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my @pkgs = qw[ mainpackage-1.0 ];
my %deps;
...
    $deps{$pkg} = \@deps;
    push @pkgs, @deps;
}

sub traverse {
    my ($deps, $root, $depth) = @_;
...
}

traverse( \%deps, "mainpackage-1.0" );

mainpackage-1.0
  dependency1-1.3
...
    dep2_of_dep2
    dep3_of_dep3
  dependency3