Prevent UI hang on long tool confirmations.

Problem:
When a tool confirmation dialog appeared for a potentially long-running
operation (e.g., `npm install`), accepting the confirmation would cause
the UI to appear to hang. The confirmation dialog would remain visible,
and no further UI updates would occur until the long-running task
completed. This provided a poor user experience as the application
seemed unresponsive.

Fix:
This change addresses the issue by ensuring the UI is updated to remove
the confirmation dialog *before* the long-running operation begins.
It also marks the tool as executing so a spinner can be shown.

Fixes https://b.corp.google.com/issues/415844994

Signed, sealed, delivered, it's yours!
   - Gemini, your friendly neighborhood code-slinger

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