1. A computer-implemented method for updating a current version of a configuration file which controls an agent which monitors an application, the method comprising: creating a merged version of the configuration file based on the current version of the configuration file, an updated version of the configuration file, and rules; and using the merged version of the configuration file to control the agent, the creating the merged version of the configuration file comprises: identifying an entry in the current version of the configuration file for which there is a corresponding entry in the updated version of the configuration file; selecting one of: (a) the entry in the current version of the configuration file and (b) the corresponding entry in the updated version of the configuration file, as a selected entry, based on at least one preference in the rules; and based on the selecting, adding the selected entry to the merged version of the configuration file.