This simple ImageJ 1.x plugin allows running scripts packaged in a jar file
by adding a simple plugins.config file that calls
sc.fiji.script.Script_Launcher("jar:<script-filename>")
This approach was originally developed to maintain compatibility with plain ImageJ 1.x.
However, if you are running ImageJ2, you can
simply place your scripts in the scripts/ subtree inside your JAR file,
and they will be automatically discovered and added to the menus by the
SciJava Common script framework.
See this forum post for details.