Inconsistency between flux2 in AMRClaw and GeoClaw

[mandli]

I am not sure where this should be fixed but I was doing some modifications to step2 and flux2 recently and noticed that the calling sequences are not the same between GeoClaw and AMRClaw. At some point we started declaring space for the cqxx and other arrays inside of flux2 rather than further up the call stack and passing it as an argument into each routine. We should probably make this consistent between both GeoClaw and AMRClaw.

[rjleveque]

I see there are other things that could also be cleaned up, e.g. amdq and apdq are declared in step2 and passed to flux2 but are only needed in flux2 I think.

[mandli]

Some of these changes were due to threading concerns but some of these are simply just simpler allocations of space on the stack that acts differently than the single grid code. @mjberger and I are in the midst of taking a long look at parallelization at the step2/flux2 level so it may be prudent to wait a bit before committing to something.