Git subprojects can't be merged

[LiamClark]

If a group pushes the framework into their repository on GitHub, merging pull requests fails.
Because the mirror has dirty state.
Git thinks we deleted the subproject. because the JGIT clone does not recursively clone this subproject.

Proposed solutions:

1. disallow a push that contains subprojects / submodule (might be too SQTE specific).
2. update the clone in the branchapi impl that we do clone recursively.

[jwgmeligmeyling]

You mean a repository with submodules? We probably should initialize submodules after pulling the repo... Not sure if thats possible with JGit though