Fix miscellaneous bugs

[jhamrick]

A few things have changed upstream causing the tests to fail. In debugging I also found a fixed a few other miscellanous bugs:

• Test notebooks shouldn't use python 2 kernels
• All nbextension tests should be marked as such
• pytest now requires custom marks to be configured in a pytest.ini file
• doc testing can fail if nbgrader_config.py already exists and defines the submitted directory to be submitted_zip, so clean up the config file first