From a quick look, I don't see what is generating your output, but I do see a few things that will definitely slow you down.

1. You are reading filenames from the directory "/mnt/data/Programming", but opening those files in the current directory. If you are not in "/mnt/data/Programming", this should not open the files you intend.

2. You are modifying the directory you are reading by creating a file there. That is probably going to cause some confusion.

3. Since you are opening your output file with '>', you would overwrite it each time instead of accumulating output in that file. If you want to reopen each time, use '>>' instead.

4. You seem to be processing data one line at a time and also putting those lines in an array. I would probably only do one or the other.

I would probably get the list of files all at once and then process them from an array. For instance,

opendir ( my $dir, "/mnt/data/Programming")
   or die "Can't open directory: $!\n";
my @files = readdir( $dir );
closedir( $dir );
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You can now process the files independently. The file open should really contain the path as well:

foreach my $file ( grep { -f "$path/$_" } @files )
{
    open( my $fh, '<', "$path/$file" )
       or die "Unable to open '$file': $!\n";

    while( <$fh> )
    {
        # process each line here.
    }
}
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It's a good idea to check the names you get from readdir() to make sure they are files. You can't read directories as files (in general). Notice that I used lexical file and directory handles. Although not critical in this case, it will definitely save troubleshooting nasty problems in the future. Start on good habits early.

Update: Corrected file test to use path as shmem observed.