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.

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).

Phase 6: Compile and Verify

1. Compile to out/ with latexmk
2. Fix all warnings (overfull/underfull)
3. Check page count against target journal limit
4. Verify all citations resolve
5. Visual check: does the formatting look right for the target venue?

Phase 7: Confirm

Report a summary:

Retargeted [Paper Name]: [Old Journal] → [New Journal]

Changes made:
- Folder: [old path] → [new path]
- Symlink: updated to [new Overleaf project]
- Bibliography: [N] citation keys updated
- Sections added: [list]
- Sections removed: [list]
- Page count: [N] pages (limit: [M])
- Compilation: clean (0 warnings)

Updated: CLAUDE.md, README.md, vault

Important Rules

• Never delete the old .bib file — rename it to old-journal.bib.bak as a safety copy
• Verify citation key mappings with the user before bulk-replacing — automated matching can misfire on common surnames
• Don't restructure content without approval — some retargets only need formatting changes, not rewriting
• Preserve git history — commit the retarget as a single, well-documented commit

Venue Style Guides

When retargeting, the writing style often needs to change too — not just the formatting. Read the appropriate guide from the shared venue-guides resource:

• Master overview: skills/shared/venue-guides/venue_writing_styles.md — style spectrum and adaptation tips
• Formatting requirements: skills/shared/venue-guides/journals_formatting.md (journals) / conferences_formatting.md (conferences)
• Venue-specific style: nature_science_style.md, ml_conference_style.md, cs_conference_style.md, cell_press_style.md, medical_journal_styles.md — all in skills/shared/venue-guides/
• Writing examples: skills/shared/venue-guides/examples/ — abstract and introduction formats by venue type

Cross-References