Add a patch file off development

[mcmehrtens]

• Fixes Diffs stored in simulation output are useless if base commit doesn't exist #188
• Implements a development-diff.patch that makes a patch based on the merge-base of HEAD and origin/development.

This feature makes the actual working tree recoverable in a couple of scenarios that otherwise wouldn't be:

• If the simulation was run based on commits that were never pushed to GitHub
• If the simulation was run based on commits that were squashed when merging into origin/development
• If the simulation was run based on commits that were dropped or overwritten by a rebase