Patch Set 1: Looks good to me, but someone else must approve

I have verified that this works ok for my test case. On second merge we will get a conflict and that's way better than mismerge or null pointer exception. Command line git would merge this using recursive algorithm but that's another story.

$ ./test-case.sh
...
+ jgit merge d1/master
Fast-forward
+ jgit merge d2/master
CONFLICT(content): Merge conflict in x
Automatic merge failed; fix conflicts and then commit the result