proagents 1.0.0

package/proagents/cli/commands-reference.md

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+# CLI Commands Reference
+
+Complete reference for all ProAgents CLI commands.
+
+---
+
+## Core Commands
+
+### `proagents init`
+
+Initialize ProAgents in a project.
+
+```bash
+proagents init [options]
+
+Options:
+  --type <type>        Project type (web-frontend, fullstack, mobile, backend)
+  --template <name>    Use specific template
+  --force              Overwrite existing configuration
+  --minimal            Minimal setup (config only)
+```
+
+**Examples:**
+```bash
+# Interactive initialization
+proagents init
+
+# Specify project type
+proagents init --type fullstack
+
+# Use template
+proagents init --template nextjs
+
+# Minimal setup
+proagents init --minimal
+```
+
+---
+
+### `proagents status`
+
+Show current workflow status.
+
+```bash
+proagents status [options]
+
+Options:
+  --all                Show all features (active, paused, completed)
+  --feature <name>     Show specific feature status
+  --json               Output as JSON
+  --verbose            Detailed status
+```
+
+**Examples:**
+```bash
+# Current feature status
+proagents status
+
+# All features
+proagents status --all
+
+# Specific feature
+proagents status --feature user-auth
+```
+
+**Output:**
+```
+┌─────────────────────────────────────────────────────────────┐
+│ ProAgents Status                                            │
+├─────────────────────────────────────────────────────────────┤
+│ Current Feature: user-authentication                        │
+│ Mode: Full Workflow                                         │
+│ Phase: Implementation (5/9)                                 │
+│ Progress: 60%                                               │
+├─────────────────────────────────────────────────────────────┤
+│ Files Modified: 8                                           │
+│ Tests: 12 passing, 0 failing                               │
+│ Time Elapsed: 2h 15m                                        │
+└─────────────────────────────────────────────────────────────┘
+```
+
+---
+
+### `proagents help`
+
+Show help information.
+
+```bash
+proagents help [command]
+
+Arguments:
+  command              Command to get help for
+```
+
+**Examples:**
+```bash
+# General help
+proagents help
+
+# Feature command help
+proagents help feature
+
+# Analyze command help
+proagents help analyze
+```
+
+---
+
+### `proagents doctor`
+
+Check system health and configuration.
+
+```bash
+proagents doctor [options]
+
+Options:
+  --fix                Auto-fix issues where possible
+  --check-conflicts    Check for command conflicts
+  --verbose            Detailed output
+```
+
+**Output:**
+```
+┌─────────────────────────────────────────────────────────────┐
+│ ProAgents Health Check                                      │
+├─────────────────────────────────────────────────────────────┤
+│ ✅ CLI Version: 1.0.0                                       │
+│ ✅ Node.js: v18.17.0                                        │
+│ ✅ Git: v2.40.0                                             │
+│ ✅ Configuration: Valid                                     │
+│ ⚠️  Missing optional: Figma API token                       │
+│ ✅ Workspace: Initialized                                   │
+└─────────────────────────────────────────────────────────────┘
+```
+
+---
+
+## Feature Commands
+
+### `proagents feature start`
+
+Start a new feature development.
+
+```bash
+proagents feature start <name> [options]
+
+Arguments:
+  name                 Feature name or description
+
+Options:
+  --mode <mode>        Workflow mode (full, bug-fix, quick)
+  --branch <name>      Custom branch name
+  --from <branch>      Base branch (default: develop)
+  --checkpoint <level> Checkpoint level (all, critical, none)
+  --skip-analysis      Skip codebase analysis
+  --no-branch          Don't create git branch
+```
+
+**Examples:**
+```bash
+# Start with auto-detected mode
+proagents feature start "Add user profile page"
+
+# Force full workflow
+proagents feature start "Add payment integration" --mode full
+
+# Custom branch
+proagents feature start "Login fix" --branch hotfix/login-fix
+
+# Skip analysis (use cached)
+proagents feature start "Quick update" --skip-analysis
+```
+
+---
+
+### `proagents feature status`
+
+Show current feature status.
+
+```bash
+proagents feature status [name] [options]
+
+Arguments:
+  name                 Feature name (optional, defaults to current)
+
+Options:
+  --json               Output as JSON
+  --verbose            Detailed status
+```
+
+---
+
+### `proagents feature list`
+
+List all features.
