1. A method of fault protection for applications distributed across multiple computer nodes, comprising: taking checkpoints, by at least one high-availability application service, of one or more sub-programs within applications executing across multiple computer nodes; flushing and halting a transport connection during said taking checkpoints in response to execution of a transport control layer interposed between a distributed application and the transport connection; and restoring said one or more sub-programs from said checkpoints in response to initiating recovery of one or more said applications by said at least one high-availability application service which is provided to said one or more sub-programs running on a primary node, while at least one backup node stands ready in an event of a fault and subsequent recovery; wherein the transport connection itself is not responsible for the flushing and the halting of transport traffic.