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=make doctor= scans =~/.claude/= and reports drift against the repo + settings.json. Read-only diagnostic. Eight checks cover skills, rules, default hooks, claude config, settings.json hook references, enabledPlugins, MCP server registrations, and dangling symlinks. Each line prints =ok= / =WARN= / =FAIL= with a final summary. Exit 1 on any FAIL.
A sweep last night found =~/.claude/hooks/= didn't exist on this machine even though =settings.json= referenced a PreCompact hook there. Compaction would have silently failed to invoke it. doctor catches that kind of drift in one command instead of relying on a manual look.
The MCP drift check reads =~/.claude.json= directly rather than parsing =claude mcp list=. The CLI has no JSON output and runs a per-server health probe (~10s). The JSON file is the user-scope source of truth for registrations and parses in well under a second.
I verified by injecting four drift scenarios — removed hook symlink, removed skill symlink, moved-aside plugin data dir, unregistered MCP server. Each produced the expected =FAIL= line and exit 1. After restoring state, doctor came back clean (33 ok).
Bundling four other improvement TODOs from the same sweep — =mcp/README.org=, =make uninstall-mcp= and =mcp/install.py --check=, a README.org section for the MCP install pipeline, and a token-rotation helper for =@a-bonus/google-docs-mcp= OAuth refresh. Plus a stale-bullet note on the existing =make remove= TODO (the bridge symlink it references was removed earlier).
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