Review and revise uses of the ApplicationSingletonProviderI model in 2.12

We need to have clear documentation and use docs for singletonprovider and related mechanisms that allow unified use of JalviewJS as a multi-instance applet and the single context JalviewJS/Jalview Desktop apps.

Questions:
- Is assuming a global context really sensible ? (ie should singletons be avoided entirely)
- what are the implications for compatibility of scripts (ie JS or Groovy) between JalviewJS and Jalview desktop.