$outfilePRE =~ s/.phase$//;

One other little cautionary note. In a regex (as in the  s/// quoted above), the  . (dot) is a "metacharacter", a regex operator that, by default, matches any character except a newline (see perlre). I don't understand the purpose of the quoted substitution, but if it's to remove a literal  .phase substring extension from the end of a file name, you may be surprised:

c:\@Work\Perl\monks>perl -wMstrict -le
"my $filename = 'foo.xyphase';
 print qq{'$filename'};
 ;;
 $filename =~ s/.phase$//;
 print qq{'$filename'};
"
'foo.xyphase'
'foo.x'
[download]

To have the regex match a literal period character, escape the dot:
    $outfilePRE =~ s/\.phase$//;

Good luck with this program.