Use shallow checkout for Git

A full checkout is not required for the initial parsing step, even if it is necessary eventually to generate the Research Object Bundle

Significant loading time reduction could be gained by doing a 'shallow clone' (with argument `--depth 1`) initially, which does not download the history of the repository. Later the full history could be downloaded before checking the `git log` to get details for the Research Object - as this step is asynchronous.

However, JGit does not currently support this feature ([open feature request here](https://bugs.eclipse.org/bugs/show_bug.cgi?id=475615)). The [Jenkins git-client-plugin](https://wiki.jenkins.io/display/JENKINS/Git+Client+Plugin) does support this option and could be used in place of JGit to implement this improvement.