Manuscript scaffold

<Purpose> Set up a LaTeX manuscript directory with optional journal-template customization and optional Overleaf Git integration. The heaviest, riskiest sub-flow inside /start-research (filesystem mutation, external archive fetches, credential handling, network push) — extracted into its own skill so the four sub-steps live in dedicated phase files for clarity, easier security review, and safer maintenance. </Purpose>

<Use_When>

• /start-research reaches phase 6 and the user did not opt out of manuscript scaffolding.
• A project that was set up with Manuscript dir empty later wants to add a manuscript directory without re-running the full /start-research interview.
• An existing manuscript directory needs to be wired up to a fresh Overleaf project (re-invoke with the new URL — the skill detects existing state and asks before clobbering). </Use_When>

<Do_Not_Use_When>

• The user wants only journal-template metadata captured in CLAUDE.md without creating files (no skeleton, no commit) — that is a CLAUDE.md edit, not this skill.
• The manuscript dir already has substantive content and the user is not asking to scaffold (phase 1 will stop anyway, but don't invoke if you already know).
• The project explicitly opted out of LaTeX (e.g. plain-markdown-only workflow). This skill is LaTeX-shaped. </Do_Not_Use_When>

<Configuration> Inputs are resolved by the caller (typically `/start-research`) from the project's `CLAUDE.md` blocks, or passed directly when the skill is invoked standalone.

Input	Required	Source	Used by
MANUSCRIPT_DIR	yes	## Research stack → Manuscript dir (default paper/)	all phases
TARGET_VENUE	no	## Project context → Target venue	phase 2 (journal lookup)
OVERLEAF_GIT_URL	no	## Research stack → Overleaf git URL	phase 3 (clone), phase 4 (push target)
WORKING_TITLE	no	## Project context → Working title	phase 3 (README seed)
CLAUDE_PLUGIN_ROOT	yes	env var (set by Claude Code)	phase 2 (registry path), phase 3 (skeleton source)

When invoked standalone (not from /start-research), if MANUSCRIPT_DIR is not given, read the project's CLAUDE.md ## Research stack block. If still missing, stop and ask the user. </Configuration>

Phases

Execute in order. Each phase is a separate file — read it, follow it exactly, then return here for the next phase.

1. Phase 1 — State check. Read phases/01-state-check.md. Decide whether to proceed, stop and ask the user, or skip (existing-content path).
2. Phase 2 — Journal template lookup. Read phases/02-journal-template.md. Match TARGET_VENUE against the bundled registry; on user-confirmed match, prepare the documentclass / bibstyle rewrite values for phase 3. Skip if no venue.
3. Phase 3 — Skeleton (with or without Overleaf). Read phases/03-skeleton.md. Branches internally on whether OVERLEAF_GIT_URL was provided.
4. Phase 4 — Commit and ask before push. Read phases/04-commit-push.md. Always commit locally; only push on explicit user confirmation (default no on empty input).

If phase 1 stops the flow (existing content, user declines), do not run phases 2–4. Report what happened and return control to the caller.

Security invariants (apply across all phases)

• No .cls files bundled in this plugin. Phase 2 may swap a \documentclass line in the skeleton copy only; any .cls archives a user opts into fetching go into the user's MANUSCRIPT_DIR, never into the plugin repo.
• No silent network calls. Phase 2's URL-fetch fallback runs WebFetch only when the user passes an https:// URL and confirms the SHA256 of the downloaded archive before extraction.
• No fuzzy venue matching. Phase 2 matches case-insensitive exact against the registry name and aliases. A near-miss is a miss.
• Overleaf token never written to a tracked file. Phase 3 stores the token only in git credential-store (scoped to git.overleaf.com) or ~/.netrc. Never write the token into CLAUDE.md, agent memory, the project repo, or this plugin. When referencing the token in any output, mask all but the last 4 chars.
• No auto-push. Phase 4 always asks; default on empty input is no. On push failure, leave the local commit in place and surface the exact retry command.

Return value (for the caller)

After phase 4 (or early stop), return a structured summary in this shape so the caller can fold it into its own report:

Manuscript scaffold: <created | skipped | stopped at phase N>
  Manuscript dir:    <path> (<created | existed empty | existed with content — skipped | overleaf clone>)
  Journal template:  <applied <class> + bibstyle <style> | not applied | no venue>
  Overleaf:          <connected to <masked URL> | local only | not configured>
  Branch / commit:   <branch> @ <short-SHA> (<pushed | push deferred | no remote>)
  Deferred push:     <exact `git -C <dir> push origin <branch>` command, only if push deferred>

The caller (e.g. /start-research phase 6) merges this into its end-of-run report.