Verify Hopper cancellation, timeout, mutation readback, and shutdown

[morluto]

Run real-Hopper verifier tests for cancellation, timeout, database save/reopen mutation readback, and clean shutdown.

Acceptance:

• Cancellation and timeout stop analysis without leaks.
• Database save, close, reopen, and readback preserve names/comments/bookmarks.
• Owned shutdown completes and does not terminate unrelated Hopper instances.

Part of #25.