FYI. It appears the link in the following paragraph of the webpage on Maven stuff (http://wiki.imagej.net/Maven) is broken...
Producing multiple JAR files So what if you have multiple .jar files you want to build in the same project? Then these need to live in their own subdirectories and there needs to be a common parent POM, a so-called aggregator POM (only this POM needs to have the scijava POM as parent, of course). For an example, look at Fiji's src-plugins/pom.xml. Basically, it is adding the <packaging>pom</packaging> entry as well as a couple of subdirectory names to the <modules> section. Cheers, Jay
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