1. A computer-implemented method of finding a root cause of one or more problems with a deployment of a software application within a managed computer system, comprising: discovering, after installation of the deployment, information about the deployment and software services that are not provided by the deployment, by sending software probes onto a communication network; using the discovered information to create an application model describing the deployment, the application model comprising: an object graph representing hardware and software elements of the managed computer system, the elements represented as objects of the graph; configuration data about the elements; and information about relationships between the elements; dynamically modifying the application model on an ongoing basis in response to detected changes of configuration of the deployment; accessing a repository of logic rules generated from analyses of reference materials for the software application and empirical analyses done on a plurality of different deployments of the software application, each rule corresponding to a known problem associated with the software application, each rule configured to be used to test for satisfaction of one or more possible conditions of the deployment; using at least one of the rules to determine that one or more of the possible conditions are satisfied by the deployment; marking objects of the application model that are associated with the satisfied conditions; and using pattern-recognition on a portion of the application model that includes some of the marked objects to identify one or more root cause candidates associated with the marked objects, the root cause candidates comprising elements of the application model, at least some of the root cause candidates not being marked objects; wherein said discovering, using the discovered information, dynamically modifying, accessing, using at least one of the rules, marking, and using pattern-recognition are executed based on code that is separate from code of the software application of the managed computer system.