Ensure code matches naming conventions

[laurenmarietta]

In the review for #172, it was mentioned a couple times that there are discrepancies between code naming conventions and what is written into the code. Namely:

• In yaml_generator.py, around line 400, the code is pulling the incorrect indices from the file name. (See comment here.)
• In the table that is generated by apt_inputs, the visit number (V***) is recorded but not the filename (jw***). See discussion here.

Each of these might be resolved by using a filename parser, such as what JWQL uses.