/setup -- Configure and verify Grainulator

The user wants to set up Grainulator or verify that all MCP servers and dependencies are working correctly.

Arguments

$ARGUMENTS

Instructions

Phase 1: Verify core MCP servers

Grainulator bundles three core MCP servers that run locally via npx. Check each one in order:

1. Wheat (research claims engine)

   • Purpose: Manages typed claims (claims.json), compiles sprint state, resolves conflicts, and searches across claims. This is the backbone of every research sprint.
   • Verify: Call wheat_status. If it returns sprint data or a "no sprint found" message, the server is healthy.
   • If it fails: The @grainulation/wheat npm package may not be accessible. Ask the user to run npx -y @grainulation/wheat manually to check for npm/network issues.
   • Sprint data (claims.json, compilation.json) lives in the project root.

2. Mill (format conversion engine)

   • Purpose: Converts between document formats (Markdown, HTML, PDF). Used by /brief and /present to produce output artifacts.
   • Verify: Call mill_formats. If it returns a list of supported formats, the server is healthy.
   • If it fails: The @grainulation/mill npm package may not be accessible. Same troubleshooting as Wheat.

3. Silo (knowledge storage)

   • Purpose: Stores and retrieves knowledge packs, manages a graph of connected concepts, and integrates with Confluence. Used by /research and /pull for knowledge reuse across sprints.
   • Verify: Call silo_list. If it returns a list (even empty), the server is healthy.
   • If it fails: The @grainulation/silo npm package may not be accessible. Note that Silo uses ${CLAUDE_PLUGIN_DATA}/silo for persistent storage.

Report the status of each server:

MCP Server Status:
  wheat  ✓ running  (claims engine)
  mill   ✓ running  (format conversion)
  silo   ✓ running  (knowledge storage)

If any server fails, show the error and suggest a fix. Do NOT proceed to Phase 2 until all three core servers are confirmed running.

Phase 2: Check optional dependencies

4. DeepWiki (external, optional)
   • Purpose: Provides read access to public GitHub repository documentation via MCP. Used by /research when investigating open-source projects. This is an HTTP MCP server hosted at https://mcp.deepwiki.com/mcp -- Grainulator does not control it.
   • Verify: Check if mcp__deepwiki__ask_question appears in the available tools list. If the tool is listed, the server connected successfully.
   • If unavailable: This is expected and non-blocking. DeepWiki is a convenience for researching public repos. All core Grainulator functionality works without it. Tell the user:

     DeepWiki is optional. If it's unavailable, /research will use WebSearch and direct code reading instead. No action needed.

   • Do NOT treat DeepWiki failure as a setup failure.

Report:

Optional Dependencies:
  deepwiki  ✓ connected  (GitHub repo docs -- optional)

or:

Optional Dependencies:
  deepwiki  ✗ unavailable  (GitHub repo docs -- optional, not required)

Phase 3: Check for existing sprints

5. Look for an existing sprint by checking for claims.json in the project root. If a sprint exists, show its question and phase:

Existing sprints:
  marketplace-submission  (phase: research, 22 claims)
  gamification-playbook   (phase: define, 3 claims)

6. If no sprints exist, offer to initialize one:

No sprints found. Would you like me to start one? Tell me your research question and I'll run /init to set it up.

If the user provides a question (either as $ARGUMENTS or in conversation), proceed to run the /init workflow to create the first sprint.

Phase 4: Summary

Print the final setup report:

Grainulator setup complete.

Core servers:    3/3 running
Optional deps:   1/1 connected (or: 0/1 -- deepwiki unavailable, non-blocking)
Active sprints:  <count>

You're ready to go. Try:
  /research <topic>  -- start investigating
  /status            -- view sprint dashboard
  /init <question>   -- start a new sprint

Important: Do NOT manually register MCP servers

Do NOT run claude mcp add wheat, claude mcp add mill, or claude mcp add silo. The Grainulator plugin already registers all three MCP servers automatically via plugin.json. Adding them manually creates duplicate server entries, which causes tool name collisions and nondeterministic behavior.

If MCP servers are not connecting, use /reload-plugins to refresh the plugin's server registrations instead of manually adding them.

If you suspect a duplicate exists (e.g., you previously ran claude mcp add wheat), remove the manual entry:

claude mcp remove wheat

Then restart Claude Code to pick up only the plugin-provided servers.

Troubleshooting notes

• All three core servers use npx -y, so they download on first run. First-run latency of 5-15 seconds is normal.
• Node.js is required. If npx is not found, the user needs to install Node.js (v18+ recommended).
• Network required for first run since packages are fetched from npm. After the first run, npx caches them locally.
• Silo persistence: Silo stores data in ${CLAUDE_PLUGIN_DATA}/silo. This survives plugin updates but is deleted on uninstall (unless --keep-data is used).