In geanydoc/src/Makefile.am:

> @@ -7,7 +7,7 @@ geanydoc_la_SOURCES = \
>  	geanydoc.c \
>  	geanydoc.h
>  
> -geanydoc_la_CFLAGS = $(AM_CFLAGS)
> +geanydoc_la_CPPFLAGS = $(AM_CPPFLAGS) -DG_LOG_DOMAIN=\"GeanyDoc\"

AM_CFLAGS is the default for when there is no traget-specific CFLAGS, so yeah should be fine.

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