Add -lociFromFile argument to Commmon

 * Any caller that uses Common.Loci set of arguments now supports a -lociFromFile argument that accepts a path to a file giving loci to call at. Closes #232.
 * Loci parsing now ignores all whitespace (including newlines, etc.) instead of just spaces.
 * Add a test for parsing a file with containing loci
Remove unused import
upgrade args4j and add forbids argument to loci args
Merge pull request #237 from hammerlab/add-loci-from-file-common-argument-forbids

Upgrade args4j and add forbids argument to loci args
Merge pull request #235 from hammerlab/add-loci-from-file-common-argument

Add -lociFromFile argument to Common