Adds Auto Start Bots Feature.

Bots can be configured to not start when the Application is loaded.

Also add some comments to the Configuration object.
Adds a per-Bot Auto Start Option

Only works when the top-level option is false. This also defaults to true because it is not required by the Json Serializer. Users don't have to add anything to their config other than the top-level option from previous commit.
Adds AutoStartBots and AutoStart options to Template.

Based on FunkyLoveCow's pulls. Sets template options to sensible defaults.
Merge pull request #252 from cwhelchel/feature/autostart

AutoStart Configuration Option (closes #250)