retarget-journal

name	retarget-journal
description	Retarget an active manuscript to a different journal by reconciling venue identity, files, bibliography, citations, and submission-facing metadata. Use when a new target journal has already been chosen and the paper package must change. Not for choosing a venue; use the venue-fit workflow.
allowed-tools	Bash(latexmk*), Bash(pdflatex*), Bash(xelatex*), Bash(mkdir*), Bash(ls*), Bash(cp*), Bash(mv*), Bash(git*), Read, Write, Edit, Glob, Grep, Task
argument-hint	[target-journal-name]
skill-dependencies	[]

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:

Check	What to compare
Word/page limit	Does the draft fit? Need to cut or can expand?
Required sections	Does the target need sections the current draft lacks? (e.g., "Relevance Statement", "AI Disclosure")
Citation style	Author-year vs numbered? natbib vs biblatex?
Formatting	Template class? Column layout? Font requirements?
Supplementary material	Online appendix conventions?

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

Skill	When to use alongside
Installed bibliography validator	Optional deeper metadata validation after Phase 3
latex	Default compiler — use for compilation with auto error resolution
latex	For manual compilation config and .latexmkrc setup
proofread	After retarget to check for remnants of old journal formatting
vault sync (edit vault files directly)	After Phase 5 to sync with central context library