Framework and Executable Changes (Code Cleanup)

[DavidJoy8]

This contains changes to address Issue #1 plus some related framework changes:

• Removed END_TIME. This made sense for the summer work, but is a flawed concept for general use. To specify dt, users now specify the number of timesteps per unit of simulation time they wish to use. Users now specify dt directly.
• Added methods for running until a certain simulation time or number of timesteps. This comes in handy for doing the free energy.
• Removed prestep and poststep. Similar to above, these were a relic of a previous iteration of the framework. Now everything is done during step.
• Removed finalize. With the framework no longer caring about the end time, this method no longer makes sense. Users are free to call an output method at any time.
• Merged the PFHub1aBenchmark and PFHub1aPeriodic executables, as requested. A command line argument is now used to distinguish which one to run.
• Added command line arguments for dt and end time to the Grid Timer/Performance Runs executable.

Things left for other PRs/future work:

• These changes restrict dt to be of the form 1/integer. We could consider how to generalize this to allow things like dt=.4 or even allow changing dt during a run.
• With the addition of variable output times, the grid output filenames are now ambiguous. This will be addressed in my PR for Use new Cabana grid output #10 since that contains a partial rework of file saving.

Closes #1

[stvdwtt]

Looks good to me!