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I've determined that we are not caught in an infinite loop, and it will end eventually.
The problem is that changes are being detected in entitlement cert directory multiple times per file (including any key files that exist as well). Looks like approx 3 change detections per file. So for me that was 90 changes detected.
For EACH change that is detected, ALL product certs are read from the disk and are sorted (CertSorter). Then the UI is updated with info from the sorter. This is very expensive, and i would guess that with a large number of products, on a slower machine, this would take quite some time.