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Compartmentalised catkin_make

Given our large 100+ package project and a rather slow target machine, the CMake file regeneration step is painfully slow, but it is made doubly slow by a feature of CMake described here that means that any package that includes a CUDA file will force the whole project to require two configurations.

Is there any way to avoid this double reconfiguration? Or somehow build the offending packages in isolation so we can localise the rebuild?

I know we could switch to catkin build, but changing tools would be a harder sell...