Stuck agent assistants cause main agent to hang when performing multiple parallel edits

### Describe the bug

When using the CLI agent to perform multiple file edits in quick succession (especially with parallel tool calling across multiple files), one of the agent assistants occasionally becomes stuck/hangs, which causes the main agent to hang indefinitely.

### Affected version

0.0.358 Commit: f5a8b1e76

### Steps to reproduce the behavior

> This happens frequently when:
> - Multiple agents are being used to perform edits across multiple files in quick succession
> - Using parallel tool calling to edit multiple files simultaneously
> - It seems to only be one agent that hangs, not all of them

1. Request a simple edit that will need to be applied across multiple files (10+)
2. Wait for the main agent to build up a queue of permission requests to edit the files in question
3. Rapidly approve all the requests in quick succession
4. Wait until the end of time...

### Expected behavior

- Agent assistants should have a timeout mechanism
- Main agent should detect hung assistants and either:
- Retry the operation
- Skip the hung assistant and continue with other operations
- Provide clear error messaging about which assistant is stuck
- Should not require force quit to recover

### Additional context

- Operating System: Linux (Ubuntu Desktop 24.04)
- CPU Architecture: x86_64
- Shell: bash