Make Setup.hs configure more CWD-independent.
Previously, we were checking the package with a hard-coded root directory of ".". This was not a problem before, but with #5372 we have started to expand globs while checking packages, which breaks if the CWD is not the directory containing the `.cabal` file and causes snowleopard/hadrian#634. Luckily, this is an easy fix: the correct directory is easy to determine. Writing a test and making sure it's tickling the failing case took longer than writing the fix! "." is hard-coded as the root directory passed to `checkPackageFiles` in a few other places, but those are (a) non-trivial to test, and (b) already in places that have other assumptions about their CWD, so I have simply documented the CWD requirement for those.
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