+
+```bash
+proagents feature list [options]
+
+Options:
+  --active             Show only active features
+  --completed          Show only completed features
+  --paused             Show only paused features
+  --json               Output as JSON
+```
+
+**Output:**
+```
+┌─────────────────────────────────────────────────────────────┐
+│ Features                                                    │
+├─────────────────────────────────────────────────────────────┤
+│ Active:                                                     │
+│ • user-authentication (Phase 5/9, 60%)                     │
+│ • dashboard (Phase 3/9, 30%)                               │
+├─────────────────────────────────────────────────────────────┤
+│ Paused:                                                     │
+│ • notifications (Phase 2/9) - Waiting for API             │
+├─────────────────────────────────────────────────────────────┤
+│ Completed (Last 7 days):                                   │
+│ • user-settings (Jan 15)                                   │
+│ • profile-page (Jan 12)                                    │
+└─────────────────────────────────────────────────────────────┘
+```
+
+---
+
+### `proagents feature pause`
+
+Pause current feature.
+
+```bash
+proagents feature pause [name] [options]
+
+Arguments:
+  name                 Feature name (optional)
+
+Options:
+  --note <text>        Add pause note
+  --reason <reason>    Reason for pausing
+```
+
+**Examples:**
+```bash
+# Pause current feature
+proagents feature pause
+
+# Pause with note
+proagents feature pause --note "Waiting for design review"
+
+# Pause specific feature
+proagents feature pause dashboard --reason "dependency-blocked"
+```
+
+---
+
+### `proagents feature resume`
+
+Resume a paused feature.
+
+```bash
+proagents feature resume [name] [options]
+
+Arguments:
+  name                 Feature name (optional, defaults to last paused)
+
+Options:
+  --from-phase <phase> Resume from specific phase
+  --refresh            Refresh codebase analysis
+```
+
+**Examples:**
+```bash
+# Resume last paused
+proagents feature resume
+
+# Resume specific feature
+proagents feature resume dashboard
+
+# Resume from earlier phase
+proagents feature resume --from-phase analysis
+```
+
+---
+
+### `proagents feature complete`
+
+Mark feature as complete.
+
+```bash
+proagents feature complete [name] [options]
+
+Arguments:
+  name                 Feature name (optional)
+
+Options:
+  --skip-checks        Skip completion checks
+  --archive            Archive feature files
+```
+
+---
+
+## Bug Fix Commands
+
+### `proagents fix`
+
+Start bug fix mode.
+
+```bash
+proagents fix <description> [options]
+
+Arguments:
+  description          Bug description
+
+Options:
+  --issue <id>         Link to issue/ticket
+  --priority <level>   Priority (low, medium, high, critical)
+  --files <files>      Specific files to fix
+  --upgrade            Upgrade to full workflow if needed
+```
+
+**Examples:**
+```bash
+# Simple bug fix
+proagents fix "Login button not responding"
+
+# With issue reference
+proagents fix "Auth token expiring early" --issue PROJ-123
+
+# Critical priority
+proagents fix "Security vulnerability in auth" --priority critical
+
+# Specific files
+proagents fix "Button styling issue" --files "src/components/Button.tsx"
+```
+
+---
+
+### `proagents hotfix`
+
+Emergency hotfix for production issues.
+
+```bash
+proagents hotfix <description> [options]
+
+Arguments:
+  description          Issue description
+
+Options:
+  --issue <id>         Link to issue/ticket
+  --from <branch>      Branch to hotfix from (default: main)
+  --skip-tests         Skip tests (not recommended)
+```
+
+**Examples:**
+```bash
+# Production hotfix
+proagents hotfix "Critical auth bypass"
+
+# From specific branch
+proagents hotfix "Payment failure" --from release/v2.0
+```
+
+---
+
+## Analysis Commands
+
+### `proagents analyze`
+
+Analyze codebase.
+
+```bash
+proagents analyze [path] [options]
+
+Arguments:
+  path                 Path to analyze (optional, defaults to project root)
+
+Options:
+  --depth <level>      Analysis depth (full, moderate, lite)
+  --focus <areas>      Focus areas (structure, patterns, dependencies)
+  --output <file>      Output file path
+  --refresh            Force refresh (ignore cache)
+  --module <name>      Analyze specific module
+```
+
+**Examples:**
+```bash
+# Full project analysis
+proagents analyze
+
+# Moderate depth
+proagents analyze --depth moderate
+
+# Specific path
+proagents analyze ./src/auth --depth full
+
+# Focus on patterns
+proagents analyze --focus patterns,dependencies
+
+# Output to file
+proagents analyze --output analysis-report.md
+```
+
+---
+
+## Testing Commands
+
+### `proagents test`
+
+Run tests.
