I close the issue.

I pushed commit 83d46e0622d2efdf5f3bf8bf8904d0dcb55fc322 which should not be controversial. In short, the fix is to remove two unused imports :-D

The fix doesn't remove module.__spec__ nor avoid usage of _weakref, it only fix this issue (reference leak) by copying code from _bootstrap.py to _bootstrap_external.py. In fact, modules like _io were already correctly imported by _bootstrap_external._setup(). Only _thread, _weakref and winreg imports caused this bug.

I don't think that it's worth it to backport the change to stable branches 3.7 and 3.8, since stable branches don't use multiphase initialization for _weakref. The two unused imports don't cause any harm in importlib._bootstrap_external.


> Can I ask why you suddenly want to throw __spec__ objects out due to a leak tied back to _weakref switching to multi-phase initialization?

I was thinking just aloud to try to find a solution for this reference leak.