Форумы / Cotonti / Support / How do i upgrade from 0.9.13 to 0.9.16?

I was wondering the same, if there was a way on github to download only the changed files, of course while maintaining the file structure.. because i've changed a few files here and there including heavily modifying all the tpl files in the modules for pages / forums etc and i would hate to accidentally overwrite them or loose something there..