How to get doxygen to run faster?

There is a DOT_NUM_THREADS options which may increase the performance on multicore machines. Unfortunately doxygen itself is just single threaded.

Another approach would be to organize your code into modules run for each module a separate doxygen instance and link the resulting tags together: http://www.doxygen.nl/manual/external.html

I found that turning off the option SEARCH_INCLUDES made a big difference. It was looking through the whole platform SDK and include paths for the compiler which were not documented anyway and would not appear in the generated documentation.

From Doxygen documentation:

How can I exclude all test directories from my directory tree?

Simply put an exclude pattern like this in the configuration file:

EXCLUDE_PATTERNS = /test/

So, you should be using patterns to exclude files. It's been a long time since I've used Doxygen, but i don't remember any option to process only changed files.