Answer
The Capabilities request to the WMS connector on a MapService (for example, SanFrancisco) first looks for a user defined capablities file called "SanFrancisco.XML" in the capabilities directory. If the file does not exist, the capabilities are generated dynamically, but an exception "The system cannot find the file specified" is written to the log file. This exception can be ignored as the response to the request was created dynamically.