When returning/downloading working directory contents allow subdirectories.

Download $output.files_path files from working directory.
Include output directory's contents in finish response.

Hopefully, will allow client to better infer what was created and not attempt to download empty outputs and pull down output extra files.
'Extra' files improvements.

Allow outputs to $output.extra_files_path (limited support for $input.extra_files_path already existed). Extend the LWR server to report everything in outputs directory at end of job to support this. Extend $input.extra_files_path to allow nested such files. Add some client utilities for path and directory logic to support this.

Add integration testing of input and output multiple files.
Allow LWR to use tools with version_command.