A subversion repository contains the html, latex and man directories that doxygen generates from the source code. Even for small source code changes, new files are being generated with random names which makes for large changes in the version control system.
Is there are way around this? How can I minimize the changesets between revisions while still including doxygen-generated documentation? Alternatively, how could I find which of the doxygen-genrated files are no longer being used and should be removed?
I hate to answer a question without providing an answer to the specific question, but its generally a bad idea to track doxygen docs in your repository. The same thing holds true for autoconf generated configure scripts.
If you are worried about people not being able to generate the docs due to a lack of doxygen, its better to host them in their own private repo in your language and locale of choice.
You could modify build scripts to do this for you, with not too much effort. In my experience after working on free/open source software for a number of years, those who actually care about the docs will be able to generate them.. but your mileage may vary.
Eliminating redundant merge conflicts (i.e. Joe changed the comments AND the docs and now has to merge both) IMHO justifies externalizing the generated docs.