Add proper implementation of methods in JnaUtils.

Implement the methods getFilemode and setFilemode
in JnaUtils. Not using the libc names as we don't
necessarily use JNA and because it is not necessarily
a one to one mapping.
Implement adjusting file permissions for shared repositories.

Implement adjusting file and directory permissions for shared
repositories in JGitUtils.
Add new property git.createRepositoriesShared.
Add JavaDoc.