Fix remaining getDirectoryFiles[IO] call-sites.
This fix addresses the fact that paths returned by `getDirectoryFiles` and `getDirectoryFilesIO` are always relative to their first argument; an empty directory defaulting to the "current directory". To avoid any ambiguity, this change ensures that the first argument in any call to those functions is either set to `top` -- if the files are expected to be in the source tree -- or `root` -- if they are expected to be in the build artifact tree.
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