Add __init__.py files to git repo.
Add __init__.py files to repo.
Add __init__.py files to github repo.
Fixed some bugs related to multidimensional inputs.
Fixed a logic bug when testing to create HDF5 files.
Generalized the input deck.  Now there “should” be no hard ties to shot numbers.
Added function to create dictionary automatically.

Also general clean up and fixes.
Merge pull request #7 from ezekial4/dev

Dev