Command Reference¶

17 Registered Commands | 19 Skill-Invoked Commands | Version: 3.5.2

Commands fall into two categories:

Registered commands are declared in plugin.json and available as user-facing /slash-commands.
Skill-invoked commands exist on disk but are not registered in manifests — they are triggered by skills, not directly by users.

Registered Commands¶

Agent Core Suite (`agent-core`) — 2 Commands¶

Command	Description
`/ultra-think`	Comprehensive analysis with full reasoning framework execution
`/team-assemble`	Generate ready-to-use agent team configurations from pre-built templates

Dev Suite (`dev-suite`) — 10 Commands¶

Command	Description
`/docs`	Unified documentation management — generate, update, and sync
`/double-check`	Multi-dimensional validation with automated testing and security scanning
`/eng-feature-dev`	End-to-end feature development with customizable methodologies
`/fix-commit-errors`	Diagnose and fix CI/CD failures by analyzing logs and rerunning workflows
`/merge-all`	Merge all local branches into main and clean up
`/modernize`	Legacy code migration using Strangler Fig pattern
`/run-all-tests`	Iteratively run and fix all tests until zero failures
`/smart-debug`	Intelligent debugging with multi-mode execution and automated RCA
`/test-generate`	Generate comprehensive test suites with scientific computing support
`/workflow-automate`	Automated CI/CD workflow generation for GitHub Actions and GitLab CI

Research Suite (`research-suite`) — 3 Commands¶

Command	Description
`/lit-review`	Systematic literature review with PRISMA-compliant search and evidence synthesis
`/paper-implement`	Reproduce a research paper end-to-end: theory → code → validation
`/replicate`	Computational replication of published experiments with deviation analysis

Science Suite (`science-suite`) — 2 Commands¶

Command	Description
`/md-sim`	Molecular dynamics simulation setup, running, and trajectory analysis
`/benchmark`	Scientific code benchmarking across backends and hardware targets

Skill-Invoked Commands¶

These commands exist on disk and are triggered by skills during workflows. They are not available as direct /slash-commands.

Agent Core — 4 Skill-Invoked¶

Command	Description
`agent-build`	AI agent creation, optimization, and prompt engineering
`ai-assistant`	Build production-ready AI assistants with NLU and response generation
`docs-lookup`	Query library documentation using Context7 MCP
`reflection`	AI reasoning analysis, session retrospectives, and research optimization

Dev Suite — 13 Skill-Invoked¶

Command	Description
`adopt-code`	Analyze and modernize scientific computing codebases
`c-project`	Scaffold production-ready C projects with Makefile/CMake
`code-analyze`	Semantic code analysis using Serena MCP for symbol navigation
`code-explain`	Detailed code explanation with visual aids
`deps`	Dependency management — security auditing and safe upgrades
`fix-imports`	Fix broken imports across the codebase
`github-assist`	GitHub operations using GitHub MCP for issues, PRs, repos
`monitor-setup`	Set up Prometheus, Grafana, and distributed tracing
`multi-platform`	Build and deploy features across web, mobile, and desktop
`onboard`	Onboarding orchestration with 30/60/90 day plans
`profile-performance`	Performance profiling with perf, flamegraph, and valgrind
`scaffold`	Project and component scaffolding for TypeScript, Python, React, Julia
`tech-debt`	Technical debt analysis with ROI-based roadmaps

Science Suite — 2 Skill-Invoked¶

Command	Description
`analyze-data`	Analyze data files with statistical tests, visualization, and reporting
`run-experiment`	Design and execute computational experiments with hypothesis tracking

Research Suite — 0 Skill-Invoked¶

No on-disk command files. All research workflows are skill-driven (scientific-review, the 8-stage research-spark pipeline, research-practice hub, and the 3 registered slash commands above).

Execution Modes¶

Most commands support three execution modes via --mode=<mode>:

Mode	Scope	Description
quick	Fast	Syntax checking, basic scaffolding
standard	Full	Complete implementation with testing
comprehensive	Deep	Advanced features, compliance, CI/CD

Hub Skill Routing¶

Commands often invoke hub skills, which route to specialized sub-skills automatically. For example, /smart-debug may trigger the debugging-toolkit sub-skill through the dev-workflows hub. See the suite reference docs for full hub → sub-skill mappings.

Resources¶

Agent Reference
Quick Reference Cheatsheet
Integration Map — Suite dependencies and MCP server roles
Glossary — Key terms (Hub Skill, Sub-Skill, Routing Decision Tree)

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