no-src jars do not add entries for directories

#289 changed the behavior of zipping a no-src jar in the sense that the zipper doesn't create entries for the directories. I guess that we're just using it wrong and that we need to also feed it the directories entries themselves but haven't gotten around to verifying and fixing it.
This is a problem for example when you want to get all files from a directory on the classpath. In that case the directory isn't found.
Current workaround: use java_library.

Start by reviewing the behavior changed in #289 and reproducing a no-src jar lookup for a directory on the classpath. Compare it with the java_library workaround; done means no-src jars include directory entries so files can be found through that directory.

Written by the indexing model from the issue text.