DirCacheCheckout: Fix handling of files not in index

DirCacheCheckout: Fix handling of files not in index

When a file is not in the index and neither contents nor mode differ
between "head" and "merge", the index state should be kept. If they
differ, a checkout conflict should occur. This is described in Git's
git-read-tree.txt.

JGit used to replace the index state with "merge" in both of the above
cases.

A confusing effect of this was that when one removed a file and then did
a rebase, the file silently reappeared again.

The changes to dir/file conflict handling are a consequence of this
change, as the index handling change made tests in DirCacheCheckoutTest
break. I compared these cases to C Git and the new behavior there also
matches what C Git does.

Bug: 387390
Change-Id: I5beb781f12172a68f98c67d4c8029eb51ceae62d
Signed-off-by: Robin Stocker <robin@nibor.org>