I set library_import_dir to a path and tried uploading a directory of bam files. After fixing the situation so galaxy could find samtools in that subshell, I was able to upload links to the history. But moving things to one directory did not appear to be terribly useful, so I tested what happened if I had subdirectories existing in library import directory.
Test 1 I used folders u1 and u2, each with data, and some data in the root library_import_directory. After clearing the samtools eror I was presented with a drop-down list with choices 'None', 'u1' and 'u2'. Selecting 'None' did not result in seeking data but a sharp reminder that I had to pick a directory. Selecting those directories led to uploads, with the Non-Copy correctly sized and even downloadable from the data library, but NOT usable in the history, because upload.py decided the file did not exist (probably the 'path' variable in os.path.exists() line 99).
It also became apparent that the upload would look one level down from the root directory and no further (tested by adding u3 with data and a subdirectory of u3 called v3, also with data.
So the current state of affairs is that it is a single directory to which one must move files in order to upload links to a galaxy library or folders thereof.. OR, alternatively, make a directory of links called directory A, and then another directory of links to the links in directory A at the library_import_dir and then ask Galaxy to copy the data. (Not fully tested yet).
But it is apparent from the UI that more utility was intended. If I have time, I will help with that.
Michael Moore