Merge development of Example 1 (and various train/infer/eval scripts) into Master

Major changes:

• Large code additions to each stage, these may not be compatible yet with the version that Sylvain will write, but should be able to merge in quite easily
• train.py, infer.py, eval.py complete as version 1. These may also need to change after Sylvain overall's class updates
• examples/Example_1 now has a set of .yaml files for each stage's train/infer/eval process