Follow the Google API design guide for structuring Protobuf files

See the proposed order in https://cloud.google.com/apis/design/file_structure:

• Copyright and license notice if needed.
• Proto syntax, package, import and option statements in that order.
• The API overview documentation which prepares the readers for the rest of the file.
• The API proto service definitions, in decreasing order of importance.
• The RPC request and response message definitions, in the same order of the corresponding methods. Each request message must precede its corresponding response message, if any.
• The resource message definitions. A parent resource must be defined before its child resource(s).

Also add README in api folder.