submodules: add failing test for stale module entries

We consider an entry in .gitmodules to mean that we have a submodule at
a particular path, even if HEAD^{tree} and the index do not contain any
reference to it.

We should ignore that submodule entry and simply consider that path to
be a regular directory.
iterator: submodules are determined by an index or tree

We cannot know from looking at .gitmodules whether a directory is a
submodule or not. We need the index or tree we are comparing against to
tell us. Otherwise we have to assume the entry in .gitmodules is stale
or otherwise invalid.

Thus we pass the index of the repository into the workdir iterator, even
if we do not want to compare against it. This follows what git does,
which even for `git diff <tree>`, it will consider staged submodules as
such.
Merge pull request #2691 from libgit2/cmn/submodule-and-dir

submodules: stale module entries