The following makes no assumption about which of your input files has duplicates. It demonstrates the use of a hash of arrays to capture multiple values for each key. You may be able to adapt it to produce the results you need.

my %data;

foreach my $line (@ge_data) {
    my ($id, $rest) = split(/\s+/,$line,2);
    push(@{$data{$id}{ge_data}}, $rest);
}
foreach my $line (@file_data) {
    my ($id, $rest) = split(/\s+/,$line,2);
    push(@{$data{$id}{file_data}}, $rest);
}

foreach my $id (sort keys %data) {
    next unless(exists $data{$id}{ge_data});
    next unless(exists $data{$id}{file_data});
    print "$id:\n";
    print "\tge_data:\n";
    print "\t\t" . join("\t\t",@{$data{$id}{ge_data}});
    print "\tfile_data:\n";
    print "\t\t" . join("\t\t",@{$data{$id}{file_data}});
}
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