Exclude subdirectories

I would like to add exclusion of subdirectories to `cindex`. For example indexing of chromium `/src` takes about 50 seconds while only 20 seconds if I exclude `/src/out` and `/src/third_party`.
Right now it works like `cindex --exclude /src/out --exclude /src/tmp /src` plus I have to pass excludes if I want to re-index. As I understand the way to integrate that is to modify index format to store list of excluded directories. Is it OK to introduce such backward incompatible changes?