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I just ran into the situation where a directory contained Gadget hdf5 snapshot files from a previous run with a larger NumFilesPerSnapshot. Since gen-pk loops up to 1000 and looks for matching files, gen-pk picked up the files from the old run as well.
I have fixed the issue with commit 674a190.
Unfortunately, I merged in my Makefile changes into that branch so I probably should not directly issue a pull request. And I am not sure if git cherry-pick will let you cherry-pick just that commit across a fork.
Please let me know if you would like to merge the changes and/or if you have a preferred way of merging this update. Thanks again!
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