Thank you for your answer.
If I remove the old jar, I get the plugin to work, but the updater will always try to install it. My concern is that I'd like this change to be permanent when the update site is installed, to make it easier for users.
Maybe there is a possibility to have this change permanent for my update site, using the "mark as obsolete" command (specifically for the update site) in the updater. When I tried, the updater asked to break dependency on scifio-0.27.1.jar, and then I get an error from the updater: "missing upload information for site http://update.imagej.net/ "
Is there another way, or how can I get this to work?
About the idea of making a pull request, I guess this is a decision from the developers, because the version 3 has major changes. Notably the files produced by version 1 are not compatible with version 3 it seems (headers vary between versions).