research-manuscript-workflow

Governs LaTeX manuscript workflows including Overleaf git sync, generated artifacts, and rebuttals.

Updated Jul 3, 2026
One-click install
npx skills add https://github.com/mnazaal/dotfiles --skill research-manuscript-workflow-mnazaal
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: research-manuscript-workflow
Source: https://github.com/mnazaal/dotfiles/tree/main/.agents/skills/research-manuscript-workflow
Command: npx skills add https://github.com/mnazaal/dotfiles --skill research-manuscript-workflow-mnazaal

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve? Writing ML and scientific papers involves fragile coordination between LaTeX source, generated figures and tables, citation tooling, and external hosts like Overleaf. This Skill sets the safety and portability boundaries for that work: it prevents agents from editing human-owned .tex files, keeps synced manuscript directories compile-standalone, and provides the exact git subtree procedures for Overleaf bridges that reject force-pushes and non-fast-forward updates. ## Core Features & Use Cases - Human-owned .tex guardrail: Agents read, compile, and review LaTeX but never edit .tex directly; edits are delivered as proposals in planning notes or scaffold scripts the human runs. - Overleaf git bridge sync: One-time subtree re-seed for pre-existing subdirectories, recurring push-then-pull rules, conflict diagnosis, and post-push scope checks confirming no parent-repo paths leak to the host. - Portable manuscript boundary: Rules for compile-standalone directories, committed generated figures/tables as the pipeline interface, byte-deterministic artifacts, and reference self-containment for arXiv and coauthor handoff. - Use Case: A researcher's git subtree push to Overleaf is rejected as non-fast-forward. The Skill walks through the one-time re-seed (git rm, subtree add, restore, push), then wires make overleaf-push to push-then-pull so shared ancestry advances and future syncs stay clean. ## Quick Start Ask the agent to set up a synced manuscript directory for your research project, including the claims ledger, build targets, and Overleaf subtree sync procedure.

Frequently Asked Questions about research-manuscript-workflow

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I fix a rejected git subtree push to Overleaf?

A non-fast-forward rejection on a pre-existing subdirectory requires a one-time re-seed: git rm the prefix, delete leftover untracked files, run git subtree add from the Overleaf remote, restore your content, commit, and push. Force-push is forbidden on the bridge, so re-seeding is the only fix.

How do I sync a monorepo subdirectory with Overleaf using git subtree?

Use git subtree pull and push with the --prefix flag naming the manuscript subdirectory, wrapped as make targets. Always commit before pushing, push then immediately pull to advance shared ancestry, and verify the remote tree with git ls-tree to confirm no parent-repo paths leaked.

Can an AI agent edit my LaTeX .tex files directly?

Under this workflow, no. Agents may read, compile, and review .tex files but must deliver changes as prose proposals or planning notes. A scaffold script the human runs can create structural stubs, and only an explicit project policy naming permitted paths can override the guardrail.

Should generated figures and tables be committed to git for Overleaf?

Yes. Generated artifacts are the interface between the reproducibility pipeline and the paper, and the Overleaf host cannot regenerate them. Commit figures/generated and tables/generated, make outputs byte-deterministic, and check with git check-ignore that no parent rule silently excludes them.

Why does a git subtree pull show conflicts right after a push?

Subtree push records nothing locally, so the next pull replays your own pushed commits as if the host wrote them. Diff the host tree against your matching local commit; if empty, abort the merge and push instead of resolving phantom conflicts.

How should I organize a rebuttal and camera-ready revision?

Keep reviewer-response plans outside the synced manuscript directory in project notes. Classify comments by must-fix, should-fix, optional, misunderstanding, or out-of-scope, triage by weight on the decision within the deadline, and maintain a claim-by-claim map from reviewer point to evidence to text change.