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
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 it to rhq-plugin.xml in the agent plugin's <resource-configuration>
You might have to add it to *-configuration.xml test/agentspawn files (in the agent module and agent plugin module) unless the hardcoded default is safe for the tests to use
Add it to the agentspawn.properties agentspawn module (probably don't need to do this anymore)
If appropriate, add an upgrade step to AgentConfigurationUpgrade
(if we support embedded agent again) Put it in embedded-agent-configuration.xml - fully document it in the comments like the rest
If you added the configuration to the comm stuff (client sender config or service container config):
You modify ClientCommandSenderConfiguration or ServerConfiguration[Constants]
Modify rhq-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