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Please see the colcon documentation about colcon.pkg files: https://colcon.readthedocs.io/en/released/user/configuration.html#colcon-pkg-files

If you would pass the argument on the command line you would involve it with --cmake-args -DCMAKE_TOOLCHAIN_FILE=.... therefore your yaml file must look like this:

{
  "cmake-args": ["-DCMAKE_TOOLCHAIN_FILE=..."]
}