New --rebase option for git-ensembl.

We now support rebasing your pull requests. This can be useful
when wanting to avoid merges when pulling changes in.
Adding a --cmd mode to git-ensembl.

Requested at the retreat. People want to be able to give git-ensembl
arbitary commands. This does mean that a lot of the pain like
automation and looping is taken out of your hands leaving you to specify the command.
Merge remote-tracking branch 'origin/feature/cmd_mode'
Merge remote-tracking branch 'origin/feature/rebase_pull'