Organizational changes

[abarret]

This is mostly code movement.

• I've put different executables into separate directories.
• I've moved input files associated with those executables into the directories as well.
• I deleted any input file that I was unsure of which executable with which it paired (so input2d, input2d.five, etc.).
• Removed the solver executable because it's the same as multigrid with USE_PRECONDITIONER=FALSE.
• Updated some input files functions to be correct manufactured solutions.
• Added @bindi-nagda's time_stepping input files.

There's currently a bug in the FAC operator with how restricting works. Currently the solver crashes unless the FAC solver uses V_CYCLE with zero pre smooths. I think this is related to #44 and the recent changes to the IBAMR master branch.

[abarret]

@bindi-nagda when you get a chance, I'd like your feedback on the changes, especially the removal of the input files.

[bindi-nagda]

@bindi-nagda when you get a chance, I'd like your feedback on the changes, especially the removal of the input files.

The input file organization looks good. I made a few corrections to the input files for time_stepping. input2d.varThn now matches what I'm using for convergence testing.

I also brought back input2d.var_theta.trans_vel and input2d.var_theta.norm_vel as I found them useful in the past for testing multigrid.

[abarret]

Note this fixes the case when the number of presweeps > 0. Also fixes the case when the number of sweeps = 1.