/doctor: make findings atomic — never bundle unrelated changes behind one confirmation

Problem: /doctor currently groups unrelated proposed changes — disk cleanup, unused-plugin removal, and checked-in CLAUDE.md content migration — behind a single "Clean up everything" option. Approving that one option applies all of them, even though they have wildly different risk and reversibility profiles: deleting a stale local install is nothing like rewriting a file the whole team reads.

Impact: A user who's happy to approve the low-stakes items (plugins, disk space) gets no natural pause point before a higher-stakes one (editing shared project instructions) also gets applied, because it's hidden inside the same bundle. Discovered this the hard way — approved the bundle, didn't register that it included a CLAUDE.md rewrite until afterward, had to revert.

Request: Present every finding as its own atomic, independently-confirmable action. Never collapse unrelated categories into one combined yes/no, even as a labeled "recommended" shortcut — granularity should be the default, not something only available via a secondary "let me pick" path.