Refactored update panel

Now a separate class away from main view
Fixed logging in gui
Refactored shutdown process to be more robust
upgraded shutdown message log in model
Fixed logger ignoring config file
Added max wait before shutdown option in config
View now follows correct shutdown process

View now tells the controller->model to shutdown its processes
before it does. This is a handy safety feature if we ever needed
to save data before shutdown.
Progress Panel now updates all relavent info