Change from deprecated manifest erasure to runtimeClass
Fix Scalariform issues and Maven warnings

We had some Unicode characters in our comments which were causing
Scalariform to throw an exception during processing.  Also, Maven
requires an empty "relativePath" attribute in the parent POM, otherwise
it was trying to resolve parent artifacts in some invalid location.
Merge pull request #207 from massie/erasure-cleanup

Change from deprecated manifest erasure to runtimeClass
Merge pull request #209 from hammerlab/maven-warning-and-scalariform-fixes

Fix Scalariform issues and Maven warnings
fasta contig search bugfix; fasta converter refactor; split to functions;