When comparing the index and a tree, we used to read the contents of the
tree into stage #1 of the index and compared them with stage #0. In order
not to lose sight of entries originally unmerged in the index, we hoisted
them to stage #3 before reading the tree.
Commit
d1f2d7e (Make run_diff_index() use unpack_trees(), not read_tree(),
2008-01-19) changed all this. These days, we instead use unpack_trees()
API to traverse the tree and compare the contents with the index, without
modifying the index at all. There is no reason to hoist the unmerged
entries to stage #3 anymore.
Signed-off-by: Junio C Hamano <gitster@pobox.com>