merge-tree: fix "same file added in subdir" inconsistency

When the same file is added with identical content at the top level,
git-merge-tree prints "added in both" with the details.  But if the file
is added in a subdirectory, threeway_callback() bails out early because
the two trees have been modified identically.

The documentation says that "the output from the command omits entries
that match the <branch1> tree", so the subdirectory behaviour is
correct.  Change the top-level behaviour to match.

Signed-off-by: John Keeping <john@keeping.me.uk>