Fix bug importing from a special remote into a subdirectory more than one level deep

Fix bug importing from a special remote into a subdirectory more than one level deep

Which generated unusual git trees that could confuse git merge,
since they incorrectly had 2 subtrees with the same name.

Root of the bug was a) not testing that at all! but also
b) confusing graftdirs, which contains eg "foo/bar" with
non-recursively read trees, which would contain eg "bar"
when reading a subtree of "foo".

It's worth noting that Annex.Import uses graftTree, but it really
shouldn't have needed to. Eg, when importing into foo/bar from a remote,
it's enough to generate a tree of foo/bar/x, foo/bar/y, and does not
include other files that are at the top of the master branch. It uses
graftTree, so it does include the other files, as well as the foo/bar
tree. git merge will do the same thing for both trees. With that said,
switching it away from graftTree would result in another import
generating a new commit that seems to delete files that were there in a
previous commit, so it probably has to keep using graftTree since it
used it before.