Notebook text and bug fixes

[jlvdb]

Problem & Solution Description (including issue #)

• Fixed a number of issues related to accessing configuration parameters from within stages and aliasing of stages.
• Improved the subclassing API which generates the parameter list and class documentation.
• Added descriptions to the example notebook.

Code Quality

• My code follows the code style of this project
• I have written unit tests or justified all instances of #pragma: no cover; in the case of a bugfix, a new test that breaks as a result of the bug has been added
• My code contains relevant comments and necessary documentation for future maintainers; the change is reflected in applicable demos/tutorials (with output cleared!) and added/updated docstrings use the NumPy docstring format
• Any breaking changes, described above, are accompanied by backwards compatibility and deprecation warnings