Run a shell command inside the workspace.

Usage:
- `command` is executed in the workspace root unless `workdir` is provided.
- Use `workdir` instead of embedding `cd ... && ...` in the command.
- Prefer dedicated tools (`read`, `glob`, `grep`, `edit`, `write`) for file inspection and editing.
- Use this tool for build, test, git, package manager, and other terminal workflows.
- `timeout_ms` controls command runtime; timed out commands return partial output and a timeout marker.
- Large stdout or stderr is truncated in the response and the full output is saved to a workspace file.
