Add `batch` option to not copy all files in top-level directory

Why this feature is necessary:
It's inefficient (and potentially problematic) to copy all files form the top-level directory into the sub-directories, especially is a careless user stores a large file in the main directory.

A possible solution is:
Add a key to the batch config that allows the user to set a copy behavior. The default can still be 'all' (though maybe this is worth reconsidering). However, a new option can be "config" or something similar, which reads all the config files in the pipeline config and only copies files that the config "mentions". This is not perfect, since there can be a files that a user wants to be copied into the sub-directories that does not appear in any config files, but this is a rather fringe example which can still be handled by the original "all"
copy method. The "config" method is likely sufficient for most typical use-cases.

Urgency / Timeframe
Not super urgent, just a nice-to-have

Locate the batch configuration handling and the logic that copies files from the top-level directory into sub-directories. Review how pipeline config files are read; done means preserving the default 'all' behavior while adding an option that copies only files mentioned by the configuration.