Fix cleanup for deleted projects and worktrees

[jsgrrchg]

Summary

• remove modern and legacy data scoped to deleted worktrees and projects
• clear persisted project settings and workspace contexts without affecting other scopes
• migrate worktree-owned SQLite foreign keys to cascade on deletion

Validation

• cargo test -p comando-persistence -p comando-projects -p comando-native-backend -p comando-ai
• pnpm run typecheck
• pnpm exec vitest run src/renderer/src/app/store/workspace-store.test.ts