Propagated the native shell working directory in ShellRunResult so AgentSession can refresh cwd without running a hidden pwd command in the persistent shell.
Added regression coverage for cd plus a failing command followed by echo $?, proving cwd sync no longer overwrites the user's last shell status.
Fixes#3958
Updated interactive bash execution to query the persistent shell PWD after commands and move the session cwd when it changes, keeping the status line and session-scoped settings aligned with shell navigation.
Added regression coverage for syncing persistent shell directory changes back to the owning session.
Fixes#3958