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So basically running tox -r would reset tox's cache. However, when it wraps other things with their own caches, those won't be affected. One example is pre-commit.
It'd be nice to have some sort of a pre_cache_clean setting in tox.ini where additional commands could be put and would be executed right before tox deletes .tox/{envname}. In case of pre-commit, I'd put pre_cache_clean = {envpython} -Im pre_commit clean into the config and it would always purge both caches.