Improve script error checking/control flow

[johnegarza]

Currently, there is little built-in error checking in optitype_script.sh. For example, during development, there were several occasions where some steps silently errored and did not produce output, but did not stop the script, leading to confusing error messages further on as downstream tools tried to access nonexistent files, and in turn did not stop execution despite errors. Additionally, the script currently assumes each step is successful and removes inputs as soon as a step is complete, complicating debugging in the above situation. How should we reconfigure the script to be safer in these situations?