Add seed location for offvertex seeding case and cleanup

[bradyrx]

This PR adds the seed location (either "offvertex" or "center"). This will also do some refactoring and various bug fixes.

[bradyrx]

To address:

• Run ./check_input_data and exit out if this fails (Custom input_data dir breaks it #14)
• Declare an output directory for simulations (declare output directory for simulations #13)
• Exit out of particle build script fails (Shut down automate_mpas if the particle build script fails #12)
• Allow just surface seeding (Allow just surface seeding #10)