If you want to add a new configuration preference to the agent, do the following:
Put it in agent-configuration.xml - fully document it in the comments like the rest
Put it in embedded-agent-configuration.xml - fully document it in the comments like the rest
Add a getter to AgentConfiguration
Add a constant to AgentConfigurationConstants
If this is a plugin container configuration, you probably just need to modify AgentConfiguration.getPluginContainerConfiguration() rather than creating a standalone AgentConfiguration.getXXX() method
If this is a comm sender config, edit AgentConfiguration.getClientCommandSenderConfiguration appropriately
Add the ability to set it by adding code to SetupPromptCommand
Add AgentSetupInstructions as appropriate
Add the prompt text to any wiki page that shows the advanced help text (if there is any)
Add it to on-plugin.xml in the agent plugin's <resource-configuration>
Add it to test-agent*-configuration.xml test files (in the agent module and agent plugin module)
Add it to the perftest-agent-configuration.xml, perftest.properties and build.xml of the etc/perftest module
Add it to template-configuration.xml in etc/perftest2 and possibly update AgentSpawn class
If you added the configuraton to the comm stuff (client sender config or service container config):
You modify ClientCommandSenderConfiguration or ServerConfiguration[Constants]
Modify on-container-build.xml so it generates the new setting in rhq-server.properties
Edit server-comm-configuration.xml and server-comm-service.xml as appropriate