Appendix B: Quick Command Reference

Essential Commands

Command	Description	Example
`pmat --version`	Display version	`pmat --version`
`pmat help`	Show help	`pmat help analyze`
`pmat init`	Initialize project	`pmat init --template=enterprise`
`pmat status`	Check project status	`pmat status --detailed`

Analysis Commands

Command	Description	Example
`pmat analyze`	Run standard analysis	`pmat analyze .`
`pmat scan`	Quick scan	`pmat scan --focus=security`
`pmat watch`	Continuous monitoring	`pmat watch --on-change`
`pmat analyze tdg`	Technical debt grading	`pmat analyze tdg --detailed`
`pmat complexity`	Complexity analysis	`pmat complexity --by-function`
`pmat similarity`	Code similarity	`pmat similarity --threshold=0.8`
`pmat dead-code`	Dead code detection	`pmat dead-code --export-list`
`pmat satd`	SATD detection	`pmat satd --priority=high`

Configuration

Command	Description	Example
`pmat config list`	List configuration	`pmat config list`
`pmat config get`	Get config value	`pmat config get quality.min_grade`
`pmat config set`	Set config value	`pmat config set analysis.parallel true`
`pmat config reset`	Reset to defaults	`pmat config reset --all`
`pmat config profiles`	Manage profiles	`pmat config profiles switch prod`
`pmat config export`	Export config	`pmat config export > config.toml`
`pmat config import`	Import config	`pmat config import config.toml`

Memory Management

Command	Description	Example
`pmat memory stats`	Memory statistics	`pmat memory stats --verbose`
`pmat memory cleanup`	Clean up memory	`pmat memory cleanup --force-gc`
`pmat memory configure`	Configure limits	`pmat memory configure --max-heap 500`
`pmat memory pools`	Pool statistics	`pmat memory pools`
`pmat memory pressure`	Memory pressure	`pmat memory pressure`

Cache Management

Command	Description	Example
`pmat cache stats`	Cache statistics	`pmat cache stats --verbose`
`pmat cache clear`	Clear cache	`pmat cache clear --all`
`pmat cache optimize`	Optimize cache	`pmat cache optimize`
`pmat cache warmup`	Warmup cache	`pmat cache warmup`
`pmat cache configure`	Configure cache	`pmat cache configure --eviction lru`

Security

Command	Description	Example
`pmat security scan`	Security scan	`pmat security scan --severity=critical`
`pmat dependencies`	Dependency check	`pmat dependencies --check-vulnerabilities`

API Server & Roadmap

Command	Description	Example
`pmat serve`	Start API server	`pmat serve --port 8080`
`pmat serve --metrics`	Server with metrics	`pmat serve --metrics --verbose`
`pmat roadmap init`	Initialize sprint	`pmat roadmap init --sprint v1.0`
`pmat roadmap todos`	Generate todos	`pmat roadmap todos --format markdown`
`pmat roadmap start`	Start task	`pmat roadmap start PMAT-001`
`pmat roadmap complete`	Complete task	`pmat roadmap complete PMAT-001 --quality-check`
`pmat roadmap status`	Sprint status	`pmat roadmap status --format json`
`pmat roadmap validate`	Validate release	`pmat roadmap validate`
`pmat roadmap quality-check`	Quality validation	`pmat roadmap quality-check PMAT-001`

Agent Management

Command	Description	Example
`pmat agent start`	Start background agent	`pmat agent start --project-path .`
`pmat agent stop`	Stop agent daemon	`pmat agent stop`
`pmat agent status`	Show agent status	`pmat agent status --verbose`
`pmat agent health`	Health check	`pmat agent health`
`pmat agent monitor`	Monitor project	`pmat agent monitor --project-id main`
`pmat agent unmonitor`	Stop monitoring	`pmat agent unmonitor --project-id main`
`pmat agent reload`	Reload configuration	`pmat agent reload`
`pmat agent quality-gate`	Quality gate via agent	`pmat agent quality-gate --strict`
`pmat agent mcp-server`	Start MCP server	`pmat agent mcp-server --debug`

AI-Powered Refactoring

Command	Description	Example
`pmat refactor auto`	Automated refactoring	`pmat refactor auto --quality-profile extreme`
`pmat refactor interactive`	Interactive refactoring	`pmat refactor interactive --target-complexity 8`
`pmat refactor serve`	Batch processing server	`pmat refactor serve --port 8080`
`pmat refactor status`	Refactoring status	`pmat refactor status`
`pmat refactor resume`	Resume from checkpoint	`pmat refactor resume --checkpoint state.json`
`pmat refactor docs`	Documentation cleanup	`pmat refactor docs --dry-run`

