Yes, this was discovered and discussed on the mailing list during the 1.2.0 release process. These "extra" files were actually introduced in earlier releases, but not noticed until the 1.2.0 release. There are some benefits to having both the source and binaries in a single jar as an aid with debugging in an IDE. To resolve this issue, we've discussed the idea of possibly separating everything into their own jars – source, binaries, manuals, and javadoc. It's makes for smaller jar files, but then development shops will probably need all four jars for their job. Catch-22.
Thanks for opening the Issue.