You are not saying everything at once, this is the cause of misunderstandings.

You only need to amend slightly the Schwartzian Transform solution by 2teez to accomodate the new rules. 

use strict;
use warnings; 

my @files = map { $_->[0] } 
            sort { $a->[1] <=> $b->[1] ||  $a->[2] <=> $b->[2]} 
            map { [ $_, /\.(\d{12})\-/, /.+?-(\d+)\..+$/ ] } <DATA>;

print $_,$/ for @files; 

__DATA__ 
abcd1_abc_123456.abc1a_A.201307290800-0900-0.gz
abcd1_abc_123456.abc1a_A.201307290800-0900-1.gz
abcd1_abc_123456.abc1a_A.201307290800-0900-10.gz
abcd1_abc_123456.abc1a_A.201307290800-0900-11.gz
abcd1_abc_123456.abc1a_A.201307290800-0900-2.gz
abcd1_abc_123456.abc1a_A.201307290800-0900-3.gz
abcd1_abc_123456.abc1a_A.201306290800-0900-0.gz
abcd1_abc_123456.abc1a_A.201306290800-0900-1.gz
abcd1_abc_123456.abc1a_A.201306290800-0900-10.gz
abcd1_abc_123456.abc1a_A.201305290800-0900-11.gz
abcd1_abc_123456.abc1a_A.201308290800-0900-2.gz
abcd1_abc_123456.abc1a_A.201302290800-0900-3.gz

[download]

Output:

$ perl schwartz.pl
abcd1_abc_123456.abc1a_A.201302290800-0900-3.gz
abcd1_abc_123456.abc1a_A.201305290800-0900-11.gz
abcd1_abc_123456.abc1a_A.201306290800-0900-0.gz
abcd1_abc_123456.abc1a_A.201306290800-0900-1.gz
abcd1_abc_123456.abc1a_A.201306290800-0900-10.gz
abcd1_abc_123456.abc1a_A.201307290800-0900-0.gz
abcd1_abc_123456.abc1a_A.201307290800-0900-1.gz
abcd1_abc_123456.abc1a_A.201307290800-0900-2.gz
abcd1_abc_123456.abc1a_A.201307290800-0900-3.gz
abcd1_abc_123456.abc1a_A.201307290800-0900-10.gz
abcd1_abc_123456.abc1a_A.201307290800-0900-11.gz
abcd1_abc_123456.abc1a_A.201308290800-0900-2.gz

[download]

I guess that's what you need.

Update 21:42 UTC: 2teez was faster than me by about 8 minutes producing a new solution in accordance with the new rules.

Update 2 22:15 UTC: you had a third additional requirement (also use the 4-digit group after the date for the sort) that I had not seen. I've just posted a newly amended version in my answer below.

In reply to Re: Custom Sort Array by Laurent_R
in thread Custom Sort Array by omegaweaponZ

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