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use strict;
use warnings;
...
       { my $ver = $2; ( defined $1 ? $1 : q{} ) . ++ $ver }e;
    say qq{$version => $newVersion};
}

1.2.3.4 => 1.2.3.5
2.6 => 2.7
3_4_9 => 3_4_10
4-2-13-5 => 4-2-13-6
5 => 6