The reason I had done this is because all the files are symbolic links in lib -- and they don't necessarily work when qualimap runs them.

So, for example:, batik-1.5-fop-0.20-5.jar gets defined as this:
lrwxrwxrwx 1 jeremy jeremy 53 Sep 13 17:24 /home/jeremy/.linuxbrew//lib/batik-1.5-fop-0.20-5.jar -> ../Cellar/qualimap/0.7.1/lib/batik-1.5-fop-0.20-5.jar

which is AWESOME if you're in the special magic directory when you run the qualimap command.  If you aren't in the right directory, it fails with a "java.lang.NoClassDefFoundError" -- and I _think_ this is because it can't navigate its way to the actual directory.  Is there a way to get brew to either symlink them with absolute pathnames, or to copy them into the lib directory, so it'll work?