Clean up examples

This PR makes a lot of small improvements to the examples.  Most of them are merely simplifications of the code, addition of docstrings, or removal of redundant comments. I've also:

- Fixed a few small bugs
- Used `grid.p_centers` instead of meshgrid to get coordinates in multiple dimensions
- Fixed some bugs in the routines for computing ghost cell centers and edges in geometry.py
- Removed the redundant file `shockbubble_scipy.py`.