Testing this on our own git repo is not working very well because we are not going to be ignoring most of the folders when it's used in a real project, so we need to figure out how we're going to place yukon within the project folder.

This is what I'm thinking: We make a folder inside the .git directory called yukon and install everything there. Then for stuff like the Dox exe, which needs a code directory, the code is just in ../.. and also the .git folder is automatically ignored so there is no chance of them accidentally committing yukon-specific files.

Do you guys like this or do you think we should put it somewhere else?

Question for Sarah: "DoxygenParse (...) s" takes two input files (one for use cases, the other for edited files). How do you want me to output them?

Right now, it just dumps out to console.