mergeConfigurations accumulates old defines/etc. after they are changed

Set mergeConfigurations to true in c_cpp_properties.json with a configurationProvider set (e.g. "configurationProvider": "ms-vscode.cmake-tools").
Change one of the mergeable properties in c_cpp_properties.json like a define in defines.
Do something to retrigger another config update, e.g. CMake: Configure.

Bug: The new define/etc. is added and the old define still exists. It should be replacing the old define with the new define.

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