Something like this might get you started?

#!/usr/bin/perl

use warnings;
use strict;

while (my $line = <DATA>){
  next unless $line =~ /\S/;
  chomp $line;
  my @cats = $line =~ /(\d+)/g;
  my $rec = join(q{.}, @cats);
  print qq{$rec\n};
}

__DATA__
Category1

Category1--Subcategory1--subsubcategory1--etc.

Category1--Subcategory1--subsubcategory2--etc.

Category1--Subcategory2--subsubcategory1--etc.

Category1--Subcategory2--subsubcategory2--etc.

Category2

Category2--Subcategory1--subsubcategory1--etc.

Category2--Subcategory2--subsubcategory1--etc.
[download]

1
1.1.1
1.1.2
1.2.1
1.2.2
2
2.1.1
2.2.1
[download]