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Absorb module_context extraction into pipeio (merge with pipeio_mod_resolve or add pipeio_mod_context)

Problem

pixecog retains a project-local MCP tool module_context(module_doc_path) that extracts structured sections from pipeline module documentation markdown files: goal, assumptions, parameters, I/O contracts, limitations. This is implemented in code/utils/pixecog_mcp/module_docs.py.

pipeio already has pipeio_mod_resolve which returns mod metadata, but it doesn't extract structured content from the mod's documentation file. The module_context pattern is general — any pipeline project with documented mods would benefit from being able to query "what does this mod assume?" or "what are its parameters?" programmatically.

Proposal

Either: 1. Extend pipeio_mod_resolve to optionally include parsed doc sections (add a include_docs=True flag) 2. Add pipeio_mod_context(pipe, flow, mod) as a separate tool that extracts structured doc sections

Option 1 is cleaner if the doc parsing is lightweight. Option 2 is better if the extraction is heavy or if agents frequently need metadata without docs.

The doc parser should handle standard section headers: - Goal / Objective - Assumptions / Prerequisites - Parameters / Configuration - Input / Output (I/O contracts) - Limitations / Caveats - Notes

Reference implementation

pixecog:code/utils/pixecog_mcp/module_docs.py — extract_context(module_doc_path) function

Migration path

  1. Add doc extraction to pipeio
  2. Remove module_context from pixecog_mcp server
  3. pixecog_mcp server may become fully redundant (pipeline_registry → pipeio_flow_list/mod_list, modkey_resolve → pipeio_mod_resolve + mod_context)

Context

From pixecog cleanup — last of three legacy utilities identified for projio absorption. If all three land, pixecog_mcp server can be fully retired.

Source context: pixecog

PixEcog (pixecog): Neuropixels and ECoG dataset and analysis

Recent commits: 

2601c54 Cleanup: remove legacy tooling superseded by projio ecosystem (pixecog_mcp modules, RAG system, foam templates, workflow makefiles, context builder, dead CLI scripts)
1cdc964 Pre-cleanup checkpoint: update bib and docs subdatasets, indexio config v3
6429574 untrack

README:

type: readme

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