How do I install the Cite Sync skill?

Run npx skillmds@latest add hsigstad/cite-sync in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Cite Sync safe to use?

This skill has not completed SkillMD's automated safety review yet. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Cite Sync?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Cite Sync free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Cite Sync?

hsigstad (@hsigstad) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Cite Sync by hsigstad — Agent Skill

Name: Cite Sync
Author: hsigstad

Cite Sync

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'.

hsigstad 4db6237 3.3 KB Updated Sep 17, 2026

File contents

/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.

---name: cite-syncdescription: 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'.---# /cite-sync — Regenerate project citation manifestsAction skill: regenerates `docs/refs/manifest.toml` for each project fromthe workspace citation registry at `research/refs/registry.toml`. Thinwrapper over `research-kit/tools/citations.py --sync`.This is a **write action**, not an audit. To validate citation tokenswithout writing anything, use `/check cite`.## What the manifest doesThe project manifest is a privacy/scoping boundary. Coauthors who clone aproject repo without access to the full workspace registry needhuman-readable titles for every external citation. `/cite-sync` buildsthat file by:1. Walking the project's `docs/` and `paper/` for `[ns:key]` tokens with **external** namespaces (`method`, `catalog`, `pipeline`, `var`, `idea`, `proj`, `inst`).2. Looking each up in the workspace registry.3. 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 acitation, `/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:```bashpython3 ~/research/research-kit/tools/citations.py [<slug>] --sync```## Procedure### 1. Run in dry-run mode first```bashpython3 $ROOT/research-kit/tools/citations.py [<slug>] --sync --dry-run```Surface the per-project diff: which projects would change, and theadded/removed entries. If nothing would change, exit cleanly with"manifests already in sync."### 2. Ask before writingIf any project would change, present the diff and ask for confirmation.Don't auto-apply — even though `/cite-sync` is an action skill, themanifests live in git and the user should see what's about to land.### 3. Apply```bashpython3 $ROOT/research-kit/tools/citations.py [<slug>] --sync```Report what changed per project.### 4. Suggest commitAfter writing, list the projects with modified manifests and ask whetherto 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.## Related- `/check cite` — validate citation tokens (no writes).- `/check` — full project-conventions audit.- Citation registry spec: `workspace/research/rules/citations.md`.

Frequently asked questions