Fix shared module read bucket for proto file refs and include_package_files #3512
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In the case where multiple modules have shared module roots
due to the
includes
key in the module configuration, when usinga proto file ref with the
includes_package_files
option (https://buf.build/docs/reference/inputs/?#protofile)the proto file ref may not exist in the module. We need to check for
that and skip accordingly.