I'm not qualified to comment on the variations among systems or the lack of determinism, but as far as coding defensively, you could just put a filter on the files with grep :
foreach my $file ( grep { !/^\.{1,2}$/ } readdir DIR ) {
munge($file);
}
perl -e 'print "How sweet does a rose smell? "; chomp ($n = <STDIN>);
+$rose = "smells sweet to degree $n"; *other_name = *rose; print "$oth
+er_name\n"'
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