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Save and commit all pipeio changes from 2026-03-30 session

Goal

Commit all code changes made during the 2026-03-30 session to both the pipeio submodule and the projio parent repo.

Context

Changes made today in pipeio (packages/pipeio/src/pipeio/): - mcp.py: config_patch ruamel round-trip fix, unreferenced anchor preservation (_ruamel_preserve_anchors, _ruamel_dump_str, _ruamel_deep_update), rule_insert params double-wrap fix (_config_path_to_expr), new mcp_nb_update, new mcp_mod_context, notebook metadata in nb_create and nb_status - notebook/config.py: added kind, description, status fields to NotebookEntry - tests/test_mcp.py: 12 new tests

Changes in projio (src/projio/): - mcp/pipeio.py: pipeio_nb_update and pipeio_mod_context wrapper functions - mcp/server.py: registered pipeio_nb_update and pipeio_mod_context tools - init.py: 2 new agent instruction rows - CLAUDE.md: updated tool list

Also: idea notes, issue resolutions, task notes in docs/log/.

Prompt

Save and commit all changes from the 2026-03-30 session. This is a commit task — run tests, then save.

  1. Run pipeio tests first: 

    cd /storage2/arash/projects/projio/packages/pipeio && PYTHONPATH=src python -m pytest tests/ -q
    Expect 234 passed. If any fail, investigate and fix before saving.

  2. Save pipeio submodule with datalad_save:

  3. message: "Fix config_patch ruamel round-trip, add nb_update and mod_context tools, fix rule_insert params"

  4. dataset: "packages/pipeio"

  5. Save projio root with datalad_save:

  6. message: "Add pipeio_nb_update and pipeio_mod_context MCP tools, v2 roadmap notes, bug fixes"

  7. Include all modified files: src/projio/mcp/pipeio.py, src/projio/mcp/server.py, src/projio/init.py, CLAUDE.md, docs/log/ notes

  8. Verify no uncommitted changes remain with git_status().

Acceptance Criteria

  • [ ] pipeio tests pass (234)
  • [ ] pipeio submodule saved
  • [ ] projio root saved
  • [ ] Clean git status

Result

(Filled in after execution)