pom.xml reformatting and minor refactoring

After this, I still have a few questions:

 - Should jdk.version be 1.7?  I don't think this will run on jdk 1.6 due to dependencies that require 1.7.
 - Should the ADAM dependency version be bumped to 0.13.1-SNAPSHOT?
 - Can some of the plugin configuration be moved from module poms to parent?  Things like ```<source>${project.build.sourceDirectory}/../gen-java</source>``` would lead me to think not.

I'll try irc.