FlexDeploy download zip contains plugin jar files (application/plugins for Tomcat download and plugins for Weblogic download). You just need to 1) copy plugins from download zip to plugins folder in your installation (details explained below) and 2) all files will be automatically uploaded and 3) activated on the server startup.

This auto upload process is very useful during initial install as well as when upgrading FlexDeploy, but you can use the procedure any time.