This is not always a viable solution, but we avoid changes to rviz configuration files by always trying to start rviz via launch files. We have an rviz.launch file that points to a custom configuration file when starting the node. That custom configuration file is under version control. If we mess with the rviz layout after launching and then kill the launch command, and rviz with it, the rviz configuration file changes are not saved. This results in a clean repository.
For the rviz launch file we try to write it such that we can include it from other launch files or run it stand-alone after launching other parts of our system.
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