What is you end goal?
If you want to use code from GanttProject as library in your own application then most likely you will not suffer from plugins machinery, because it is used in just a small number of user interface points, such as building a list of available importerts or exporters.
Repackaging JARs with the goal of launching GanttProject UI is not the best idea, sorry. It is still possible to package a single JAR as a single plugin, craft your own plugin.xml file with all extensions and configure Eclipsito appropriately, but not sure if it worth the efforts comparing to just using GanttProject distro and launcher scripts as is.