Add proper support for application logging
Convert old logging to use the new centralized logger

Also remove many print statements; these should never be used.
Clean minor style issues
Upgrade some package requirements
Disable email logging

This will be re-enabled once the logger has been verified as stable.
Merge branch 'logging'

* logging:
  Disable email logging
  Upgrade some package requirements
  Clean minor style issues
  Convert old logging to use the new centralized logger
  Add proper support for application logging