Repo cleanup round 2

[sweverett]

We are now starting the next stage of pipeline development, with the move towards data-ready modules and modern mcal API. As we are bringing in new collaborators it would be a good time for a quick repo cleanup

• Remove unnecessary or old files
• SmallShearCode cleanup #93
• Restructure submodules to be a bit less confusing (e.g. do we need separate dirs for medsmaking classes & scrips?)
• Update README for new collaborators

[mcclearyj]

#93 closed with commit facca08