By default the ant scripts will not combine the main PLPTool jar archive and its dependencies. PLPTool currently has two libraries it depends on: commons-compress for PLP project file and the rxtx java component. If PLPTool is built with "ant jar" command, the PLPTool archive will be in dist/PLPTool.jar and the libraries will be in the dist/lib directory.
The "ant package-for-store" command, in addition to building PLPTool, will include the libraries into PLPToolStatic.jar and generate the correct manifest for the archive. This JAR file then can be distributed by itself to be run anywhere. The native RXTX library (dll for windows, .so for Linux) will need to be distributed separately, however. I don't know if it is possible to actually include native libraries into the JAR file.