Possibility to apply plugin by instance, not only by id/type

This pull requests adds possibility to apply plugin by instance, not only by id/type.
This is important, when building more complicated plugins (like our Ameba - mobile builds support), with potential dependency injection, that makes us using the internal API (example: https://github.com/apphance/Apphance-MobilE-Build-Automation/blob/master/src/main/groovy/com/apphance/ameba/plugins/PluginMaster.groovy ).

Ameba: http://ameba.apphance.com/