For version control, I would grab everything in the project directory as well as the Dave, Libraries, and Startup folders. We also have a DAVE_modified directory where we tweak some of the XMC library files that I get as well. I skip .settings folder.
In the Debug and Release directories, I check in just the makefile and .mk files. This allows me to do automated/nightly builds without the DAVE IDE running. The script I have sets up the environment, runs make, and logs all output to a file. If you don't plan on anything like that, the Debug and Release can be skipped completely.
