add/move more options of CLI to config

```
as a user
i want all the options to be stored in the config
so that i don't have to remember anything if i need to rerun a simulation
```

- [ ] raw data path
- [ ]  prepped data path
- [ ] column name mapping - a separate data schema might be useful here. it'd be great if we could abstract column names out of the code #36 
- [ ] output directory?