Shouldn't $RCfile, $fixtarget, and $midlopts be passed to GetOptions() as references?

If you want to allow unspecified options to not cause warnings/errors, use the 'pass_through' option on Getopt::Long::Configure(), but that will leave the unspecified options in @ARGV, so if you want to remove them from @ARGV, you could also use Getopt::Std like so:

# Configure here or with Getopt::Long::Configure()
use Getopt::Long qw(:config pass_through);
use Getopt::Std;

my ($verbose, @linkfiles, $RCfile, $fixtarget, $midlopts);

GetOptions (
   'help|?|h' => \&show_options,
   'verbose!' => \$verbose, 'v' => \$verbose,
   'L=s' => \@linkfiles,
   'RC=s' => $RCfile,
   'fixtarget!' => $fixtarget,
   'midlopts=s' => $midlopts
) or die;
# If you don't want '$opt_*' variables
# springing into existence, supply a hashref to getopt.
# Of course there's an ambiguity about whether
# or not your 'bad' options are supposed to take an
# argument, so there isn't really any perfect solution here.
my %other_opts;
getopt('', \%other_opts);

print "ARGV: @ARGV\n";
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