I start Geronimo using this command,

java -jar bin/server.jar org/apache/geronimo/DebugConsole org/apache/geronimo/RuntimeDeployer org/apache/geronimo/DefaultDatabase org/apache/geronimo/SystemJMS

The Debug, Deployer, JMS, and Database GBeans are started. As stated var/config/config.list contains the last stable config therefore subsequent restart is done using this command,

java -jar bin/server.jar

Geronimo EAR Deployment is done using this command,

java -jar bin/deployer.jar deploy ~/agentis/agentis/Agentis370_350IDE/work/SimpleProjectTest/dist/SimpleProjectTest-agent.ear