Merge with sbliven

This adds some pom cleanups:
- Use vecmath 1.3.1
- Take JDK version from the parent pom

Also some code changes:
- Improvements to CrystalTransform class & xtal package
- Warnings and logging improvements

Conflicts:
	biojava3-alignment/pom.xml
	biojava3-core/pom.xml
	biojava3-modfinder/pom.xml
	biojava3-phylo/pom.xml
	biojava3-protein-disorder/pom.xml