cleanup DSL generated expression for readability

[isaacsas]

This introduces a bunch of intermediate variables to store inputs to make_ReactionSystem_internal, with the goal of making the generated expression easier to read when debugging. It also makes the creation of t the first thing in the generated code, which should be a first step to allowing time-dependent parameters (something MTK is working on better supporting).

[TorkelE]

Looks good.

Ideally I'd prefer to not do any non-required changes to the DSL file until after #985 is merged (I've already had to do one messy merge thing to get that one back functioning with master). The removing Catalyst. things might work with a simple merge, but not sure about the other changes. If you thing there won't be any problems then feel free to merge, but otherwise I wouldn't might waiting until #985 (with neither of these being very urgent)