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Update agent-safety

Update agent-safety.md write-tool list — incomplete vs actual implementation.

Scope

docs/explanation/agent-safety.md line ~105 lists write tools to prompt on, but is missing: biblio_docling, biblio_grobid, indexio_sources_sync, biblio_rag_sync, codio_rag_sync, plus all pipeio write operations.

docs/tutorials/agent-orchestration.md lines ~196-200 has incomplete tool categorization by access level, missing ~20 write tools.

Approach

Cross-reference the actual MCP tool decorators in server code against the documented write-tool lists and update both files.

  • [[issue-arash-20260331-172245-820267.md]] — Both are documentation gap issues for MCP tools — that issue covers 61 undocumented tools, this one covers missing write-tool entries in agent-safety.md
  • [[issue-arash-20260331-172307-095605.md]] — Both are documentation update issues filed in the same session; CLI reference gaps and write-tool list gaps are parallel documentation debt
  • [[issue-arash-20260327-155921-977015.md]] — Mentions codio_rag_sync specifically, one of the write tools missing from the agent-safety.md list in the current note

Batch Result

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