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questio docs_collect generates both README.md and index.md in docs/plan/ — should only produce index.md

Problem

questio_docs_collect generates 6 files including both docs/plan/index.md and docs/plan/README.md. mkdocs warns: "Excluding 'plan/README.md' from the site because it conflicts with 'plan/index.md'." In strict mode this is a build-blocking WARNING.

Expected behavior

Only generate index.md. mkdocs uses index.md as the directory landing page. README.md is a GitHub convention that has no role in the mkdocs build and creates a conflict.

Workaround

Manually delete docs/plan/README.md after each questio_docs_collect run.

Source context: pixecog

PixEcog (pixecog): Neuropixels and ECoG dataset and analysis

Recent commits: 

8dc0d9d Pipeline docs: gitignore docs/pipelines/, relocate hand-authored files
96cd1ec Refactor sharpwaveripple/contracts: extract generic helpers to utils/io, remove pipelines __init__.py
36f9326 Add result note directory and sample note

README:

type: readme

Quick Start for Collaborators

Follow this checklist to get started with Pixecog documentation and workflows.

🐀 Pixecog Project — Compact Overview

Core principles

  • One immutable BIDS raw dataset (raw/) as the canonical baseline
  • Each analysis pipeline ha