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Online upgrades can strand users on stale desktop UI state or malformed local persistence. This adds a deny-by-default Doctor path that resets only regenerable desktop UI state, reports protected local files with redacted metadata, and keeps protected repair as a dry-run no-op until a reviewed backup-first flow exists. Constraint: Chat transcripts, model/provider config, Skills, MCP, IM bindings, adapter sessions, OAuth tokens, plugins, and team/session records are user-owned protected state. Rejected: Automatically rewrite malformed protected JSON | unsafe without schema-specific migrations and backups. Rejected: Continue relying only on startup migrations | users need an explicit recovery action after a white screen. Confidence: high Scope-risk: moderate Directive: Keep Doctor repair deny-by-default; do not mutate protected state without an explicit reviewed backup-first manual repair flow. Tested: bun test src/server/__tests__/doctor-service.test.ts Tested: cd desktop && bun run test src/components/ErrorBoundary.test.tsx src/lib/doctorRepair.test.ts src/__tests__/diagnosticsSettings.test.tsx src/components/layout/StartupErrorView.test.tsx Tested: cd desktop && bun run lint Tested: bun run check:server Tested: bun run verify (failed only existing agent-utils coverage baseline; changed-lines coverage 97.62%) Not-tested: Packaged desktop manual Doctor click path.