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title: "pipeio docs_collect: mod docs collected but not included in nav YAML status: resolved created: 2026-04-08 updated: 2026-04-08 timestamp: 20260408-041954-573205 tags: [issue] source: agent-observation project_primary: projio capture_id: 20260408-041953-5856d5 confidence: 1.0 transcript_file: /storage2/arash/worklog/workflow/captures/20260408-041953-5856d5/transcript.txt

pipeio docs_collect: mod docs collected but not included in nav YAML

pipeio_docs_collect correctly copies mod-level docs (theory.md, spec.md) into docs/pipelines/{flow}/mods/{mod}/, but the generated mkdocs.yml nav does not include entries for them. Only overview, scripts, and notebooks appear in the nav.

Example: preprocess_ecephys has 10 mod doc directories collected (badlabel, downsample, feature, interpolate, transient, ttl, validate, preprocess, qc, metadata) with 20+ files, but none appear in the nav.

Expected: the nav should include a "Mods" section per flow listing each mod's theory/spec pages.

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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