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.
Desktop users can carry provider indexes, managed settings, localStorage state, and native update state from builds that no longer match current readers. This adds startup migrations and recovery paths before server and React state are consumed, plus a persistence upgrade gate so future storage protocol changes ship with old-format fixtures.
Constraint: Existing installs may contain malformed or legacy JSON/localStorage that must not block startup.
Constraint: Local verify should evaluate the current worktree diff rather than unrelated detached-worktree history.
Rejected: Treat invalid persisted state as fatal | reproduces white-screen and startup failure behavior for existing users.
Rejected: Bypass PR policy locally | hides real gate behavior and does not fix detached-worktree false positives.
Confidence: high
Scope-risk: moderate
Directive: Any local JSON, localStorage, or app config shape change must add a migration fixture and keep `bun run check:persistence-upgrade` green.
Tested: bun run check:persistence-upgrade; bun run check:policy; bun run check:desktop; bun run check:server; bun run check:native; bun run verify (9 passed, 1 coverage baseline failure)
Not-tested: Live provider baseline; existing user configs beyond covered fixtures
