Deprecate GitIndex more by using only DirCache internally.

Deprecate GitIndex more by using only DirCache internally.

This includes merging ReadTreeTest into DirCacheCheckoutTest and
converting IndexDiffTest to use DirCache only. The GitIndex specific
T0007GitIndex test remains.

GitIndex is deprecated. Let us speed up its demise by focusing the
DirCacheCheckout tests to using DirCache instead.

This also add explicit deprecation comments to methods that depend
on GitIndex in Repository and TreeEntry. The latter is deprecated in
itself.

Change-Id: Id89262f7fbfee07871f444378f196ded444f2783
Signed-off-by: Robin Rosenberg <robin.rosenberg@dewire.com>