1. An integrated circuit device comprising: a first partition and a second partition; and a boundary scan system configured to control at least a portion of the integrated circuit device via a plurality of logic signals, wherein the boundary scan system comprises: a boundary scan interface configured to receive the plurality of logic signals; a boundary scan hub instantiated in the first partition and being communicatively coupled to the boundary scan interface; boundary scan-based logic instantiated in the second partition; and an interface instantiated in the first partition configured to communicatively couple the boundary scan hub to the instantiated boundary scan-based logic; wherein the second partition is configured to be reconfigured by: loading a partial reconfiguration file in the second partition while the first partition concurrently runs an application; and instantiating the boundary scan-based logic in the second partition while the first partition concurrently runs the application in response to loading the partial reconfiguration file in the second partition.