Cleans up some of the app delegate's code

When getting bool values out of defaults you don't need to check for the object, then pull the object and convert it to bool i.e. 
```
if ( [defaults objectForKey:kCheckForRepoUpdatesAutomaticallyEnabled] ) {
    if ([defaults objectForKey:kCheckForRepoUpdatesAutomaticallyEnabled] bool value]) {
        ... do something ...
    }
}
```
it's a lot cleaner to just do this
```
if ([defaults boolForKey:kCheckForRepoUpdatesAutomaticallyEnabled]) {
     ... do something ...
}
```

i've refactored the occurrences of these in the app delegate file.  If you like I could go over the rest of the project and work on those a little bit too.

In addition this was built on top of Mitchel Blake's pull request #93, which I tested and works well. 

I've taken it one step further to completely remove the setupConfigurationWindow: method, which could be bypassed pretty cleanly by putting the LGConfigurationWindowController initializer in the showConfigurationWindow: method.