Why do you need to add an atexit handler after all dlopens if you need to refer to the globals in the handler itself anyways. Assuming you don't add a function from the library you dlopen explicitly, you could add the handler at any time before exit.
Anyways, I think your argument about the exit sequence is a good one and I don't contest that. I was just wandering if you could run GarbageCollect from an atexit handler and if would not solve the problem in the majority of cases.
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