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It leaves it up to the user to cleanup. If it crashed then I want to know why and that usually means having a look at what's in the temp directory. So sorry, but I don't really want to change this.
Does the temp directory class in Python have a way to ensure cleanup in the case of killed job (eg. CTRL-C). Can you trap the signal?
eg.
pilon.fixstart.tmp.circlator.fixstart.xn4xwx51/
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