Replace a pair of patches with updated ones for subproject support.

This series of three patches is a *replacement* for the patch series of
two patches (plus one-liner fixup) I sent yesterday.

It fixes the issue I noted with "git status" incorrectly
claiming that a non-checked out subproject wasn't clean - that
was just a total thinko in the code (we were checking the
filesystem mode against S_IFDIRLNK, which obviously cannot work,
since S_IFDIRLINK is a git-internal state, not a filesystem
state).

It then re-sends the two patches on top of that, with the fix
for checking out superprojects (we should *not* mess up any
existing subproject directories, certainly not remove them - if
we already have a directory in the place where we now want a
subproject, we should leave it well alone!)

The first one really is a fix, and it makes the commit
commentary about a remaining bug in the patch I sent out
yesterday go away.