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refactor: move go2proto configuration from flags to comment directives (
#3832) This makes the source files more self-contained, which is nice, but is also a step towards being able to support multiple packages - when we import a Go package with directives, we will know that it is a protobuf package, and we won't generate types for it in the current package. Next I'll move the definition of the "roots" into code.
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