nix-prefetch-git: set deepClone if leaveDotGit is set

Without deepClone, things like "git describe" doesn't work. To make
leaveDotGit more useful, this commit enables deepClone if leaveDotGit is
set.

You can still disable deepClone by adding --no-deepClone after the
--leave-dotGit flag. No such option exist for fetchgit, but I cannot
think of a reason to not have deepClone if you have leaveDotGit.

Update the hash of libcouchbase, the only package in nixpkgs that uses
leaveDotGit.