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Look for documentation only in specific directories
Generate the documentation from include and doxygen/input only. Don't get snared by files containing Doxygen comments that lie in other directories such as tests, yotta, crypto/include, ... The only difference this makes in a fresh checkout is that the documentation no longer lists target_config.h. This file is from yotta, does not contain any Doxygen comment, and its inclusion in the rendered documentation was clearly an oversight.
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