Put all the pieces together

[babayagaofficial]

• [x] workflow the workflows
• [x] API: decide which arguments/inputs are required, what commands to have, what defaults to give parameters, how much choice to allow the user, etc
• [x] move various utility functions (e.g. reading in/out of files) into one global script (rather than duplicated across multiple scripts)
• [x] unify all config files into one global config file