Template Generation & Scaffolding

Command	Description	Example
`pmat list`	List available templates	`pmat list --format json`
`pmat search`	Search templates	`pmat search "web" --limit 10`
`pmat generate`	Generate single template	`pmat generate rust cli -p name=app`
`pmat validate`	Validate template params	`pmat validate rust web`
`pmat scaffold project`	Scaffold complete project	`pmat scaffold project rust-api --name api`
`pmat scaffold agent`	Scaffold MCP agent	`pmat scaffold agent deterministic --name agent`
`pmat scaffold list-templates`	List agent templates	`pmat scaffold list-templates`
`pmat scaffold validate-template`	Validate agent template	`pmat scaffold validate-template agent.yaml`

System Diagnostics

Command	Description	Example
`pmat diagnose`	Run system diagnostics	`pmat diagnose --verbose`
`pmat diagnose --format json`	JSON diagnostic output	`pmat diagnose --format json > report.json`
`pmat diagnose --only`	Test specific features	`pmat diagnose --only cache --only analysis`
`pmat diagnose --skip`	Skip features	`pmat diagnose --skip telemetry`
`pmat diagnose --timeout`	Set timeout	`pmat diagnose --timeout 30`
`pmat diagnose --troubleshoot`	Troubleshooting mode	`pmat diagnose --troubleshoot`
`pmat diagnose --repair-cache`	Repair cache	`pmat diagnose --repair-cache`
`pmat diagnose --serve`	Start diagnostic server	`pmat diagnose --serve --port 8090`

Performance Testing

Command	Description	Example
`pmat test performance`	Run performance tests	`pmat test performance --verbose`
`pmat test property`	Property-based testing	`pmat test property --cases 10000`
`pmat test memory`	Memory usage testing	`pmat test memory --detect-leaks`
`pmat test throughput`	Throughput testing	`pmat test throughput --rps 1000`
`pmat test regression`	Regression detection	`pmat test regression --threshold 5`
`pmat test integration`	Integration tests	`pmat test integration --full-stack`
`pmat test all`	Run all test suites	`pmat test all --timeout 300`
`pmat test --baseline`	Create baseline	`pmat test performance --baseline`
`pmat secrets`	Secret detection	`pmat secrets scan --all-history`
`pmat compliance`	Compliance check	`pmat compliance --standard=SOC2`
`pmat audit`	Security audit	`pmat audit --comprehensive`

Reporting

Command	Description	Example
`pmat report`	Generate report	`pmat report --format=html`
`pmat report executive`	Executive summary	`pmat report executive --period=monthly`
`pmat export`	Export data	`pmat export --format=json`
`pmat import`	Import data	`pmat import results.json`
`pmat compare`	Compare analyses	`pmat compare baseline.json current.json`
`pmat diff`	Show differences	`pmat diff --from=main --to=feature`
`pmat merge`	Merge reports	`pmat merge *.json --output=combined.json`

Performance

Command	Description	Example
`pmat performance analyze`	Performance analysis	`pmat performance analyze`
`pmat performance hotspots`	Find hotspots	`pmat performance hotspots --top=10`
`pmat performance memory`	Memory analysis	`pmat performance memory --leak-detection`
`pmat performance compare`	Compare performance	`pmat performance compare --baseline=main`

Architecture

Command	Description	Example
`pmat architecture analyze`	Architecture analysis	`pmat architecture analyze`
`pmat architecture deps`	Dependency analysis	`pmat architecture deps --circular`
`pmat architecture patterns`	Pattern detection	`pmat architecture patterns --detect=all`
`pmat architecture validate-layers`	Layer validation	`pmat architecture validate-layers`
`pmat architecture graph`	Generate graph	`pmat architecture graph --output=deps.svg`

Quality Gates

Command	Description	Example
`pmat quality-gate`	Check quality gates	`pmat quality-gate --min-grade=B+`
`pmat repo-score`	Repository health score	`pmat repo-score . --format json`
`pmat rust-project-score`	Rust-specific quality score	`pmat rust-project-score --full`
`pmat popper-score`	Popper falsifiability score	`pmat popper-score --verbose`
`pmat perfection-score`	Unified 200-point quality score	`pmat perfection-score --fast --breakdown`
`pmat validate`	Validate project	`pmat validate --strict`
`pmat check`	Run all checks	`pmat check --all`

