Fixing distribution information
Switching to biojava 3.1.0-SNAPSHOT
Updating pom to biojava 3.1.0

Also update log4j to 2.0.2 and
downgrade vecmath to 1.3.1 from maven central
Adding unit test cases

These shouldn't be different, and someone should track down when they
changed. But for now I want the tests to stop changing things.
Updating ResourceListTest to stop modifying xml files

Now it cleans up after itself