reformat and fix examples

- remove imports that are not needed
- remove spaces at the end of lines
- convert tabs to spaces
- fix indentation
- always use pythonic style for line continuation
reformat and fix misc/*py

It looks like a lot of our latest changes broke the paper*py files. Also
reformat all this crap.
Merge pull request #10 from tjhei/fix_format_examples

Fix and format examples
Move examples into new directory
Remove latex table stuff for the moment, not sure how to distribute, licensing, etc.
Add output_figures directory to git repo so that the examples run without the user needing to make it
Update gitignore
Move test outputs, update testing scripts.  What does gen_doc do?