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Hacky work-around: putting random characters in front of a real model file will run annotate on the real model, for example the following command will ignore "invalid-non-whitespace" and run on just "valid_thing.rb":
Separate problem, annotate does not seem to understand relative path names to a file e.g. app/models/valid_thing.rb is not found but valid_thing.rb is found.
I tried
and
and in both cases, all models are annotated.
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