Clarifying Environment Specifications

[atravitz]

Issue Description

It's not clear which arguments should be passed directly to signac and which should be passed as "additional arguments."

Proposed change (optional)

In the docs we should introduce the exisiting templates first. Right now it jumps right into defining your own. We should give some example use cases that are common for us.

Additional context (optional)

Things that (we know) have caused confusion so far:

• --walltime should be passed directly to signac
• --partition can be passed as optional to the default environment, but is passed directly to signac for specific templates (like great lakes)
• additional arguments will not show up when using --pretend