build-sys: Configure doxygen.conf.in a bit differently
This change prepares for adding a doxygen target to the Meson build system. The DOXYGEN_OUTPUT_DIRECTORY substitution variable is needed so that the output will go to the build directory. I also replaced @srcdir@ with @top_srcdir@. I think it looks cleaner, since the ".." parent directory traversal is avoided. It also happened to make writing the Meson rules easier.
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