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Rename InputPort to InputPortValue (RobotLocomotion#5533)
* Rename InputPort to InputPortValue and clarify some comments. * Rename Context::Set/GetInputPort to Set/GetInputPortValue. Line length, variable name, and comment fixes. * Minor name fix. * Line length fixes. * Renamed system_input files to input_port_value. * Realphabetize header file lists. * Fix odd indentation & sorting. * Renamed system_output files to corresponding output_port_value files. * CMake fix. * Change dangerous version of FixInputPort to be safe with respect to invalidation.
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