Replace doc code

In the ReStructuredText (*.txt) files, many of the copies of Python code were out of date. Replaced copies of Python code with links to sections of the corresponding files. This dramatically reduced the number of lines of code to maintain. This will help keep documentation in sync with code (but will not guarantee synchronization). Renamed two ReStructuredText files to match corresponding Python files. Modified code files for improved readability. Modified .gitignore to ignore tmp directories.
This does not include the line `class DBN(object)`, which should be there.