Something like the following, untested, code:

my @top_level;
my %seen;
my @cache;

while (<>) {
    chomp;
    my ($key, @thingies) = split /\t/;
    unless ($seen{$key}) {
        push @top_level, $key;
        $seen{$key} = {};
    }
    push @{$cache{$key}}, grep {!$seen{$key}{$_}++} @thingies;
}
foreach my $key (@top_level) {
    say join "\t", $key, @{$cache{$key}};
}
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