warnings are not correctly removed and CLI exits with code 1 when warnings are filtered out by `--level` argument and running in github actions

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This also impacts the exit status, i.e. if you have 0 errors and a non-zero amount of warnings, the exit status will be 1 even using --level error (but only in GitHub workflows, or rather when GITHUB_ACTIONS is truthy). This made it pretty hard to figure out why my new workflow was failing only in CI 😵

Originally posted by @BHSPitMonkey in #1351