Health-check the user's Claude Code setup and fix issues: diagnose installation health — what the claude doctor terminal diagnostics cover — from local data (duplicate or leftover installs, PATH, unparseable settings files, broken or colliding agent definitions); find unused skills, MCP servers, and plugins versus their context cost and disable dead weight; deduplicate local CLAUDE.md files against checked-in ones; trim checked-in CLAUDE.md files by cutting content a session could derive from the codebase (directory layouts, tech-stack lists, architecture overviews) while keeping gotchas, rationale, and non-standard conventions; migrate always-loaded CLAUDE.md guidance into lazy skills and nested CLAUDE.md files; flag slow hooks and context-heavy extensions; check the installed version is current; make auto mode the default permission mode; and pre-approve frequently denied read-only commands. Use when the user asks for a doctor run, checkup, audit, tune-up, or cleanup of their Claude Code setup or configuration.