Fix submodule remote URLs after cloning
Identify existing submodules and check them out
Fix checking out submodules previously committed

If you commit a submodule, then remove its directory, we can run into
an error trying to `git submodule add` it again. Ignore those.
Allow Git callers to filter submodules to clone
Ignore Carthage.checkout folders in submodules
Replace submodule dependencies using Carthage

Conflicts:
	Cartfile
	Cartfile.lock
	Carthage.checkout/LlamaKit
	Carthage.checkout/Nimble
	Carthage.checkout/Quick
	Carthage.checkout/ReactiveCocoa
	Carthage.checkout/xcconfigs