What config files can be managed programmatically, and which require file system access?

For example, in ./server/default/deploy/jms/jbossmq-destinations-service.xml there are the JMS queues and topics. Is the only way to add, edit or remove queues and topics to edit this file manually on the file system, or can I do this from an app running inside the same container?

In the ./server/default/deploy directory, files are automatically interpreted into the running configuration, but how can I add or remove files in the JBOSS_HOME directory structure from an application running within the app server itself?

Another example would be how to create an EJB JAR programmatically (that is, from an app running inside the container), then copy it to the deploy directory?

TIA!