Getopt::Long can parse command-line options from a string. So my proposal is to take all options as a string, split on --job, and then parse whatever was in front of it. Like this:

use strict;
use warnings;
use Getopt::Long qw(GetOptionsFromString);
use Data::Dumper;

my ($args, $job) = split /--job /, join( ' ', @ARGV );
my %opts;
my $ret = GetOptionsFromString( $args, \%opts, "file=s", "dir=s" );
$opts{"job"} = $job if $job;

print Dumper \%opts;
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