Allow Repository.getDirectory() to be null

Allow Repository.getDirectory() to be null

Some types of repositories might not be stored on local disk.  For
these, they will most likely return null for getDirectory() as the
java.io.File type cannot describe where their storage is, its not
in the host's filesystem.

Document that getDirectory() can return null now, and update all
current non-test callers in JGit that might run into problems on
such repositories.  For the most part, just act like its bare.

Change-Id: I061236a691372a267fd7d41f0550650e165d2066
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>