When developing something, Visual Studio looks to see if the output file is older than the input file.
You added index.html as the input file when it is actually the output file. Adding Doxyfile will not work either, because it will not change often. That's why project recovery works (because it ignores the age of the files and builds anyway).
It modifies the C ++ files you want to catch. If (as I suspect) doxygen does incremental builds anyway, you'd better just add the doxygen step as a Post-build event.
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