Fairly substantial update

- Moved private methods to public where they can be overridden by child classes or where methods are accessed out of classes
- Added deprecation warnings for private methods
- New Logging class for accessing and running Logging config from other modules or sub-processes
- New behavior for foreground:
  - Does not attempt to change user/group
  - Does not write or remove a pidfile
- New behavior for stack trace on unhanded exceptions to have optional, top-level constant to turn this behavior on and off
- Controller.config accesses full config file
- Controller.application_config accesses application section
- Controller.logging_config accesses logging section