Make conversion functions in AlleleConversions.scala not implicit.

Better to avoid implicits when possible, and these functions were never used as implicits anyway.
Variant caller renaming

 * Rename "callers" package to "commands"
 * Rename individiual callers to have more appropriate names. Closes #200.
 * Drop somatic threshold caller.
 * Move GenotypesEvaluator to Concordance, and make it no longer a Command.

Closes #200.
minor comment fixes
Merge pull request #208 from hammerlab/rename-callers

Rename callers
Add NOTICE file. Closes #22.
Add license notice to files that were missing it

One liner to find files that are missing the header:

for i in $(find . | grep '\.scala') ; do echo $i $(head -n 2 $i | tail -n 1 | grep Licensed) ; done | grep -v Licensed
Fix package names