Currently, the notebook saves file paths to things like the output directory and the config path.
This is not needed since this information is given by the user when they start a pipeline run. This information should never be saved as a hard absolute file path, so users can easier change tile directory, change output directory, and change config location without dealing with crashes.
The least intrusive solution will be to not add the notebook page 'file_names' to the notebook, so it never saves to disk and is computed on-the-fly each time coppafish is called.