Retarget Journal

Retarget Journal Skill

Switch a paper manuscript from one journal to another. Handles folder renaming, bibliography swaps, citation key updates, formatting changes, and compilation verification.

When to Use

• Switching a paper's target venue (e.g., Journal A to Journal B, Journal C to Journal D)
• After a rejection when resubmitting to a different journal
• When strategic decisions change the target venue mid-drafting

Before Starting

Ask the user for:

1. Current project path — where is the paper?
2. Target journal — full name and abbreviation
3. What changes? — some retargets are minor (formatting), others are major (restructuring)

Read the project's CLAUDE.md and README.md to understand current state.

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Workflow

Phase 1: Assess Scope

Read the current manuscript and compare against the target journal's requirements:

Present the assessment to the user before proceeding.

Phase 2: Rename and Restructure

1. Rename project folder if it references the old journal:

   mv "old-journal-name/" "new-journal-name/"

2. Update Overleaf symlink if one exists:

   # Remove old symlink
   rm paper/
   # Create new symlink to the correct Overleaf directory
   ln -s "/path/to/Overleaf/new-project" paper

3. Update folder references in CLAUDE.md, README.md, .gitignore

Phase 3: Bibliography

1. Swap .bib file if the user provides a new export from Paperpile
2. Update citation keys across all .tex files:
   • Read the new .bib to get the new key format
   • Find all \cite{...}, \citet{...}, \citep{...}, \citeauthor{...} commands in .tex files
   • Map old keys to new keys (match by author + year)
   • Replace all occurrences
3. Validate — cross-reference every manuscript citation key against the .bib files and report missing or unused keys. Use an installed bibliography validator for deeper metadata checks when available.

Phase 4: Formatting

1. Switch document class/template if needed
2. Add required sections (e.g., data availability, AI disclosure, conflict of interest)
3. Adjust page layout (margins, columns, font size)
4. Update \bibliographystyle{} if citation style changes
5. Update abstract — check word limit for target journal

Phase 5: Update Documentation

1. Project CLAUDE.md — update target journal, formatting notes
2. Project README.md — update journal reference, submission info
3. MEMORY.md — carry forward any learnings, update journal-specific notes
4. vault research pipeline — update the Target Journal and Status fields. If the retarget closes a live venue event (rejection or withdrawal), append the closing history: row (event: decision, outcome: reject or event: withdrawn) to the OLD venue's submission entry per rules/submission-file-archive.md § history — the new target's entry gets its own history: when it is actually submitted, not at retarget time
5. atlas topic outputs[] — update the retargeted output's venue (slug must resolve to a ~/vault/venues/ file). Refresh or clear cycle: if the new venue is a Conference/Workshop and the output is submission-active, set cycle: <NewVenue> <edition-year>; if the new venue is a journal, remove any stale cycle — per rules/atlas-status-vocabulary.md § submission-join completeness. A stale cycle from the old venue must never survive a retarget. If the retarget also changed the paper's title, update paper_title here and the registry canonical_title together (keep them aligned per paper-vault-alignment.md).