fix(jar): Add directory entries to the jar file

According to the [jar file specification](http://docs.oracle.com/javase/7/docs/technotes/guides/jar/jar.html)

> For resource files with non-empty directory prefixes, mappings are also
> recorded at the directory level.  Only for classes with null package
> name, and resource files which reside in the root directory, will the
> mapping be recorded at the individual file level.

If needed, directory entries may be excluded using `:jar-exclusions`
regex like `#"^.*/$"`.
Merge branch 'jar-directory-entries' of https://github.com/dm3/leiningen
Reorder the skip/added file check.

Also document internals and decouple the skip/added file check.