Why is the _ folder named that?

[Jorenm]

Also, is inc folder inside of it a customized version of the options framework plugin? If so, what was changed about it?

[murtaugh]

I can't speak to the inc folder (maybe @ckhicks can), but the underscore folder was so named so that it would always float to the top of the list when looking at a site's directory.

I recently gave up on the underscore folder in the main repo, it was causing problems in some scenarios (specifically, working with Jekyll).

[ckhicks]

What Tim said. I've been working on an update to how we're handling options framework, which will be included with an updated folder structure to match the main repo. Good questions - more soon!