fix regression in #352
close #365
close #367

@edani's fix to close #377

simpler isJar/isArchive

only strip trailing dollar in classname
Merge pull request #376 from fommil/source_jars

Fix reference sources in jars and zips
Merge pull request #380 from fommil/flatten_regression

fix scala 2.9 regression in #352
Merge pull request #381 from fommil/transitive_src_roots

Fix for transitive source roots
close #378