Currently, you can set scijava.app.directory, which is the path to the base directory of the SciJava application. And you can set scijava.app.subDirectory, which is the relative path to a subdirectory beneath jars or plugins inside the SciJava application folder structure. But there is no way (AFAICT) to override the copy-jars mojo's assumption to copy artifacts into the jars folder (or plugins folder in the case of ImageJ 1.x plugins).

I propose a new property that defines this value. Then all the legacy ImageJ 1.x plugins in Fiji can override this property with plugins instead of jars, and we can get rid of the hacky ImageJ1 and Bio-Formats hardcoded code blocks, in favor of declarative POM goodness.