Additional formatting and refactoring

Created by: pmpowers-usgs

Some classes are incorrectly formatted, mostly wrt indentation. We also want to move classes like SourceElement and SourceAttribute to util and disable javadoc generation of the util package; the classes it contains are generally for internal use only but are public so as to be accessible by other projects.

Created by: pmpowers-usgs

created 'internal' package to hold privately used classes with public exposure so that 'util' can be javadoc-ed

Created by: pmpowers-usgs

Should also more classes/enums like Site, Sites, Vs30 to 'util' package

Created by: pmpowers-usgs

updated build.xml javadoc to use packages -- more performant and doesn't throw errors for classes in packages that won't be documented but that are referenced by public classes in other packages