Correct ONNX and Protobuf version in vcpkg build (#23285)
### Description
Changes vcpkg manifest and configuration file (vcpkg.json &
vcpkg-configuration.json)
* Update vcpkg version to
https://github.com/microsoft/vcpkg/releases/tag/2024.12.16
* Use protobuf 3.21.12(= `v21.12`) to sync with
[cmake/deps.txt](https://github.com/microsoft/onnxruntime/blob/main/cmake/deps.txt)
* Resolve https://github.com/microsoft/onnxruntime/issues/22750
* Add `onnx` to vcpkg manifest so `find_package(ONNX)` and
`find_dependency(Protobuf)` can work as expected.
* Currently, It uses 1.16.2
* v1.17.0 will become available after
https://github.com/microsoft/vcpkg/pull/42942
However, `onnx` in vcpkg doesn't configure
`ONNX_DISABLE_STATIC_REGISTRATION` build option.
* https://github.com/microsoft/vcpkg/pull/38879
* Create "cmake/vcpkg-triplets/" folder and triplet files which use
`VCPKG_CMAKE_CONFIGURE_OPTIONS` for the option
* This requires `VCPKG_OVERLAY_TRIPLETS` environment variable for CI
steps, which is a bit inconvenient.
I will try to find simple way to get same result
### Motivation and Context
* Help #23158
* "ONNX is not consumed from vcpkg"
* "Mismatch protobuf version. When vcpkg is enabled , we should not
fetch protoc from Github which may cause version mismatches."
* https://github.com/microsoft/vcpkg/pull/43126
* #21348
