Update MCP tools reference docs — 61 of 95 tools undocumented

Update MCP tools reference docs — 61 of 95 tools undocumented.

Scope

docs/reference/mcp-tools.md currently documents 34 tools. Missing sections:

1. Pipeio (40+ tools) — entirely absent. Add organized sections: flow management, notebook lifecycle, module/rule ops, config, execution/monitoring, docs/nav
2. DataLad (5 tools) — datalad_save, datalad_status, datalad_push, datalad_pull, datalad_siblings
3. Biblio gaps (3) — biblio_docling_status, biblio_graph_expand, biblio_rag_sync
4. Indexio gaps (4) — indexio_build_status, indexio_sources_list, indexio_sources_sync, indexio_status
5. Codio gaps (3) — codio_add, codio_func_doc, codio_rag_sync
6. Notio gaps (2) — note_resolve, notio_reindex
7. Context/meta — agent_instructions, module_context, git_status, skill_read

Approach

Read each tool's docstring from the MCP server implementation (src/projio/mcp/server.py and sub-modules) and generate reference entries matching the existing format in mcp-tools.md. Group by subsystem.

Related Notes

• [[issue-arash-20260327-155921-977015.md]] — Mentions codio_rag_sync and 'unclear MCP docs' — codio_rag_sync is one of the 3 codio gaps listed in the current note
• [[issue-arash-20260328-174906-119594.md]] — Tracks adding biblio_graph_expand MCP tool — listed as one of the 3 biblio gaps needing documentation
• [[issue-arash-20260326-232746-941302.md]] — Implements notio_reindex — one of the 2 notio gaps listed as undocumented
• [[issue-arash-20260326-232732-019412.md]] — Implements pipeio — the largest undocumented subsystem (40+ tools) in the current note
• [[issue-arash-20260328-192146-858687.md]] — Tracks indexio_build_status bug — this tool is one of the 4 indexio gaps listed as undocumented

Batch Result

• status: done
• batch queue_id: 2dfdd2e244d7
• session: 4ff59117-10a7-42f1-8cbe-1b1300021fe4
• batch duration: 444.5s