Update Gradle plugin to only repackage main jar

Previously, Repackage would attempt to repackage every jar in the
project. This would cause it to incorrectly attempt to repackage source
and javadoc jars.

This commit updates Repackage so that it ignores any jar with a
classifier. Hopefully this is a reasonable approximation for ignoring
'special' jars that should not be repackaged such as sources and
javadoc.