Add capability to package files such as input decks or any file paths when submitting a workfow from a directory

[pagrubel]

Currently there is no way of defining extra files to package with the workflow. It has to be done manually.
When submitting a workflow from a directory, beeflow currently moves everything to a temporary directory. This was previously implemented to be able to use external yml files for the submit command. If we add a way to include a yml file describing any other file paths that we want to include we can copy those files (and possibly directories) into that temporary directory and they will be available in the packaged workflow.

Think about how they will be used for the workflow.