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Just ran into the same problem, while choosing between docker or cri parsers. Since the standard is moving from dockerd to containerd, I'd be satisfied with changing the default from docker to cri.
Edit: Just realized that the fluent-bit chart is deprecated...
Currently I'm unable to overwrite or add the INPUT section from fluent-bit.
It would be much more helpful if you could overwrite the complete config as it is the case here. https://github.com/fluent/helm-charts/blob/master/charts/fluent-bit/values.yaml#L130
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