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.