Tools

File conversion

The wiki works with Markdown. If your sources are in other formats, two conversion scripts handle the rest:

# Batch-convert any supported format in a directory
python tools/file_to_md.py --input_dir raw/

# PDFs and arXiv papers
python tools/pdf2md.py paper.pdf
python tools/pdf2md.py 2401.12345                          # arXiv by ID
python tools/pdf2md.py https://arxiv.org/abs/2401.12345    # arXiv by URL
python tools/pdf2md.py paper.pdf --backend marker          # for complex layouts

Once converted, ingest normally: ingest raw/papers/my-paper.md

Standalone usage

The Python scripts in tools/ can also run standalone from terminal, without a coding agent.

# Run any tool directly
python tools/ingest.py raw/doc.md
python tools/query.py "what are the main themes?"
python tools/health.py
python tools/lint.py
python tools/build_graph.py
python tools/heal.py
python tools/refresh.py
python tools/validate_domain.py --doc raw/doc.md --tag project-alpha

try it

“Run stats and show me which projects have the most pages”

All scripts accept --help for full options. Most support --json for machine-readable output and --save to write results to the wiki.

Knowledge graph

Running build graph (or python tools/build_graph.py) extracts all connections between pages — both explicit [[wikilinks]] and implicit relationships inferred by the agent — and renders them in a self-contained graph/graph.html you can open in any browser. No server needed.

The graph uses Louvain community detection to cluster related pages, and vis.js for interactive visualization with search, filtering, and a detail drawer for each node.