I donβt like answering a question without answering a specific question, but overall it is a bad idea to track doxygen documents in your repository. The same is true for configure scripts created by autoconf.
If you are worried that people cannot generate documents due to the lack of doxygen, it is better to place them in your own repo in your language and language choice.
You can modify build scripts to do this for you, with less effort. In my experience, after working on free / open source for several years, those who really care about documents will be able to generate them, but your mileage may vary.
Eliminate redundant merge conflicts (i.e. Joe has changed the comments AND docs and should now combine both). IMHO justifies externalizing created documents.
Tim post
source share