Update2: I think I got something working can someone check if its OK?

It looks like you've still got some issues to me.

You should probably chomp your file names, for one.

And you're not building your array of arrays right. Your line:

push @allfiles, <FILE>;
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Will push all of the lines from all of the files on one array, @allfiles. You want:

push @allfiles, [ <FILE> ];
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instead.

BTW, if you want to keep the filenames, you can use a hash of arrays instead... then the line would look like:

$allfiles{ $filename } = [ <FILE> ];
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