Specification Management

Command	Description	Example
`pmat spec score`	Popperian spec validation	`pmat spec score docs/spec.md --verbose`
`pmat spec comply`	Auto-fix spec issues	`pmat spec comply docs/spec.md --dry-run`
`pmat spec create`	Create specification template	`pmat spec create "Feature Name" --issue "#123"`
`pmat spec list`	List all specifications	`pmat spec list docs/specifications/ --failing-only`

Team Collaboration

Command	Description	Example
`pmat team setup`	Setup team	`pmat team setup`
`pmat review prepare`	Prepare review	`pmat review prepare --pr-number=123`
`pmat dashboard serve`	Start dashboard	`pmat dashboard serve --port=8080`
`pmat retrospective`	Generate retrospective	`pmat retrospective generate`

Integration

Command	Description	Example
`pmat serve`	Start HTTP API server	`pmat serve --port=8080 --cors`
`pmat webhook`	Manage webhooks	`pmat webhook create`
`pmat notify`	Send notifications	`pmat notify slack --channel=#alerts`
`pmat pipeline`	Pipeline integration	`pmat pipeline validate`

Plugins

Command	Description	Example
`pmat plugin list`	List plugins	`pmat plugin list`
`pmat plugin install`	Install plugin	`pmat plugin install swift-analyzer`
`pmat plugin update`	Update plugins	`pmat plugin update --all`

AI Features

Command	Description	Example
`pmat ai analyze`	AI analysis	`pmat ai analyze --explain-violations`
`pmat ai suggest`	Get suggestions	`pmat ai suggest-improvements`
`pmat ai refactor`	AI refactoring	`pmat ai refactor --preview`
`pmat ai review`	AI code review	`pmat ai review-pr --number=123`

AI Prompt Generation (Phase 4)

Command	Description	Example
`pmat prompt show`	View workflow prompts	`pmat prompt show code-coverage`
`pmat prompt show --list`	List all prompts	`pmat prompt show --list`
`pmat prompt generate`	Generate defect-aware prompt	`pmat prompt generate --task "Add auth" --summary org.yaml`
`pmat prompt ticket`	EXTREME TDD ticket workflow	`pmat prompt ticket ticket-123.md --summary org.yaml`
`pmat prompt implement`	Spec-based implementation	`pmat prompt implement docs/spec.md`
`pmat prompt scaffold-new-repo`	New repo setup	`pmat prompt scaffold-new-repo docs/spec.md --include-pmat`

Organizational Intelligence (Phase 4)

Command	Description	Example
`pmat org analyze`	Analyze GitHub organization	`pmat org analyze --org mycompany --output report.yaml`
`pmat org analyze --summarize`	Analyze and summarize	`pmat org analyze --org mycompany --summarize --strip-pii`

Utilities

Command	Description	Example
`pmat doctor`	Diagnostics	`pmat doctor --fix`
`pmat debug`	Debug mode	`pmat debug --trace`
`pmat benchmark`	Benchmarking	`pmat benchmark --iterations=100`
`pmat info`	System info	`pmat info --environment`

Custom Rules

Command	Description	Example
`pmat rules init`	Initialize rules	`pmat rules init`
`pmat rules create`	Create rule	`pmat rules create --name=no-console-log`
`pmat rules test`	Test rules	`pmat rules test --all`
`pmat rules validate`	Validate rules	`pmat rules validate`

Auto-clippy

Command	Description	Example
`pmat clippy enable`	Enable clippy	`pmat clippy enable`
`pmat clippy run`	Run clippy	`pmat clippy run --format=json`
`pmat clippy fix`	Auto-fix issues	`pmat clippy fix --safe`

Hooks

Command	Description	Example
`pmat hooks install`	Install hooks	`pmat hooks install --pre-commit`
`pmat hooks run`	Run hooks	`pmat hooks run pre-commit`
`pmat hooks configure`	Configure hooks	`pmat hooks configure`

Global Options

Option	Description	Example
`--config <path>`	Use specific config	`--config custom.toml`
`--profile <name>`	Use profile	`--profile production`
`--format <type>`	Output format	`--format json`
`--output <path>`	Output file	`--output report.html`
`--quiet`	Suppress output	`--quiet`
`--verbose`	Verbose output	`--verbose`
`--debug`	Debug output	`--debug`
`--dry-run`	Preview only	`--dry-run`
`--parallel`	Parallel processing	`--parallel`
`--help`	Show help	`--help`

