1. A computer-implemented method performed by a runtime engine executing on at least one computing device, the method comprising: in response to an execute command from a management process configured to direct at least a portion of the operations of the runtime engine, executing an application implemented by an application file comprising a plurality of data blocks, the management process operating independently of the runtime engine, a thread being initiated by the execution of the application, the thread having been created by a module associated with a module identifier and execution of the thread having been initiated at an offset location within the module, the module being a Dynamic Link Library file or an executable file; monitoring read operations performed by the application on the application file as the application is executing, the monitoring comprising receiving a thread discriminate value and a pseudo thread identifier from the thread when the thread performs a read operation on the application file, the thread discriminate value identifying the module identifier and on offset value identifying the offset location in the module; and sending a read message comprising the thread discriminate value and the pseudo thread identifier to the management process each time the application reads one or more of the plurality of data blocks of the application file.