Use onnx_protobuf.h to suppress some GCC warnings

[snnn]

Description

Use onnx_protobuf.h to suppress some GCC warnings.

All the changes are autogenerated by a shell command.

find . -type f -exec sed -i 's/#include\s\+<onnx\/onnx_pb.h>/#include "core\/graph\/onnx_protobuf.h"/g' {} \;

Motivation and Context

This PR is needed for making vcpkg work(without disabling all warnings)
This PR is split from another bigger PR per request from a reviewer.