Place proto files in the Xcode Sources build phase

Tuist now treats .proto files as valid source files and places them in Xcode’s Sources build phase instead of handling them as resources. This makes Xcode build tool plugins, including the gRPC Swift protobuf generator, receive the target input files they expect. Note that Xcode may still emit a no-rule-to-process warning for proto files; this change does not suppress that warning.