clean up tick.f and sync up 1d, 2d, 3d

[rjleveque]

The subroutine tick.f has complicated logic that has been added to piecemeal and needs a refactor. Various things are also done differently in 2d than in 1d or 3d since the 2d code has been more actively developed.

For example, timers were moved into tick so that they could be checkpointed for restarts, but they are not checkpointed in 1d or 3d.