Paper Writer Plugin

Personal Claude Code plugin for academic paper writing in ML / computational biology. 9 skills (procedural + reference) + 5 thin agents + 5 commands, designed so the same procedural knowledge can be invoked in main session or in an isolated subagent.

Architecture

skills/ holds all procedural knowledge. Skills are reusable: load them in main session OR have an agent load them in isolation.
agents/ are thin wrappers (~15 lines each). Each agent declares model, tools, and which skills to load — no procedure embedded.
commands/ dispatch a specific agent as a subagent (for cases where you want isolation; the same workflow can run in main session without commands).

Skills

Skill	Used by
`repo-scanning-protocol`	brainstormer
`outline-construction`	outline-architect
`peer-review-protocol`	peer-reviewer
`prose-editing-discipline`	prose-polisher
`latex-conventions`	draft-writer, prose-polisher
`claim-evidence-chain`	outline-architect, draft-writer, peer-reviewer
`academic-style`	draft-writer, prose-polisher
`reviewer-rubric`	peer-reviewer
`figure-design-patterns`	brainstormer

Agents

All agents run on opus and have WebSearch + WebFetch.

Agent	Tools (extra to web)	Skills
`writing-brainstormer`	Read, Glob, Grep, Bash, Write, Edit	repo-scanning-protocol, figure-design-patterns
`outline-architect`	Read, Write	outline-construction, claim-evidence-chain
`draft-writer`	Read, Write, Edit, Bash	claim-evidence-chain, academic-style, latex-conventions
`peer-reviewer`	Read, Glob, Grep	peer-review-protocol, reviewer-rubric, claim-evidence-chain
`prose-polisher`	Read, Edit	prose-editing-discipline, academic-style, latex-conventions

Commands

Command	Dispatches
`/paper-pipeline [slug] [stage]`	orchestrator — detects current stage from `working/` and runs the right agent; pauses at each checkpoint
`/brainstorm-paper [slug]`	writing-brainstormer
`/outline-paper [slug]`	outline-architect
`/write-section [slug] [section-id]`	draft-writer
`/review-paper [slug]`	peer-reviewer
`/polish-paper [slug]`	prose-polisher

You can also invoke any agent directly in main session without a command — the skills load identically.

Suggested Pipeline

The full flow is brainstorm → outline → draft → review → polish. Each stage produces a file in papers/<slug>/working/ that the next stage consumes; the user owns the decisions between stages.

#	Stage	Agent	Produces	You decide before this stage
1	brainstorm	`writing-brainstormer`	`findings.md`	repo path
2	outline	`outline-architect`	`outline.md`	thesis, target venue, word budget
3	draft	`draft-writer` (per section, looped)	`draft-sections/<id>.tex`	section order; you assemble `draft.tex`
4	review	`peer-reviewer`	`review.md`	review depth; optional reviewer-persona focus
5	polish	`prose-polisher`	`polished.tex` + `polish-changelog.md`	which reviewer comments to act on; scope

Two ways to drive it:

Step by step — run the per-stage command for each stage (/brainstorm-paper, /outline-paper, …). Most explicit; nothing happens you didn't ask for.
Orchestrator — run /paper-pipeline <slug>. It detects which artifacts already exist and starts at the earliest missing stage, or starts at [stage] if you pass one explicitly. After each stage it stops, summarizes, and tells you what's next — it never auto-advances. Re-run later to resume from wherever you left off.

File Conventions

papers/<paper-slug>/
├── .bibsources          # paths to your master .bib files (one per line)
├── refs.bib             # plugin-managed; agents append verified entries here
├── working/
│   ├── findings.md
│   ├── outline.md
│   ├── draft-sections/<id>.tex
│   ├── draft.tex        # you assemble from draft-sections/
│   ├── review.md
│   ├── polished.tex
│   └── polish-changelog.md
└── final/               # camera-ready (you maintain)

Markdown for findings/outline/review; LaTeX for draft and polish onward. Markdown→LaTeX handoff happens at the outline.md → draft-sections/*.tex boundary.

Citation Discipline

Hybrid .bibsources lookup chain:

Look up citation key in master .bib files listed in papers/<slug>/.bibsources → if found, use it.
Else look up in papers/<slug>/refs.bib → if found, use it.
Else search online and verify the entry has a DOI or arXiv ID.
If verified: append to papers/<slug>/refs.bib with key lastname2024firstword. Master .bib files are read-only.
If unverifiable: emit [CITE: <description>] marker and report in chat.

Repo-Write Confirmation Gate

Agents have full write access in principle, but they MUST post a chat message naming the exact file and intended change before any Write/Edit outside papers/<slug>/. Silence is not consent — they wait for an explicit "yes / ok / go ahead".

Customization

The plugin ships voice/forbidden-pattern conventions in skills/academic-style/SKILL.md. Override per-repo by:

Adding voice rules to your repo's CLAUDE.md (Claude Code loads it on top of the plugin), OR
Editing your installed copy of academic-style/SKILL.md.

The plugin itself has no CLAUDE.md — it's portable across repos, and per-repo voice belongs in your repo, not in the plugin.

Install

git clone <this-repo> ~/.claude/plugins/paper-writer

Design Principles

Skills hold procedure. Agents are thin. Procedure is shareable between main session and subagents.
One responsibility per agent. New responsibility → new skill or new agent, never bolted on.
Files are the message-passing medium. Subagents communicate via papers/<slug>/working/.
The user drives the checkpoints. The /paper-pipeline orchestrator suggests the next stage and dispatches agents, but it never auto-advances past a decision point (thesis, section order, which reviewer comments to act on). The user is still the integration layer; the orchestrator just removes the "which command do I run next" friction.

Known Limitations

No multi-persona reviewer (single persona by default).
No LaTeX compilation (handle separately via tectonic / Overleaf / latexmk).
No automatic figure regeneration; agent will ASK before touching analysis code.
No automated assembly from draft-sections/*.tex to draft.tex — you control the assembly order.

paper-writer

Install to Claude Code

README