The compare compares both sides with each other, not just from say Left to right. Selection/Deletion occurs on both sides.
The current method does use an array, The array isn't sorted any special way, it uses the same sort as the file listing.
There are two loops (one within the other) which makes it a file^2..
I tried a few things but I was unable to improve the performance. Doing a line profiler shows no bottlenecks, the main slow down is simply doing file^2
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