The link to "imagej-maven-plugin" was broken, hope this is the right one...?
= What's this: ''Property 'imagej.app.directory' unset; Skipping copy-jars'' =
This is part of the [https://github.com/
scijava/scijava-common/tree/master/imagej-maven-plugin imagej-maven-plugin] (enabled for you by pom-scijava). As you suspected, it copies your plugin's ''.jar'' file to your ImageJ plugins folder. But you have to specify where: