Wow, sorry I never saw this thread until now, @radoslaw.ejsmont.
Regarding writing SciJava plugins in Groovy: it seems that Groovy does not support Java annotation processing. There is an open issue for it but I think it would be a difficult project to implement. For SciJava only (i.e. only the
@Plugin annotation), we could perhaps implement a less general solution.
For Kotlin, there is an annotation processor (kapt), so that is an option for people who want an alternative to Java’s verbosity.
You were on the right track to look for
META-INF/json/org.scijava.plugin.Plugin in the JAR file. If that is missing, then there is no hope of it being present in the menu. If that file is present and contains your plugin metadata (you can use a text editor to check), then it should be discovered at runtime.
Probably you need to pass the
--ij2 flag as well. See the Scripting Headless page.