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Problem

The auto-generated docs/pipelines/index.md uses bare directory links like [brainstate](brainstate/) which mkdocs flags as "unrecognized relative link". mkdocs expects brainstate/index.md for explicit resolution.

Similarly, architecture.md flow table links use brainstate/ trailing-slash format.

Fix

In the pipelines index generator and any generated link to a flow landing page, use {flow}/index.md instead of {flow}/. This is the only format that works cleanly across both mkdocs (strict mode) and pandoc.

Impact

14 INFO-level warnings in mkdocs build (7 from index.md + 7 from architecture.md). Links still resolve in practice but break strict-mode clean builds.

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