2 provisos:
1) the removal of the ".doxygen" files must be added to whatever
mechanism you're using to perform a clean (e.g. CLEANFILES= or
clean-local::) in order to satisfy "make distcheck"
2) because the cfg directory is not part of $(SUBDIRS) but only
$(DIST_SUBDIRS), the generation of its ".doxygen" file has to be
special-cased in the top-level Makefile.am:
doxygen/html/index.html: cfg/.doxygen $(addsuffix /.doxygen,$(DIST_SUBDIRS))
$(DOXYGEN) ....
cfg/.doxygen:
touch cfg/.doxygen
kludgy, but it works :-)
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