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pipeio docs: two navigation/embedding issues

Observed in pixecog site docs. Both originate in pipeio's docs_collect tooling.

  • File: docs/pipelines/architecture.md:81-87 (collected from code/pipelines/architecture.md:77-83)
  • Links use: click IEEG "preprocess_ieeg/" — bare relative paths.
  • Problem: When the page is served at /pipelines/architecture/ (mkdocs trailing-slash convention), the browser resolves preprocess_ieeg/ to /pipelines/architecture/preprocess_ieeg/ instead of /pipelines/preprocess_ieeg/.
  • Fix: Change to "../preprocess_ieeg/" or absolute site paths. Since architecture.md is generated by pipeio_dag_export (or docs_collect), the link-rewriting logic in pipeio needs to emit correct relative paths accounting for the page's own location.

2. Per-flow DAG SVGs exist but are not embedded in flow overview pages

  • SVGs present in docs/pipelines/{flow}/dag.svg for brainstate, preprocess_ieeg, preprocess_ecephys, manifest_assemble.
  • Nav lists them as separate sidebar items (e.g., - DAG: preprocess_ieeg/dag.svg), but they are not inlined in the flow overview/index page.
  • Overview pages use ASCII art DAGs instead (e.g., preprocess_ieeg/index.md:16-37).
  • Expected: docs_collect or pipeio_dag_export should embed the SVG (or an ![DAG](dag.svg) reference) into the flow overview page under the "DAG Structure" heading, replacing or supplementing the ASCII art.

Summary

# Scope Owner Status
1 Mermaid link paths pipeio (docs_collect link rewriting) resolved — _rewrite_mermaid_click_links() in pipeio/docs.py prefixes bare relative click-links with ../ during architecture.md collection
2 SVG embedding in overviews pipeio (docs_collect) resolved — DagCollector now embeds ![DAG](dag.svg) in flow index.md; IndexCollector stubs include it too; standalone DAG nav entry removed

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