Added method to specify cloneOptions on the Git plugin

This pull request adds a method to specify Git cloneOptions.

Before continuing (adding unit tests, documentation, codeNarc) I would like to ask if this approach is ok?

The problem was that the git clone timeout option can only be added using the new, extensions based approach of the Git plugin. As soon as the CloneOption extensions element is present, the old elements of reference and shallowClone aren't picked up anymore, so you have to define them by using the CloneOption as well. I tried some different approaches but in the end settled on deprecating the old way.
do not move the code around