Why not use the stream classes to do the copying?
Or you could use File.rename() to move the JAR for the deploy directory.
Also, if you are going to do a copy, it is usually best to copy the file to a temporary
location on the same disk partition as the deploy directory, and then move that file to
the deploy directory. This prevents weird zip file error that can occur if the hot deploy
tries to deploy the JAR before the copy is finished.
And just to answer your question, to run an external program use Process.exec(), though
within an EJB you should not wait for the process to exit before continuing.
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