+
+```bash
+proagents test [pattern] [options]
+
+Arguments:
+  pattern              Test file pattern (optional)
+
+Options:
+  --unit               Run unit tests only
+  --integration        Run integration tests only
+  --e2e                Run e2e tests only
+  --all                Run all tests
+  --coverage           Generate coverage report
+  --affected           Test only affected files
+  --watch              Watch mode
+  --verbose            Verbose output
+```
+
+**Examples:**
+```bash
+# Run all tests
+proagents test
+
+# Unit tests only
+proagents test --unit
+
+# With coverage
+proagents test --coverage
+
+# Affected files only
+proagents test --affected
+
+# Specific pattern
+proagents test "auth/**/*.test.ts"
+
+# Watch mode
+proagents test --watch
+```
+
+---
+
+## Documentation Commands
+
+### `proagents docs`
+
+Generate documentation.
+
+```bash
+proagents docs [path] [options]
+
+Arguments:
+  path                 Path to document (optional)
+
+Options:
+  --mode <mode>        Documentation depth (full, moderate, lite)
+  --scope <scope>      Scope (project, module, folder, file)
+  --format <format>    Output format (markdown, html, pdf)
+  --output <dir>       Output directory
+  --update-only        Update existing docs only
+```
+
+**Examples:**
+```bash
+# Full project docs
+proagents docs
+
+# Moderate depth
+proagents docs --mode moderate
+
+# Specific module
+proagents docs --scope module auth
+
+# Specific file
+proagents docs --scope file ./src/services/AuthService.ts
+
+# Output as HTML
+proagents docs --format html --output ./docs-html
+```
+
+---
+
+## Quality Assurance Commands
+
+### `proagents qa`
+
+Run quality assurance checks.
+
+```bash
+proagents qa [options]
+
+Options:
+  --full               Full QA check
+  --quick              Quick QA check
+  --security           Security focused
+  --performance        Performance focused
+  --fix                Auto-fix issues
+```
+
+**Examples:**
+```bash
+# Full QA
+proagents qa --full
+
+# Quick check
+proagents qa --quick
+
+# Security scan
+proagents qa --security
+
+# Auto-fix
+proagents qa --quick --fix
+```
+
+---
+
+### `proagents lint`
+
+Run linting.
+
+```bash
+proagents lint [path] [options]
+
+Arguments:
+  path                 Path to lint (optional)
+
+Options:
+  --fix                Auto-fix issues
+  --strict             Strict mode (warnings as errors)
+```
+
+---
+
+### `proagents security`
+
+Run security scan.
+
+```bash
+proagents security [options]
+
+Options:
+  --full               Full security audit
+  --dependencies       Scan dependencies only
+  --code               Scan code only
+  --owasp              OWASP compliance check
+```
+
+---
+
+## Git Commands
+
+### `proagents commit`
+
+Create a commit.
+
+```bash
+proagents commit [message] [options]
+
+Arguments:
+  message              Commit message (optional, auto-generated if not provided)
+
+Options:
+  --type <type>        Commit type (feat, fix, docs, refactor, test, chore)
+  --scope <scope>      Commit scope
+  --breaking           Mark as breaking change
+  --staged             Commit staged files only
+  --all                Stage and commit all changes
+```
+
+**Examples:**
+```bash
+# Auto-generate message
+proagents commit
+
+# With message
+proagents commit "Add login validation"
+
+# Feature commit
+proagents commit --type feat "Add user authentication"
+
+# With scope
+proagents commit --type fix --scope auth "Fix token expiration"
+```
+
+---
+
+### `proagents branch`
+
+Branch operations.
+
+```bash
+proagents branch <action> [name] [options]
+
+Actions:
+  create               Create new branch
+  switch               Switch to branch
+  delete               Delete branch
+  list                 List branches
+
+Options:
+  --type <type>        Branch type (feature, hotfix, release)
+  --from <branch>      Base branch
+```
+
+**Examples:**
+```bash
+# Create feature branch
+proagents branch create user-auth --type feature
+
+# Switch branch
+proagents branch switch feature/user-auth
+
+# List branches
+proagents branch list
+```
+
+---
+
+### `proagents pr`
+
+Pull request operations.
