For anyone still following this thread: I tried Maven and several other approaches. I have some follow-up questions and a solution. Let’s start with the solution:
Unfortunately, I kept experiencing the same problems with the Netbeans IDE as I described above (plugin working in debug mode, but MM not loading ANY plugins when I put a new one in the mmplugins folder and ran ImageJ from my applications folder).
I tried using a lab computer to recreate my problem. I experienced the same problems with Netbeans. However, I noticed the jre folder in the MicroManager1.4 folder. I had looked for this when trying to set up with eclipse on my other computer, but it was nowhere to be found. I then used the Eclipse setup instructions (after downloading Eclipse Kepler). This allowed the plugin to be used in debug mode, and in ImageJ outside of Eclipse with the plugin in the mmplugins folder. Wonderful!
So then I thought I could use Eclipse on my original computer now that I had the jre file. I followed the same steps, except in Eclipse Neon, and a main class kept being detected when I set up the Run/Build configuration, and then not detected at run time. I kept getting an odd error message reading “The currently displayed page contains invalid issues” when I changed the compliance to 1.6. I tried to install Eclipse Kepler, the same one I used on the lab computer, but it failed to open, perhaps because it was an older version. I tried using Mars, which I was able to open on my computer, but ran into odd file permission issues for the jre that prevented debugging and running.
At the end of the day [read: week], I have a working setup for MM plugin development that, for some reason, only works on one computer. Which leads to these followup questions:
Follow up questions
Why is the jre folder not included in the version of MM that I installed? I installed the latest 1.4 for Mac OS and it was not there.
Furthermore, is this the missing piece that caused plugins to not work when they were developed using the Netbeans instructions? Also, Netbeans 7.3 is not even available for downloads. I know MM 1.4 will no longer be supported, but these instructions should be updated for the time that it is supported to avoid the issues that myself and others have run into.
If you do recommend Maven and it does make things easier, as suggested, there should also be instructions for Maven with the appropriate pom.xml specifications.