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use strict;
use warnings;
...
my @files = File::Find::Rule->file()->in($dir);

print "$_\n" for sort { lc $a cmp lc $b } @files;

.project
10B.xml
...
atom.pdb
Bio_SeqIO.pl
...

use strict;
use warnings;
...
my @files = File::Find::Rule->file()->in( $dir );

print "$_\n" for nsort @files;

5a.xml
6adh.pdb
...
atom.pdb
Bio_SeqIO.pl
Book1.xls