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Under https://fluxcd.io/flux/components/kustomize/kustomizations/#kustomize-secretgenerator
there's an example of how to encrypt an env secret:
sops -e --input-type=json config.json > config.json.encrypted
sops -e --input-type=yaml config.yaml > config.yaml.encrypted
sops -e --input-type=env config.env > config.env.encrypted
The third example is wrong, the type should be dotenv instead of env. One also have to give both --input-type dotenv and --output-type dotenv.
I didn't check yaml and json at this time, but at least this would be fixing the env case:
sops -e --input-type=json config.json > config.json.encrypted
sops -e --input-type=yaml config.yaml > config.yaml.encrypted
sops -e --input-type=dotenv --output-type=dotenv config.env > config.env.encrypted
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