chore(deepagents): clarify LocalShellBackend virtualMode behavior (#577)

## Summary

Fixes #544.

Clarifies `LocalShellBackend` path semantics without introducing a
breaking default change. This keeps legacy behavior intact while making
the bounded-workspace setup explicit in docs and examples.

## Changes

### deepagents (`LocalShellBackend`)

- Clarified `LocalShellBackendOptions` docs to explicitly note that
`rootDir` does not bound filesystem paths when `virtualMode` is `false`.
- Updated `LocalShellBackend` examples to use `virtualMode: true` when
bounded path semantics are intended.
- Added unit coverage to assert legacy behavior is preserved: with
`virtualMode: false`, absolute writes can resolve outside `rootDir`.