Upgrading a direct mode repo to v7 while it has a deleted file in it
behaves strangely. This is after my recent change to not make it commit.

A `git checkout` of the file checks out the pointer file, as the content
of the file is not present. This is as expected.

But `git whereis` thinks the content is present, which it's not any longer.
Seems that the upgrade process needs to notice when a deleted file was the
only copy of the content, and set its content as not present.

And `git fsck` doesn't find a problem, despite the content not being
present. And does not fix the location log.
This part may not be specific to this case, seems it must be some bug in
fsck?

> It was, a new bug introduced while removing the direct mode code. Fixed
> that part. --[[Joey]]