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Problem

Auto-generated questio pages (evidence.md, milestones.md, questions.md) contain cross-references with two bugs:

  1. Wrong relative depth. Links from plan/evidence.md use ../../log/result/... but the correct path is ../log/result/... (only one level up from plan/ to docs root).

  2. Missing .md extension. Result note links omit the .md extension: result-arash-20260408-011519-651113 instead of result-arash-20260408-011519-651113.md.

Examples from pixecog build

'plan/evidence.md' contains an unrecognized relative link '../../log/result/result-arash-20260408-011519-651113'
  → should be '../log/result/result-arash-20260408-011519-651113.md'

'plan/milestones.md' contains an unrecognized relative link '../../log/result/result-arash-20260409-034237-164561'
  → should be '../log/result/result-arash-20260409-034237-164561.md'

'plan/index.md' contains an unrecognized relative link '../log/result'
  → should be '../log/result/index.md'

Affected component

questio_docs_collect — the template or link generator that produces evidence dossier pages and milestone tracker pages. The relative path computation assumes one extra parent level than exists.

Separate concern: forward manuscript refs

plan/questions.md also has links to ../../manuscript/results/h1-delta-ripple etc. These are intentional forward references to manuscript sections that don't exist yet — not a bug, just placeholders. They can be ignored or suppressed.

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

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🐀 Pixecog Project — Compact Overview

Core principles

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