Common Workflows

Quick Quality Check

pmat analyze . --quick && pmat quality-gate --min-grade=B+

Full Analysis with Report

pmat analyze . --comprehensive && pmat report --format=html

Security Scan

pmat security scan --severity=high && pmat notify slack

Incremental CI/CD Analysis

pmat analyze --incremental --since=main | pmat quality-gate

Team Dashboard

pmat dashboard generate --team=backend && pmat dashboard serve

Environment Variables

Variable	Description	Example
`PMAT_CONFIG_PATH`	Config file path	`/opt/pmat/config.toml`
`PMAT_PROFILE`	Active profile	`production`
`PMAT_MAX_THREADS`	Thread limit	`16`
`PMAT_MEMORY_LIMIT`	Memory limit	`8G`
`PMAT_CACHE_DIR`	Cache directory	`/tmp/pmat-cache`
`PMAT_API_TOKEN`	API token	`your-token`
`PMAT_DEBUG`	Debug mode	`1`
`PMAT_LOG_LEVEL`	Log level	`debug`

Exit Codes

Code	Meaning
0	Success
1	General error
2	Configuration error
3	Analysis failure
4	Quality gate failure
5	Security violation
10	Invalid arguments
11	Missing dependencies
12	Network error
20	License error

Tips and Tricks

Create Aliases

alias pa='pmat analyze'
alias pq='pmat quality-gate'
alias ps='pmat status'

Batch Analysis

find . -type d -name "src" | xargs -I {} pmat analyze {}

JSON Processing

pmat analyze . --format=json | jq '.violations[] | select(.severity=="error")'

Continuous Monitoring

watch -n 60 'pmat status --detailed'

Pipeline Integration

pmat analyze . || exit $?

Running Examples

PMAT includes extensive runnable examples demonstrating various features. All examples are located in the server/examples/ directory and can be run using Cargo.

Running Examples

# From the paiml-mcp-agent-toolkit directory
cd server
cargo run --example <example_name>

Key Examples by Category

Category	Example	Description
Quality Analysis	`quality_gate`	Comprehensive quality gate demonstration
	`analyze_complexity`	Complexity analysis with CI/CD integration
	`analyze_dead_code`	Dead code detection with thresholds
	`analyze_satd`	Self-Admitted Technical Debt detection
	`quality_proxy_demo`	Quality Proxy for AI-generated code
	`perfection_score_demo`	Unified 200-point perfection score
	`work_commands_demo`	Work management commands
MCP Integration	`mcp_server_pmcp`	MCP server using pmcp SDK
	`unified_mcp_demo`	Unified MCP server architecture
	`pmcp_analyze_workflow`	MCP analyze workflow
Mutation Testing	`rust_mutation_workflow`	Rust mutation testing
	`typescript_mutation_workflow`	TypeScript mutation testing
	`python_mutation_workflow`	Python mutation testing
	`cargo_mutants_detect`	Cargo mutants integration
CI/CD	`ci_integration`	Multi-platform CI/CD examples
	`exit_codes`	Exit code behavior reference
Agent Scaffolding	`scaffold_agent_basics`	Basic MCP agent setup
	`scaffold_agent_hybrid`	Hybrid agent patterns
	`scaffold_agent_interactive`	Interactive agents
GitHub Integration	`analyze_github_repo`	Analyze GitHub repositories
	`check_github_repo`	GitHub repository checks
	`organizational_intelligence_integration`	Org-wide analysis
Semantic Search	`semantic_search_demo`	Code semantic search
	`similarity_demo`	Code similarity detection
Debugging	`recording_capture_demo`	Time-travel debugging
	`complexity_demo`	Complexity pattern testing

Quick Start Examples

# Quality gate check
cargo run --example quality_gate

# Perfection score demo (200-point scale)
cargo run --example perfection_score_demo

# Analyze complexity
cargo run --example analyze_complexity

# MCP server demo
cargo run --example mcp_server_pmcp

# GitHub repo analysis
cargo run --example analyze_github_repo

# Mutation testing workflow
cargo run --example rust_mutation_workflow

Full Example List

Run ls server/examples/*.rs to see all 67+ available examples.

Getting Help

pmat help - General help
pmat help <command> - Command-specific help
pmat <command> --help - Alternative help syntax
pmat doctor - Diagnose issues
pmat info - System information

PMAT: The PAIML MCP Agent Toolkit