils/parser.ts"]
+    },
+    "duplication": {
+      "percentage": 3.5,
+      "duplicated_blocks": 12
+    }
+  },
+  "coverage": {
+    "overall": 82,
+    "by_module": {
+      "src/auth": 95,
+      "src/api": 78,
+      "src/utils": 65
+    }
+  }
+}
 ```
 
----
+## Thresholds
 
-## Best Practices
+Default thresholds (customize in proagents.config.yaml):
 
-1. **Focus on Trends**: Individual metrics matter less than trends over time
-2. **Context Matters**: Compare metrics within similar project types
-3. **Avoid Gaming**: Use metrics for improvement, not punishment
-4. **Regular Review**: Schedule weekly metric reviews
-5. **Team Ownership**: Let teams define their own targets
+| Metric | Warning | Error |
+|--------|---------|-------|
+| Coverage | < 70% | < 50% |
+| Complexity | > 10 | > 20 |
+| File size | > 300 lines | > 500 lines |
+| Duplication | > 5% | > 10% |

package/proagents/sprints/README.md

@@ -0,0 +1,58 @@
+# Sprints
+
+This folder contains sprint tracking files.
+
+## Commands
+
+- `pa:sprint-start` - Start a new sprint
+- `pa:sprint-end` - End sprint with summary
+- `pa:sprint-status` - Show current sprint status
+- `pa:velocity` - Show velocity metrics
+
+## File Structure
+
+```
+sprints/
+├── sprint-1.json           # Sprint data
+├── sprint-1-summary.md     # Sprint summary (generated on end)
+├── sprint-2.json
+└── sprint-2-summary.md
+```
+
+## Sprint File Format
+
+```json
+{
+  "sprint_number": 1,
+  "name": "Sprint 1",
+  "start_date": "2024-03-01",
+  "end_date": "2024-03-15",
+  "status": "active",
+  "goals": [
+    "Complete user authentication",
+    "Add dashboard UI"
+  ],
+  "features": [
+    {
+      "name": "user-auth",
+      "status": "completed",
+      "points": 8
+    },
+    {
+      "name": "dashboard",
+      "status": "in_progress",
+      "points": 5
+    }
+  ],
+  "metrics": {
+    "planned_points": 13,
+    "completed_points": 8,
+    "velocity": 8
+  }
+}
+```
+
+## Velocity Tracking
+
+Velocity is calculated as the average story points completed per sprint.
+Use `pa:velocity` to see trends over time.

package/proagents/time-tracking.json

@@ -0,0 +1,19 @@
+{
+  "current": null,
+  "entries": [],
+  "_comment": "Time tracking data managed by pa:time-start/stop commands",
+  "_format": {
+    "current": {
+      "task": "feature-name",
+      "started": "2024-03-06T15:00:00Z",
+      "status": "running"
+    },
+    "entry": {
+      "task": "feature-name",
+      "started": "2024-03-06T15:00:00Z",
+      "ended": "2024-03-06T17:30:00Z",
+      "duration_minutes": 150,
+      "ai": "Claude:opus-4"
+    }
+  }
+}