# Summary
[Introduction](./index.md)
# Getting Started
- [Installation](./tutorials/installation.md)
- [License Setup](./tutorials/license.md)
- [Configuration](./tutorials/configuration.md)
- [Quick Start](./tutorials/quickstart.md)
# Tutorials
- [Your First Command](./tutorials/first-command.md)
- [SAM/BAM Processing](./tutorials/bam-workflow.md)
- [RNA-seq Walkthrough](./tutorials/rnaseq-walkthrough.md)
- [Workflow Builder](./tutorials/workflow-builder.md)
# How-to Guides
- [Add Documentation for a Tool](./how-to/add-tool-docs.md)
- [Switch LLM Provider](./how-to/change-llm-provider.md)
- [Create a Custom Skill](./how-to/create-custom-skill.md)
- [Build a Production Pipeline](./how-to/build-pipeline.md)
# Command Reference
- [run](./commands/run.md)
- [dry-run](./commands/dry-run.md)
- [docs](./commands/docs.md)
- [config](./commands/config.md)
- [history](./commands/history.md)
- [skill](./commands/skill.md)
- [workflow](./commands/workflow.md)
- [server](./commands/server.md)
- [job](./commands/job.md)
- [license](./commands/license.md)
- [completion](./commands/completion.md)
# Architecture & Design
- [System Architecture](./reference/architecture.md)
- [Documentation System](./reference/documentation-system.md)
- [Skill System](./reference/skill-system.md)
- [MCP Skill Provider](./reference/mcp-skill-provider.md)
- [LLM Integration](./reference/llm-integration.md)
- [Workflow Engine](./reference/workflow-engine.md)
- [License System](./reference/license-system.md)
- [Security Considerations](./reference/security-considerations.md)
# Development
- [Contributing](./development/contributing.md)
- [Expert Evaluation Reports](./development/evaluation-reports.md)