Use JGit in favor of shelling to git

This pull request replaces the use of `Runtime.exec` to invoke git, with the use of the [JGit](http://eclipse.org/jgit) library. This appears to result in much faster import and analysis times. Aside from the new functions, the major change to `datomic.codeq.core` is the need to pass around an instance of [`org.eclipse.jgit.lib.Repository`](http://download.eclipse.org/jgit/docs/latest/apidocs/org/eclipse/jgit/lib/Repository.html).