Fix the uber jar generation

There were three problems with it:

* the annotation indexes were not combined by default
* the annotation index combining was not prepared for SciJava-common 2.6.0 (which replaces SezPoz with a home-grown solution)
* the `META-INF/services/` files were not combined (disabling either Jython or JRuby, depending on the dependency order).

NOTE! Do *not* merge this without replacing the commit *TEMP: Use scijava-common 2.6.1-SNAPSHOT*!