Update JGit to latest 4.5.x release

JGit releases older than 4.5 are known to be prone to issues
with MissingObjectExceptions.

Since this is a major JGit version upgrade some code needs to be adapted
to changed JGit API.

Change-Id: Ia9099a5ac8fcbaf873e3354b5a47d2178c97444a
Signed-off-by: Edwin Kempin <ekempin@google.com>
45 files changed