Refactor prep config

[Dooruk]

Same thing as #324 that @danholdaway introduced with additional fixes.

This shouldn't change (and didn't change as far as I could test) any of the configuration YAML outputs. I tested creating experiments with the defaults/overrides and Callum and I tested the CLI interface.

A few highlights:

• It replicates the task_questions logic with the suite_questions so we don't have to have suite_questions in each suite folder.
• It changes Jinja2 utility slightly to add a custom "undefined" class, which essentially gives Jinja2 an option to skip certain template variables without breaking.
• It moves R2D2 config creation to utilities but again, doesn't change the configuration.
• This should help with the model dependent tasks (e.g., a variable change task only required for CICE)

I made a few minor fixes and merged with SLURM changes by @ashiklom (I had to add dashes to avoid whitespace between SLURM directives and added items to jinja2 undefined class).

So please take a look and test if you can and see if anything breaks. I'm planning on merging this next week.

[ashiklom]

@Dooruk I gave this a pretty thorough review. Functionally, I think it looks good and I didn't find any bugs. My suggestions above are primarily related to style and, in a few cases, adding additional robustness or clarity.

That said, don't let my suggestions hold up this PR. Take a quick look through them and feel free to either directly commit them (I tried to make it a one-click thing using "Suggestions") or just "resolve" the conversation without implementing the changes. Especially for the type hinting stuff (#349), I can always just open a separate PR on that later.

[Dooruk]

Thanks for your thorough review @ashiklom, I made most of the modifications you suggested and deferred some to a future PR. This is almost set to merge, except while I started fixing some issues with the CLI I encountered an error with the iso-duration type:

So make_duration in question_and_answer_cli is explicitly set to handle PT12H type entries but not D as I quickly looked at it, which should be an easy fix. I have a few meetings back-to-back now but if anyone has time to fix that that would be great.

[ashiklom]

Looks good to me!