Add ability to turn of "git clone --depth=1", it's sometimes quite expensive

This was changed in 2e9ceb9 by @kellegous. See this comment to a CocoaPods issue for why using shallow clones for things like this is a bad idea.

IMO this commit should just be reverted, it makes much more sense to do a full clone and then fetch that with the way the fetch protocol works and how shallow clones can trigger bad edgecases in it, but if not please add some config option to turn this off.

Edit: FWIW this isn't some theoretical thing, I have a very large repo that's running into this edge-case, a "pull" should take 2-3s, but sometimes takes up to 6 minutes from hound (a fresh clone is ~3m) because of the edge cases triggered by the shallow clone.