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D'oh - more issues with this not-intended-to-be-released-yet format command :)
This one is because the only output format supported is exo.hcl, which is clearly a problem when the output file is the same as the input file with a different format.
A potential workaround is to use the redirection form:
exo manifest format < docker-compose.yml
This is similar to exo manifest convert with the output format will always as "exo.hcl", which isn't what you want if you're trying to format a compose yaml file, but we don't support that yet anyway.
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