Migrating all outputs to .hdf5

[pavyedav]

Currently, most outputs and inputs of MANTA are in .csv format, which is not conducive to fast pre- and post-processing, and data analytics. We would like to convert these files to .hdf5 and create functionality in MANTA to support this.

@martjanz also suggested that we create an output/ directory from here on out to keep all outputs organized.