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.
