Update CLI options

[klwetstone]

Change CLI options to be more user friendly

In predict, have arguments / options for:

• samples_path (as is)
• model_path (as is)
• output_file: file path to save the predictions
• output_directory: if this is specified, output_file will be relative to output_directory. Default to the current directory
• keep_features: If true, we'll copy the train and test features to the output_directoy.
• overwrite: Just check whether the prediction path exists, and ask about overwriting predictions. Don't check about overwriting train / test features

In evaluate, add an overwrite flag as well