I want to link this up to a display application (web app running on the same server via apache) such that galaxy provides a URL that will enable read access to these files.  

From what I could gather, there's no straightforward way to get a stable URL from galaxy that points to the extra_files in the composite data set, such as getting links to a bunch of bam files and indexes placed there. 

Assigning each of the extra files as metadata items (ie. similar to a bam.bai file as a metadata file for a single bam file) could have been an option, but I couldn't get that to work.

For now, since my Galaxy instance and my web app are running on the same machine with access to the same file system, I'll just have my web app read the files directly from the galaxy database directory via symlinks set up by my galaxy tool during the run.  It's a clunky way of doing things but should suffice for now given my setup.

If others have better solutions, I'm definitely interested in hearing them.

many thanks,

~brian