+
+```bash
+proagents pr <action> [options]
+
+Actions:
+  create               Create PR
+  update               Update PR
+  merge                Merge PR
+  status               PR status
+
+Options:
+  --title <title>      PR title
+  --body <body>        PR body
+  --draft              Create as draft
+  --reviewers <users>  Add reviewers
+  --labels <labels>    Add labels
+```
+
+**Examples:**
+```bash
+# Create PR
+proagents pr create
+
+# Create with details
+proagents pr create --title "Add authentication" --draft
+
+# Add reviewers
+proagents pr create --reviewers "user1,user2"
+
+# Check status
+proagents pr status
+```
+
+---
+
+## Deployment Commands
+
+### `proagents deploy`
+
+Deploy application.
+
+```bash
+proagents deploy [environment] [options]
+
+Arguments:
+  environment          Target environment (staging, production)
+
+Options:
+  --skip-tests         Skip tests before deploy
+  --skip-build         Skip build step
+  --dry-run            Simulate deployment
+  --tag <tag>          Deploy specific tag
+  --rollback-on-fail   Auto-rollback on failure
+```
+
+**Examples:**
+```bash
+# Deploy to staging
+proagents deploy staging
+
+# Deploy to production
+proagents deploy production
+
+# Dry run
+proagents deploy production --dry-run
+
+# With auto-rollback
+proagents deploy production --rollback-on-fail
+```
+
+---
+
+### `proagents rollback`
+
+Rollback deployment.
+
+```bash
+proagents rollback [environment] [options]
+
+Arguments:
+  environment          Target environment
+
+Options:
+  --to <version>       Rollback to specific version
+  --quick              Quick rollback (skip confirmations)
+  --confirm            Skip confirmation prompt
+```
+
+**Examples:**
+```bash
+# Rollback production
+proagents rollback production
+
+# Rollback to specific version
+proagents rollback production --to v2.3.1
+
+# Quick rollback
+proagents rollback production --quick
+```
+
+---
+
+## Configuration Commands
+
+### `proagents config`
+
+Configuration management.
+
+```bash
+proagents config <action> [key] [value] [options]
+
+Actions:
+  get                  Get config value
+  set                  Set config value
+  list                 List all config
+  edit                 Open config in editor
+  validate             Validate configuration
+  reset                Reset to defaults
+  export               Export configuration
+  import               Import configuration
+
+Options:
+  --global             Global configuration
+  --local              Local (project) configuration
+```
+
+**Examples:**
+```bash
+# Get value
+proagents config get checkpoints.before_deployment
+
+# Set value
+proagents config set checkpoints.before_deployment true
+
+# List all
+proagents config list
+
+# Validate
+proagents config validate
+
+# Export
+proagents config export > backup.yaml
+
+# Import
+proagents config import backup.yaml
+```
+
+---
+
+## Report Commands
+
+### `proagents report`
+
+Generate reports.
+
+```bash
+proagents report <type> [options]
+
+Types:
+  velocity             Development velocity
+  quality              Code quality
+  coverage             Test coverage
+  security             Security status
+  dependencies         Dependency status
+  activity             Team activity
+
+Options:
+  --period <period>    Time period (week, month, quarter)
+  --format <format>    Output format (text, json, pdf, html)
+  --output <file>      Output file
+```
+
+**Examples:**
+```bash
+# Velocity report
+proagents report velocity
+
+# Quality report (monthly)
+proagents report quality --period month
+
+# Output as PDF
+proagents report velocity --format pdf --output report.pdf
+```
+
+---
+
+## Collaboration Commands
+
+### `proagents collab`
+
+Real-time collaboration.
+
+```bash
+proagents collab <action> [session-id] [options]
+
+Actions:
+  start                Start collaboration session
+  join                 Join existing session
+  leave                Leave session
+  status               Session status
+  invite               Invite collaborator
+
+Options:
+  --feature <name>     Feature to collaborate on
+  --role <role>        Your role (primary, reviewer, observer)
+```
+
+**Examples:**
+```bash
+# Start session
+proagents collab start --feature user-auth
+
+# Join session
+proagents collab join abc123
+
+# Invite
+proagents collab invite user@email.com
+```
+
+---
+
+## Utility Commands
+
+### `proagents clean`
+
+Clean up temporary files.
+
+```bash
+proagents clean [options]
+
+Options:
+  --cache              Clean analysis cache
+  --features           Clean completed features
+  --all                Clean everything
+  --dry-run            Show what would be cleaned
+```
+
+---
+
+### `proagents upgrade`
+
+Upgrade ProAgents CLI.
+
+```bash
+proagents upgrade [options]
+
+Options:
+  --check              Check for updates only
+  --beta               Include beta versions
+```
+
+---
+
+### `proagents version`
+
+Show version information.
+
+```bash
+proagents version [options]
+
+Options:
+  --json               Output as JSON
+  --verbose            Show all version info
+```