use strict;
use warnings; 

my @files =  map {s/-0(\d)(\.gz)$/-$1$2/; $_} 
             sort
             map {s/-(\d)(\.gz)$/-0$1$2/; $_} <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
abcd1_abc_123456.abc1a_A.201306290800-1000-1.gz
abcd1_abc_123456.abc1a_A.201306290800-1000-10.gz
abcd1_abc_123456.abc1a_A.201305290800-1000-11.gz
abcd1_abc_123456.abc1a_A.201308290800-1000-2.gz
abcd1_abc_123456.abc1a_A.201302290800-1000-3.gz

##</code><code>##

$ perl schwartz.pl
abcd1_abc_123456.abc1a_A.201302290800-0900-3.gz
abcd1_abc_123456.abc1a_A.201302290800-1000-3.gz
abcd1_abc_123456.abc1a_A.201305290800-0900-11.gz
abcd1_abc_123456.abc1a_A.201305290800-1000-11.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.201306290800-1000-1.gz
abcd1_abc_123456.abc1a_A.201306290800-1000-10.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
abcd1_abc_123456.abc1a_A.201308290800-1000-2.gz