integrate-references

name	integrate-references
description	Walks the user through the citation report, resolving each citation one at a time. Use when the user invokes /integrate-references. Expects pipeline/citation_report.md and pipeline/paper_draft.md to exist.
allowed-tools	Read, Edit, Write, Glob, Grep
disable-model-invocation	true

Startup

This skill walks you through the citation report one entry at a time — for each citation, you'll see the assessment and proposed action, then decide whether to keep, revise, replace, or remove it. Changes are applied to a new file (pipeline/paper_draft_v2.md) so the original draft from the paper-writer is preserved for traceability.

Before starting: is there anything I should know — citations you already know are wrong, new papers you've added to literature/, or sections to prioritize? If not, just say go.

Wait for the user to respond before proceeding.

Preconditions

Before starting, verify:

1. CLAUDE.md exists in the working directory.
2. pipeline/citation_report.md exists.
3. pipeline/paper_draft.md exists.

If either is missing, stop and tell the user which file is needed.

Read pipeline/citation_report.md in full before beginning. Do NOT read all of literature/ — source papers are read selectively during the process.

Then copy pipeline/paper_draft.md to pipeline/paper_draft_v2.md. All edits during this skill are made to the cited copy — never modify pipeline/paper_draft.md.

Process

Work through the citation report entry by entry, in the order they appear. For each entry:

1. Show the citation in context. Quote the relevant passage from the draft so the user can see how it's currently used.

2. Show the assessment. Present the citation assessor's verdict and proposed action (KEEP / REVISE / REPLACE / REMOVE).

3. Ask the user what to do. The user may:

   • Approve the proposed action as-is
   • Modify — accept the direction but adjust the specifics
   • Override — reject the proposal and give a different instruction
   • Skip — leave this citation unchanged for now
   • Inspect source — if the user wants to check the assessor's reading, look up the relevant passage in literature/ using Glob and Grep. Read only the specific source, not the entire folder.

4. Apply the change. Edit pipeline/paper_draft_v2.md to implement the agreed action. For REVISE or REPLACE, rewrite the surrounding sentence or passage to integrate the new or revised citation naturally — don't just swap a name.

Placeholder Citations

For [CITE: AuthorYear — reason] placeholders, the process is the same but the options differ:

• Resolve — replace with a real citation (from the assessor's suggestion or the user's choice)
• Keep placeholder — the user hasn't found a suitable source yet
• Remove — the argument doesn't actually need a citation here

Pacing

Don't rush. Present one citation at a time and wait for the user's response before moving to the next. If the report is long, offer to pause and resume later — the user can re-invoke the skill to continue where they left off.

After Completion

When all entries have been addressed, summarize what was done: how many citations were kept, revised, replaced, removed, and how many placeholders remain unresolved.