academic-agent-toolkit 0.1.0

Plug-and-play CLI for academic research agent skills and Paper Search MCP setup

Academic Agent Toolkit (AAT)

One command to install academic research skills and paper search across all your AI coding agents.

Students and researchers use different AI agents (Claude Code, OpenCode, Cursor, Copilot, Codex). Each agent needs different config formats, different file locations, and different skill setups. AAT handles all of that so you can focus on your research.

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What you get

Component	What it does
Academic Research Suite	Deep research, lit reviews, systematic reviews, paper drafting, peer review, experiment planning
Experiment Agent	Study protocol design, statistical interpretation, reproducibility validation
Paper Search MCP	Search 20+ academic sources (arXiv, PubMed, Semantic Scholar, Crossref...) and download PDFs

All configured across every supported agent in one command. No manual JSON/TOML editing.

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Quick Start

Prerequisites: Python 3.11+, uv.

# See what agents are detected and what's missing
uvx academic-agent-toolkit doctor

# Install everything (skills + MCP) with one guided command
uvx academic-agent-toolkit install

# Configure your API keys interactively
uvx academic-agent-toolkit setup-keys

# Verify the installation
uvx academic-agent-toolkit verify

The shorthand aat works everywhere:

uvx aat doctor
uvx aat install
uvx aat setup-keys
uvx aat verify

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How it works

New users — aat install downloads Academic Research Suite and Experiment Agent automatically, creates a private .env file for your API keys, and configures Paper Search MCP in every detected agent.

Existing users — AAT adopts your existing ARS installation and Paper Search MCP registrations. It skips what you already have and only manages what's missing. Use --replace-skills or --replace-mcp if you want AAT to take over an existing setup.

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Commands

Command	What it does
aat doctor	Show environment readiness and agent detection
aat install	Install skill adapters and MCP configs with a guided plan
aat setup-keys	Configure Paper Search MCP API keys interactively
aat verify	Confirm everything is in place
aat self-check	Validate runtime prerequisites (Python, uv, ARS source, env file)
aat repair	Re-apply the last saved installation
aat uninstall	Remove AAT-managed files safely (does not touch your own configs)

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API Keys

Paper Search MCP works without most keys, but some sources need credentials. AAT helps you set them up interactively with aat setup-keys.

Variable	Required?	Recommended?	Where to get it
PAPER_SEARCH_MCP_UNPAYWALL_EMAIL	yes	—	unpaywall.org
PAPER_SEARCH_MCP_CORE_API_KEY	no	yes	core.ac.uk
PAPER_SEARCH_MCP_SEMANTIC_SCHOLAR_API_KEY	no	yes	semanticscholar.org
PAPER_SEARCH_MCP_GOOGLE_SCHOLAR_PROXY_URL	no	no	Your proxy provider
PAPER_SEARCH_MCP_DOAJ_API_KEY	no	no	doaj.org
PAPER_SEARCH_MCP_ZENODO_ACCESS_TOKEN	no	no	zenodo.org
PAPER_SEARCH_MCP_IEEE_API_KEY	no	no	developer.ieee.org
PAPER_SEARCH_MCP_ACM_API_KEY	no	no	acm.org

Keys are stored in a single private file (~/.config/paper-search-mcp/.env by default). Paper Search MCP reads them automatically via PAPER_SEARCH_MCP_ENV_FILE. No keys are duplicated across agent configs.

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Supported Agents

Skill adapters (agent-optimized routers for Academic Research Suite):

• Claude Code
• OpenCode
• Cursor
• GitHub Copilot
• Codex (opt-in with --include-codex)

MCP configuration (Paper Search MCP registration):

• Claude Code
• OpenCode
• Cursor
• Codex
• VS Code (user and global)
• GitHub Copilot
• Zed

See docs/mcp-agent-matrix.md for the exact config format used per agent.

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Install flags

Flag	Purpose
--no-bootstrap	Skip automatic ARS download; requires an existing source
--ars-source PATH	Use a specific ARS source tree
--env-file PATH	Use a custom .env file path
--replace-skills	Back up and replace existing skill directories
--replace-mcp	Back up and replace existing MCP entries
--include-codex	Also install the Codex skill adapter
--dry-run --yes	Preview the full plan without writing files

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Uninstall

aat uninstall

Removes only files AAT created. Your existing hand-written configs and skill directories are never touched. Optional flags:

• --remove-env also removes the Paper Search MCP env file
• --remove-managed-ars also removes AAT's downloaded ARS source

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Where files live

What	Location
AAT config	~/.config/academic-agent-toolkit/config.json
Managed ARS source	~/.local/share/academic-agent-toolkit/ars/
Paper Search MCP env	~/.config/paper-search-mcp/.env (default)
Skill adapters	~/.claude/skills/, ~/.config/opencode/skills/, ~/.cursor/skills/, ~/.copilot/skills/

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Upstream projects

AAT is an integration layer. It bundles and configures these upstream projects with their permission:

• academic-research-skills by Imbad0202
• experiment-agent by Imbad0202
• paper-search-mcp by openags

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License

MIT — see LICENSE.