fix: keep pending-input runs alive until callbacks settle

[kesslerio]

What

• keeps active runs registered while pending input still exists
• restores an active run if questionnaire input arrives after the original settle path
• adds lifecycle logs for deferred cleanup and callback misses

Why
The first questionnaire prompt could be shown to the user, then fail on submission because the run had already been cleaned up. This branch fixes that race, but the work was later folded into #95 with broader follow-up coverage.

Tests

• pnpm test src/controller.test.ts
• pnpm typecheck
• pnpm test

AI Assistance

• Codex used for implementation and testing.

[kesslerio]

Superseded by #95. The follow-up lifecycle fixes and the broader regression coverage were moved there so the questionnaire/run-cleanup work stays in one PR.