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We've been moving away from wrapping system-installable libraries in ROS packages. It leads to less portable code, as you end up using ROS-specific linking methods to use these libraries.
Instead, as much as possible, we are now trying to:
A valid criticism of source rosdeps is that they don't come with an uninstall mechanism. That said, the main role of the source rosdeps, IMHO, is to provide a starting point to people on other platforms. They are generally equivalent to what that user would have done if they had to manually download the source and install on their own.
We try to shy away from PPAs for libraries, as Ubuntu does, as they lack safety guards to prevent downstream issues.