reformatted pom.xml
removed some unused plugins from the pom
added some elements required by sonatype
removed unneeded repository definitions
CORE-5040: updated CondorJobRequestFormatter to work with the new property value format for reference genomes
CORE-4807: fixed a couple of javadoc comments
CORE-4807: keep the default value when formatting reference genome input properties for the UI
Merge remote-tracking branch 'origin/dev'

Conflicts:
	pom.xml