Desktop app: newly-created project (git repo nested inside an already-open parent folder) never appears as its own sidebar section

What happened — Created ~/Dev/deckhand as a git repo nested inside ~/Dev (already an open project, itself not a git repo). Ran sessions rooted in ~/Dev/deckhand, but it never appears as its own sidebar section, even after ⌘Q restart.

Environment — Desktop app (macOS), version 1.12603.1.

Repro

1. Have ~/Dev open as a project.
2. Create git repo ~/Dev/deckhand.
3. Open it as a project, run a session.
4. ⌘Q and reopen.

Expected — deckhand shows as its own sidebar section like sibling projects.

Actual — Never appears. Siblings under the same parent show fine; the differentiator is the new project was opened while its parent was already registered.

Evidence (UI/cache, not missing data)

• ~/.claude/projects/-Users-milly-Dev-deckhand/ has real session .jsonl transcripts.
• ~/.claude.json lists the path.
• App session data exists under ~/Library/Application Support/Claude/claude-code-sessions/.
• Restart doesn't surface it. Looks like the sidebar reads cached Electron IndexedDB/LocalStorage state rather than live from disk.

Workaround — cd ~/Dev/deckhand && claude works and loads history.

Related — #50749, #51513, #48967