Integration with ONNX==1.20.1

[titaiwangms]

This pull request updates the ONNX dependency from version 1.19.1 to 1.20.1 across the build system, patches, and documentation. It ensures that all relevant files, patches, and metadata are consistent with the new ONNX version, and updates the operator documentation to reflect changes in ONNX opset versions.

ONNX Dependency Update:

• Updated ONNX version from 1.19.1 to 1.20.1 in cmake/deps.txt, cmake/vcpkg-ports/onnx/vcpkg.json, and the submodule reference in cmake/external/onnx. Also updated the SHA512 in cmake/vcpkg-ports/onnx/portfile.cmake to match the new ONNX release. [1] [2] [3] [4]

Patch and Build System Synchronization:

• Synchronized ONNX patches (cmake/patches/onnx/onnx.patch and cmake/vcpkg-ports/onnx/binskim.patch) to match the new ONNX version, including updates for minimal build options and source file exclusions. [1] [2]
• Updated dependency handling for Protobuf in ONNX build patches to ensure compatibility with the new ONNX version. [1] [2]
• Adjusted the onnxruntime_add_include_to_target call in cmake/onnxruntime_unittests.cmake to include ${PROTOBUF_LIB} for correct dependency propagation.

Documentation Updates:

• Updated docs/OperatorKernels.md to reflect the new opset version for the Cast operator (now 25+) and added the previous version (24) for clarity.
• Clarified the ONNX update process in docs/How_To_Update_ONNX_Dev_Notes.md to mention the importance of patch synchronization and SHA updates.

[snnn]

There appears to be a gap in the vcpkg configuration for native Linux builds regarding the protobuf library version.

The generated triplet file (e.g., x64-linux.cmake) does not currently receive a setting for ONNX_USE_LITE_PROTO.

This is because the logic in tools/python/util/vcpkg_helpers.py that adds -DONNX_USE_LITE_PROTO=ON is specific to WebAssembly builds, as shown in the add_port_configs function:

    if is_emscripten:
        # Uses ONNX_USE_LITE_PROTO=ON for WebAssembly build.
        f.write(
            r"""
    list(APPEND VCPKG_CMAKE_CONFIGURE_OPTIONS
        "-DONNX_USE_LITE_PROTO=ON"
    )"""
        )

For native Linux builds, is_emscripten is False, so this block is skipped. As a result, the onnx dependency falls back to its default (ONNX_USE_LITE_PROTO=OFF), causing a mismatch with the ONNX Runtime default build which expects the lite version. This should be addressed to ensure native builds are configured correctly.

[titaiwangms]

Need onnx/onnx#7515

Will integrate with 1.20.1

[justinchuby]

Does it still need #26597 ? Or does the PR description need update

[titaiwangms]

Does it still need #26597 ? Or does the PR description need update

Thanks. It's also included in this PR.