add a comment about CWD

add a comment about CWD

While git ls-files can actually be used on a repo that is not in the
cwd, it works inconsistently. For example, this fails:

git --git-dir=../foo/.git --work-tree=../foo ls-files ../foo

But change some of the paths to absolute and it will succeed. That seems
like a bug in git.

OTOH, this succeeds:

git --git-dir=../foo/.git --work-tree=../foo ls-files

But, that lists paths relative to the top of the --work-tree,
rather than the usual listing them relative to the cwd. Because the cwd
is not in the repo. And so anything parsing the ls-files output of that
is likely to operate on files in the wrong location. Indeed, there is
code in Upgrade/ that has this problem!