Fill the Manuscript Map
The single most important setup step — give the agent a thesis, a venue, section budgets, and key sources so it stops drifting and overclaiming.
MANUSCRIPT_MAP.md is the file Claude reads first, every session. The more precise it is, the less the agent drifts, overclaims, or invents.
If you cannot state your thesis in one sentence, the paper is not ready to draft. Writing the map is part of the thinking.
1. State the thesis in one sentence
The single claim the manuscript exists to defend. A reader should be able to dispute it.
"A pre-execution verification gate reduces hallucinated tool calls in LLM agents without lowering task completion, which post-hoc self-correction does not achieve."
2. Name the contribution
What does the reader know after this paper that they didn't before? Distinguish it explicitly from prior work.
3. Set the status and venue
Stage (idea / outline / draft / revision / responding-to-reviewers), target venue with its reference style and length limit, the main .tex file, and references.bib. The session-start hook surfaces the venue and stage every session.
4. Lay out sections with budgets
Fill the Structure table — each section names the claim it establishes, its file, and a word budget. The word-budget hook warns when a section .tex exceeds its % budget: NNN.
| Section | File | Purpose (claim it establishes) | Budget |
|---|---|---|---|
| Introduction | sections/intro.tex | gap + why it matters + what we do | 800 w |
| Methods | sections/methods.tex | reproducible account of what was done | 1500 w |
5. Pin the key sources and terminology
List the handful of references the paper stands on, and what they must NOT be overclaimed as. Lock the vocabulary — one term per concept — so the draft doesn't alternate synonyms.
Verify
Start a Claude Code session and ask it to "restate the thesis and the open section." If it parrots your map back accurately, the map is doing its job. If it hedges or invents, tighten the map.
Next: Build the Literature Vault so every claim has a source to trace to.
Recipes
Concrete how-to guides for the things you'll actually do — fill the manuscript map, build the vault, respond to reviewers, add a field overlay.
Build the Literature Vault
Ingest your sources into a grounded annotated bibliography so the cardinal rule has somewhere to trace claims to — never a fabricated source.