Auto format tools

[JoshuaSBrown]

Add auto formatting to python files using pep8 -> git pre-commit hook
Add auto formatting to md files using remark-stringify -> git pre-commit hook

[junghans]

I would honestly make this part of the make format rule in CMake and have the hook call it.

We are currently globing all *.cc and *.h files, we could do the same for *.md and *.py.

[JoshuaSBrown]

Ok, will do that instead.