Unless I'm much mistaken (which has been known to happen), you're opening the file, reading in the entire thing, closing it, opening it again for appending and writing "$count." to the file once for each line.
As you're appending to the end of the file, thats why the line numbers appear at the end. I don't know (undef) = <FILE> but it doesn't seem to be springing to the beginning of the file, which is what you would need in order to write $count to the beginning.

I suggest you try:
1. Open file, read all lines, close file.
2. Open another filename, write each $count and the line itself to the new file in a loop.
3. Unlink the old file, rename the new one to the old.
You can use @files to get the number of lines also, instead of reading the file again.

C.