Set up MkDocs documentation and wire into Github Pages

[ajtritt]

Summary

• Add MkDocs (Material theme) documentation site with full navigation structure covering architecture, MCP servers, knowledge base, tools/skills, observability, CLI reference, and use cases.
• Add GitHub Actions workflow that builds docs on every push/PR and deploys to GitHub Pages (gh-pages branch) on merges to main.
• Add docs dependency group to pyproject.toml with mkdocs-material>=9.5.

Files Added

mkdocs.yml                          # MkDocs config (Material theme, nav, extensions)
docs/index.md                       # Home: overview, supported agents, key capabilities
docs/quickstart.md                  # Quick start walkthrough and setup-kb guide
docs/architecture.md                # Architecture diagram and layer descriptions
docs/mcp-servers.md                 # Registry and Knowledge server tool tables
docs/knowledge-base.md              # Six collections, explicit/episodic memory, search
docs/tools-skills.md                # Tool spec format, bundled tools, skills system
docs/observability.md               # MLflow, trace coverage by agent, provenance
docs/cli.md                         # Complete CLI reference table
docs/developer.md                   # Tests, proxy mode, troubleshooting
docs/assets/architecture.png        # Architecture image (copied from latex/)
docs/use-cases/index.md             # Use cases overview table
docs/use-cases/microbial-isolates.md
docs/use-cases/cryoem.md
docs/use-cases/vasp.md
.github/workflows/docs.yml          # Build on push/PR; deploy to gh-pages on main

Test Plan

• Verify pip install mkdocs-material && mkdocs build --strict completes without errors.
• Confirm the GitHub Actions docs job passes on this PR.
• After merge, go to Settings → Pages → Source and select "Deploy from a branch" with gh-pages / / (root). Verify the deployed site renders correctly.

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