Internally, `FindDoxygen.cmake` uses `${PROJECT_BINARY_DIR}` to look for the top-level `CMakeDoxyfile.in` file. This breaks when `doxygen_add_doc()` is invoked in a subdirectory that also calls `project()` beforehand. This modifies the `PROJECT_BINARY_DIR` variable to point to the respective subdirectory in the binary dir tree, which will not have the Doxygen files. Instead, it should use `${CMAKE_BINARY_DIR}`. I tested this and it worked. I'll provide a PR shortly.