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docs(mcp): comprehensive MCP server documentation #775

@joshrotenberg

Description

@joshrotenberg

Summary

Write comprehensive documentation for the MCP server covering setup, configuration, safety, and the full tool catalog. Good docs are critical for adoption -- operators need to understand the safety model, and agents need to discover capabilities.

Deliverables

Getting started guide

  • Installation (binary, cargo install, Docker)
  • First run with stdio transport (Claude Desktop, Cursor, VS Code)
  • First run with HTTP transport
  • Profile setup for Cloud, Enterprise, and direct database connections
  • Verifying connectivity with profile_validate

Client configuration guides

  • Claude Desktop: claude_desktop_config.json setup with examples
  • Cursor: MCP server configuration
  • VS Code (Continue, Cline): Integration setup
  • Custom clients: HTTP/SSE transport with optional OAuth

Safety and policy guide

Tool catalog / reference

  • Auto-generated or hand-curated list of all tools
  • Grouped by toolset (cloud, enterprise, database, profile)
  • Each tool: name, description, parameters, safety annotation, example
  • Consider generating from tool metadata at build time

Audit logging guide (#767)

  • Enabling audit logging
  • Log format reference
  • Integration with log aggregation (ELK, Datadog, etc.)
  • Interpreting denied operation logs

Architecture overview

  • Feature flags and toolset composition
  • Profile resolution and credential management
  • Transport modes (stdio vs HTTP/SSE)
  • OAuth configuration for multi-tenant deployments
  • Rate limiting and concurrency control

Troubleshooting

  • Common errors and remediation
  • Credential resolution failures
  • Policy misconfiguration
  • Transport issues

Format considerations

  • Primary format: markdown files in docs/mcp/ directory
  • Consider mdBook for a structured documentation site
  • Tool catalog could be auto-generated from source annotations
  • Include in repository (version-controlled with the code)

Acceptance criteria

  • Getting started guide written and tested
  • At least two client configuration guides (Claude Desktop + one other)
  • Safety and policy guide complete
  • Tool catalog with all 199+ tools documented
  • Audit logging guide
  • Architecture overview

Context

Part of #681 (MCP epic). Documentation should be written alongside feature work, not after. Each issue in this epic should include doc updates as part of its acceptance criteria.

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