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First, thanks a lot for your article and for this repo. It helps a lot!
I made some simple modifications to your projet, in order to make it easier to use in the case of a standard project that would use a top "src" + "include" folder and demonstrate a use case with several targets.
This version should be compatible with the merged or not merged header project layout conventions, since it searches for headers in both folders (except src//internal src//details and src/**/private)
I do not think this version would be compatible with your article, so I do not think it should be merged into master. However - and if you are interested - may be you could add a branch with this version.
The resulting doc on readthedocs:
https://pthom-cpp-documentation-example.readthedocs.io/en/latest/