hsigstadhsigstad/research-kit/skills/cite-sync/SKILL.md

cite-sync

Skill0 starsChanged 4 months agoMITView on GitHub

Regenerate each project's docs/refs/manifest.toml from the workspace citation registry. Walks docs/ and paper/ for [ns:key] tokens with external namespaces, looks each up in research/refs/registry.toml, and writes the public-facing subset (title + description, no internal paths) to the project manifest. Use when the user invokes /cite-sync, /cite-sync <slug>, or asks to 'sync the manifest', 'rebuild the refs manifest', 'regenerate citations manifest'.

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The file

We split this skill into the rules it gives an agent

4 rules. About 0 are common, 1 is distinctive, and 3 are very specific to this project.

≈0
Common · estimate
Many files like this have a rule of this kind.
≈1
Distinctive · estimate
This author's own choices. Worth a look.
3
Very specific
Tied to their project's names, files or tools. Probably skip.

Common
Distinctive
Very specific

Very specific:
If any project would change, present the diff and ask for confirmation.
line 62
Very specific:
Don't auto-apply — even though /cite-sync is an action skill, the manifests live in git and the user should see what's about to land.
line 63
Distinctive:
After writing, list the projects with modified manifests and ask whether to commit per-repo.
line 76
Very specific:
Registry not found: If research/refs/registry.toml is missing, surface the path and stop.
line 81

≈ “Common” is an estimate: at least 1 in 5 of the 350,495 skill files we read have a rule of the same kind, not the same words. “Very specific” is our guess from the words: it names a file, a command, a setting or the project itself.

Keep what fits and drop the rest. Your version, ready for your agents.

Files

SKILL.md

/cite-sync — Regenerate project citation manifests

Action skill: regenerates docs/refs/manifest.toml for each project from the workspace citation registry at research/refs/registry.toml. Thin wrapper over research-kit/tools/citations.py --sync.

This is a write action, not an audit. To validate citation tokens without writing anything, use /check cite.

What the manifest does

The project manifest is a privacy/scoping boundary. Coauthors who clone a project repo without access to the full workspace registry need human-readable titles for every external citation. /cite-sync builds that file by:

Walking the project's docs/ and paper/ for [ns:key] tokens with external namespaces (method, catalog, pipeline, var, idea, proj, inst).
Looking each up in the workspace registry.
Writing the public-facing subset — title + description only, no paths, no internal pointers — to docs/refs/manifest.toml.

The manifest stays in sync with what the project actually cites: drop a citation, /cite-sync removes the entry next run; add a new one, /cite-sync adds it.

How to invoke

Form	What it does
`/cite-sync`	Regenerate manifests for every project in the workspace
`/cite-sync <slug>`	Regenerate one project's manifest
`/cite-sync --dry-run`	Show the diff per project, don't write

Raw command:

python3 ~/research/research-kit/tools/citations.py [<slug>] --sync

Procedure

1. Run in dry-run mode first

python3 $ROOT/research-kit/tools/citations.py [<slug>] --sync --dry-run

Surface the per-project diff: which projects would change, and the added/removed entries. If nothing would change, exit cleanly with "manifests already in sync."

2. Ask before writing

If any project would change, present the diff and ask for confirmation. Don't auto-apply — even though /cite-sync is an action skill, the manifests live in git and the user should see what's about to land.

3. Apply

python3 $ROOT/research-kit/tools/citations.py [<slug>] --sync

Report what changed per project.

4. Suggest commit

After writing, list the projects with modified manifests and ask whether to commit per-repo. Don't auto-push.

Common failures

Registry not found. If research/refs/registry.toml is missing, surface the path and stop. Don't try to create the registry.
Unresolved external citation. A [ns:key] token in a project doc has no matching registry entry. The token is silently dropped from the manifest (since there's nothing to write). Surface as a warning and suggest /check cite to see the full list of unresolved citations.

/check cite — validate citation tokens (no writes).
/check — full project-conventions audit.
Citation registry spec: workspace/research/rules/citations.md.

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