Make layout=="flat" Behave the Same on all Schedulers

[davi0011]

User feedback suggest that there is confusion in Flux "flat" vs Non-Flux "flat".

The layout should apply consistently to all of the schedulers supported and instead the flux allocation style run should be a different option.

[mdmosby]

@davi0011 were you working on a PR for this? I think we should remove the current flux special behavior in favor of encapsulating as proposed in #113

[davi0011]

I still needed to add the option to have a way to call flux with the encapsulating run. Did we want to do this and #113 separately? Seemed like that issue covers this as well. I might be able to get this done later tonight if needed.