Add Custom Command Timeout Configuration

[TimothyFran]

Allow the run commands tool to handle long-running processes without hitting timeout limits that force inefficient polling behavior and unnecessary costs.

Now, the timeout is the 30s default one and cannot be changed. It would be useful to add a 'Custom Timeout' field in the settings where user can set a custom value in seconds.

[IlyaKhalafi]

A 30 second default matches the VS Code background child-process path. The foreground terminal instead auto-proceeds after five minutes, so it also returns control before a long command finishes. The runtime builder assigns that path a one-hour wrapper budget, but its separate auto-proceed timer can return control much earlier. The command stays running in a busy terminal and output goes to a capped log file.

For the requested background timeout setting, two independent deadlines need wiring in the VS Code extension. createShellTool defaults bashTimeoutMs to 30,000. createShellExecutor separately defaults timeoutMs to 30,000. In that background path, raising the wrapper alone leaves the executor deadline.

The background executor is constructed without a timeoutMs override. That call site and the tool wrapper should receive the same validated setting. The background executor kills the process tree on its deadline. Foreground auto-proceed leaves its terminal process running.

This distinction is specific to the VS Code wiring. The generic SDK executor can also detach when given an execution controller and session ID. I checked source at commit b549ceb, without testing your installed extension or confirming its current UI labels.