Sorting the Preprocess config a bit

This MR adds the following:

• Removing unused Preprocessing config (Hits, GNN). Those should be moved here.
• Adding comments to preprocess configs. Also updated the preprocessing docs.
• Moving class_labels to the sampling block because it is not used in preparation.
• Moving intermediate_index_file to parameters.
• convert to bottom of the file and renamed to convert_to_tfrecord.
• Split the unit tests again.
• Removing iterations.
• Adapting the tests.

Also:

• Fixing a remnant bug of !334 (merged).
• Adapting the plotting of plotting_epoch_performance.py to the fixes made here and in !334 (merged).
• Removing the zpext test files from the tfrecords training integration test to check if this is now working (the standard integration test without tfrecords checks if it is working with zpext).