Doxygen is a bit slow - it takes about a couple of minutes to process my whole project, so for small incremental changes this is longer than actually building the rest of my
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.