test: reap native app-server fixtures after each test

[naiba]

Problem

Real test fixtures retain their app-server until worker exit. Protocol logging showed later command tests timing out during app-server initialization, before command handling.

Change

Dispose each real fixture after its owning test, close stdin first, await process exit, and use a bounded kill fallback. Keep the existing test-home cleanup on exit.

Validation

• New regression was red before cleanup: the previous test app-server remained alive. All three fixture utility tests passed after the change.
• Full local Bun suite without retries: 1493 passed, 36 pre-existing skipped. That run also included the separate idle-observer and workspace-symlink assertion changes; neither is included here.
• Typecheck and build passed.

No command assertions were removed, no timeout was increased, and no retry was added.