Academic Research Skills
A suite of Claude Code skills for rigorous academic research, paper writing, peer review, and pipeline orchestration.
## Skills Overview
| Skill | Purpose | Key Modes |
|-------|---------|-----------|
| `deep-research` v2.12.1
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Hiring**: Add 10 engineers to accelerate product development
2. **Product**: Launch AI codereview feature by end of Q2
3. **Sales**: Expand into European market
4. **Fundraising**: Begin Series
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formatting and notebook structure.
## Slash Commands
These commands are available in Claude Code and CI:
- `/notebook-review` - Review notebook quality
- `/model-check` - Validate Claude model references
- `/link-review` - Check links in changed files
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patches.
## GitHub
### Pull Requests
Use the `gh-create-pr` skill. Fallback: read `.agents/skills/gh-create-pr/SKILL.md` directly.
### CodeReview
When reviewing a GitHub PR, do NOT run `pnpm lint` / `pnpm test` / `pnpm format
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AGENTS.md` as loaded. Claude Code does not reliably inline that import.
Before any planning, coding, reviewing, or answering a project question, you MUST call the Read tool on the repo
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Last reviewed: 2026-10-17
**Project:** GitNexus · **Environment:** dev · **Maintainer:** repository maintainers (see GitHub)
Follow **AGENTS.md** for the canonical rules; this file adds Claude Code–specific deltas. Cursor-specific notes
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mode must be written as "follow-up" or "preserves codes for observability; retry wiring unverified" — never as achieved. A reviewer will verify your claim against the running system; over-claiming
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code (ruff check, mypy)
./scripts/validate.sh
```
Both scripts must pass with no errors before codereview.
**PR Title Format:**
PR titles must follow one of these formats:
- `type: description` — e.g., `feat
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inside a fenced code block are ignored, so keep them as plain numbered lines. Write each step as a numbered checkbox (`1. [ ] step`) so a reviewer can tick
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later in a separate lane.
Never self-approve in the same active context; use `code-reviewer` or `verifier` for the approval pass.
Before concluding: zero pending tasks, tests passing, verifier
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later in a separate lane.
Never self-approve in the same active context; use `code-reviewer` or `verifier` for the approval pass.
Before concluding: zero pending tasks, tests passing, verifier
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push
```
> The parent repo stores a commit SHA pointer to each submodule, not the code itself. Always push from inside the submodule first, then update the pointer in the parent
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This shows all tasks grouped by status (Completed, Done, In Progress, To Do).
### 2. Review Recent Commits
```bash
git log --oneline -20
```
Look for feature implementations, major refactors, or completed
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CLAUDE.md
This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
## Overview
Trilium Notes is a hierarchical note-taking application with synchronization, scripting
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AGENTS.md](AGENTS.md)**, imported below so Claude Code loads it automatically. They are mandatory for all content generation, pull requests, issues, comments, and reviews.
@AGENTS.md
## For maintainers
To review a pull
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shell
- ✅ README states the command, controls/options, the minimum Claude Code version and (for `games/`) the attribution
**The component-reviewer agent checks:**
- ✅ Valid YAML frontmatter and required fields
- ✅ Proper kebab-case
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A file Claude Code reads at the start of every session. It holds the commands, conventions and warnings the agent needs for this project.
Where does it go?
At the repository root. Claude Code also reads CLAUDE.md files in subdirectories when it works there.
What should it contain?
Build and test commands, the project's layout, conventions that aren't obvious from the code, and mistakes to avoid. Short files tend to work better than long ones.
CLAUDE.md or AGENTS.md?
Claude Code reads CLAUDE.md; most other agents read AGENTS.md. Many projects keep one and point the other at it.