Directory Bloat and explicit file paths

[tylerbarna]

Need to reduce bloat in main directory, particularly with respect to priors being kept in the root directory. Also need to make clear what scripts do what and what order they're called.

Current state of repo is geared explicitly towards using nmma_fitter on the msi system; at various points, the pipeline makes explicit assumptions about absolute file paths that are located in the msi directory. Work needs to be done to make these various file paths either relative paths or arguments provided when executing the scripts.

One of my ongoing projects is getting the pipeline working on local systems, which should hopefully motivate more platform-agnostic changes to the codebase

[tylerbarna]

would probably be good to pull any path references to a settings.json file or something. Could also use that as an opportunity to decouple models from the explicit definitions we make in make_jobs.py. If we define a models.json with a similar structure to the models dictionary that is currently being used, that might make it easier to dynamically add models in the future.

[tylerbarna]

May be good to try out these changes in the packaging branch and validate with localScript.py