Feature/batch inject take two

This feature is a huge feature, FYI. It's not fully debugged but all the major functionality should be working, I just need to move on now.

When I run it on the VM I get an error in testParseMiseqFile, but that seems to be because test_seqware_meta_db is not being populated by the mvn install process. Is this the correct way to run all of the tests?

mvn clean install -DskipITs=false