A technique for updating agent software which controls an agent, including how the agent adds instrumentation to an application and how the agent process data from the instrumentation. A current configuration file and an updated configuration file are evaluated in view of rules, to create a merged configuration file. The files include metadata entries. The rules can include: delete a current configuration file, not merge a current configuration file with an updated configuration file, overwrite a current configuration file with an updated configuration file, delete a metadata entry, prefer an entry in the configuration file over a corresponding entry in the updated configuration file, and prefer an entry in the updated configuration file over the corresponding entry in the configuration file. Customized entries in the current configuration file can be maintained if appropriate. Entries which are not maintained are kept in the merged configuration file as inline comments for documentation.