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.tox is already excluded by default. .env is not as commonly used as you think. Many people use autoenv and there are other .env files beyond .env directories. Without very compelling evidence to add another pattern to the default exclude, I'm closing this.
For what it's worth, you can update the default exclude globally in $HOME/.config/flake8.
In GitLab by @RonnyPfannschmidt on Feb 22, 2015, 13:29
.env is commonly used for logal venvs
.tox is tox
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