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Performance - Dupfinder is slow on lots of files

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The program takes a long time to run for large numbers of input files. The increase in run time is more than linear, though I haven't managed to characterise it as O(N^2) or otherwise.
I don't have any ideas for speed increases. Any ideas?
 
A workaround would be to partition the checks performed - compare data layer code only to other data layer code, Ui to Ui, etc.

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