Sifting through files to cleanup documentation, like fixed missed module name changes, adding automodule methods, enhancing docstrings, etc.
Updates to documentation
Removed Sandbox_doc
Updated Template Geometry a bit, mostly to fix errors in the merge, updated documentation, cleaned up a few pieces of code
Made my run_script a bit more general to work with all Geometries
Another big batch of documentation updates: cleaned up a bunch more of the autodoc directives, corrected naming and references in docstrings, and added some documentation to the geometry file.