setup

Quick definitions (T4-5; full glossary at skills/_glossary.md):

• A plugin is the code bundle this setup is configuring — a downloadable package shipped with skills, pipeline scripts, and templates that the agentic environment uses for academic-research work.
• A skill is a prose rule-book the agent loads when your request matches its trigger phrases. Skills tell the agent how to approach a task; they don't run code on their own. setup, zotero- operations, systematic-review, etc. are all skills in this plugin.
• An MCP server is a small helper program the agent talks to in the background. Example: the Zotero MCP server lets the agent read and update your Zotero library directly. The wizard checks five MCP servers (Zotero, Scopus, Semantic Scholar, OpenAlex, paper-search) and offers to register the missing ones.

Setup runs as a terminal wizard the user executes. The agent's role is only to give them the command and confirm when they are done. Do not run any tool calls — no Bash, no Read, no probes. All the information needed is already known:

• Wizard path: ${CLAUDE_PLUGIN_ROOT}/scripts/setup/wizard.py (or project-relative ./scripts/setup/wizard.py if not running inside Claude Code or Antigravity) — The active plugin version's absolute path (or project-relative fallback if ${CLAUDE_PLUGIN_ROOT} is not defined) is used, so the user has a concrete path to run.
• Config written to: ~/.config/academic-research/config.toml (mode 0600).
• Settings patched: ~/.claude/settings.json (backed up as .bak-wizard, bypassed silently if not running under Claude).
• Antigravity MCP config: if Antigravity (agy) is detected, the same MCP servers are also registered into ~/.gemini/config/mcp_config.json (backed up as .bak-wizard). Permission rules are not patched for Antigravity — only Claude Code's ~/.claude/settings.json is.
• Wizard is idempotent: re-running updates or adds keys without clobbering existing ones.

Procedure

CRITICAL: never ask the user to paste API keys into the chat. Any text typed into the chat is transmitted to the model provider. The wizard exists so keys stay local.

Paste the following message to the user (no tool calls needed — just text):

I'll hand you the setup wizard. It runs in your terminal, prompts for each API key with hidden input (keystrokes don't appear), then checks five MCP (Model Context Protocol) servers and offers to register any that are missing: Zotero (required — every citation skill uses it), at least one of Scopus / Semantic Scholar / OpenAlex (required for literature search to work), and paper-search (optional — for ArXiv / PubMed PDF retrieval). It then writes your config file locally. Your keys never pass through the chat.

Run the setup wizard in your terminal. If the ${CLAUDE_PLUGIN_ROOT} environment variable is defined:

python3 ${CLAUDE_PLUGIN_ROOT}/scripts/setup/wizard.py

Otherwise, run the project-relative command from the root of your workspace:

python3 ./scripts/setup/wizard.py

How to open a terminal if you are not already in one:

• macOS: ⌘-Space → type Terminal → Enter.
• Windows: Windows key → type PowerShell → Enter. If python3 is not recognised, try python instead.
• Linux: Ctrl-Alt-T (or your distro's terminal app).

Already running the agent in a terminal? Either open a new tab and run it there, or temporarily exit this session, run the wizard, and then resume this conversation.

When the wizard prints "Setup complete", return here and say "done" (or similar). I'll confirm and we'll continue.

After the user says they finished the wizard, respond with a short confirmation ("Setup done. Ready for the next task.") and let the next conversational turn drive the work. Do not run a verification Bash call — if something went wrong with the wizard, the user's next invocation of zotero-operations / systematic-review / etc. will hit its own pre-flight check and bounce here again.

If the wizard reports errors

The wizard prints to stdout. If the user pastes output showing a problem:

• Python missing: tell them to install Python 3.11+ — macOS can use Homebrew (brew install python), Windows can use python.org's installer (check "Add Python to PATH"), Linux uses the distro's package manager.
• Tkinter not required — the wizard is terminal-only. Any Python 3.11+ install works.
• Permission denied writing config: user's home directory has unusual permissions. Unlikely on a single-user machine.
• Can't parse existing settings.json: the file is malformed. The wizard backs up to .bak-wizard before touching; restore from there, fix manually, or delete and re-run.
• MCP register fails with "command not found": the underlying MCP binary is not installed. The wizard prints the project's homepage and the exact install command (uv tool install "zotero-mcp-server[scite,semantic]" — the extras add Scite retraction checks and semantic search; uv tool install scopus-mcp, or "requires Node.js + npm" for the npx-based servers). Install it, then re-run the wizard — it's idempotent and picks up where it left off.
• Wizard exits with code 4: Zotero MCP is not connected. No academic-research skill works without it. The wizard's summary lists the install and registration commands; run them and re-run the wizard.

Red flags

• You are about to run a Bash tool call in this skill. Don't. This skill has no Bash probes by design — they cause permission prompts for no benefit. The wizard handles everything.
• You are about to ask the user to paste a key into the chat. Never. The wizard is the only acceptable path for keys.
• You are about to log, echo, or repeat a key the user typed in any form. The wizard hides input for this exact reason; don't accidentally capture it in follow-up questions.