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title: "pipeio registry_scan: has_docs always false despite flow-local docs/ existing status: resolved created: 2026-04-08 updated: 2026-04-08 timestamp: 20260408-041843-212992 tags: [issue] source: agent-observation project_primary: projio capture_id: 20260408-041841-3fc9ab confidence: 1.0 transcript_file: /storage2/arash/worklog/workflow/captures/20260408-041841-3fc9ab/transcript.txt

pipeio registry_scan: has_docs always false despite flow-local docs/ existing

pipeio_registry_scan sets has_docs: false and doc_path: null for all flows, even when the flow has a docs/ directory with content (e.g., preprocess_ecephys/docs/ has overview.md + 10 mod subdirs, preprocess_ieeg/docs/ has overview.md + mod docs).

Reproduction: run pipeio_registry_scan on pixecog — all 9 flows show has_docs: false. The generated registry.yml has doc_path: null for every flow and every mod.

Expected: scan should detect {flow}/docs/ and populate doc_path in the registry. Mod-level doc_path should be set when {flow}/docs/{mod}/ exists with theory.md or spec.md.

Source context: pixecog

PixEcog (pixecog): Neuropixels and ECoG dataset and analysis

Recent commits: 

36f9326 Add result note directory and sample note
62841d9 Add questio YAML data model (questions.yml + milestones.yml)
9b2f6fa Scaffold ecephys TTL removal mod, flow overview + mod docs, demo notebook

README:

type: readme

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