My real problem is in not being able to open my JPanel. I was able to clean up the pom.xml file, even though I do not understand the dependency structure, by simply selecting all the text in the file, deleting it, then clicking on the little red triangle and restoring the original text.
Still, even though the build is clean and the program runs without any errors, the GUI (JPanel) never shows up — the program starts, then stops in less than a second. The JPanel never appears. There are no errors anywhere. I tried a new project in an earlier version of Netbeans, just so there would be no interference from my other project; it was simply a JPanel with a single button, but running it gave the same result: the project starts and stops within a second and the JPanel never appears. This is my problem, not the pom.xml file or the plugins.config file. The JPanel never appears and when I allow an instance of ImageJ, the plugin never appears in the plugins dropdown menu, even though it has an underscore in the name. I think I am missing something very basic, but I can’t find it!