Run setup.py -x flags in scripts/update

[jisantuc]

Once issues from #472 are resolved, create a scripts/bootstrap that gets the application into a working state

[hectcastro]

Could we tuck whatever is destined for bootstrap into update? That seems to be the convention across most projects (RF is an outlier because it was being setup while things were still being figured out, and is slowly being migrated).

[jisantuc]

Yeah that's fine, I'll update the issue title accordingly. One less script to run 👍