By "'in mice' equivalent", do you mean "a useful way to make statements about things that can't be directly measured"?
Assuming you don't mean that, that's not a gotcha. Practically all of science is "in a model". We can't observe an alternative universe where DNA doesn't mutate, but that doesn't disprove evolution.
I'd urge you to keep accessibility in mind. I have a bit of an issue with processing visual information, and the fact that the files don't have any borders on them now makes it really difficult for me to process which file has which status. Having toggleable borders (horizontally and vertically) would be a huge improvement in terms of accessibility.
It'd also be nice if you could have the bar at the side up top, or shrink it a lot. It takes up a quarter of the screen space plus padding and margin. For reading README.md files and Awesome Lists, it's extremely intrusive.
Alternatively, you could have the README.md below the longer element of the new "sidebar" and the file list, so that it can take up the whole width of the screen.
Assuming you don't mean that, that's not a gotcha. Practically all of science is "in a model". We can't observe an alternative universe where DNA doesn't mutate, but that doesn't disprove evolution.