treewide: use closedir after readdir for error checking

treewide: use closedir after readdir for error checking

Hopefully...

Neither Perl's readdir nor readdir(3posix) documents EIO as a
possible error, nor does Linux getdents(3).  So relying on
readdir to detect errors via autodie(3perl) is not supported
nor possible, it seems.

Perl's closedir is supported by autodie and uses
closedir(3posix), which doesn't document EIO, either.  However,
closedir(3posix) will use close(3posix).  Thus in theory, EIO
can still be detected if a previous readdir failed.