This Bootstrap folder is from the Twitter Bootstrap project;

http://twitter.github.com/bootstrap/

We are using a fork which has converted it to SASS. 
https://github.com/jlong/sass-twitter-bootstrap

The project is pretty active, fixing bugs, making improvements, so upgrading will mostlikely be needed. Therefore the bootstrap folder should be left as is for the most part.
Overrides and style adjustments can be made in other files, although you are free to do as you like...