Added flux limiter based on gradients

[kolosret]

New in this update:

1. Added maximum gradient for the multi dimensional petscfv limiter calculations, based on Kenny's code. (This effectively turns off projections for large gradients).
2. added MPI_Barrier for timestepper to make sure profiling results for the compute step are accurate.
3. Added the new mass flux boundary condition from Kenny.
4. Formatting all the files in repo.