EclipseHelper annotation index generation woes

[ctrueden]

In multiple scenarios we have witnessed the SciJava plugin index file generated in target/META-INF/json/org.scijava.plugin.Plugin instead of target/classes/META-INF/json/org.scijava.plugin.Plugin. I recall a couple of debugging sessions months ago where I determined that it was the EclipseHelper writing this file in the wrong place.

We also noticed that the EclipseHelper does not process nested classes (i.e. public static classes with @Plugin annotations). And furthermore we noticed that the index contains wrong package names e.g. classes.foo.Bar rather than foo.Bar sometimes.

More investigation needed to isolate and fix these bugs.