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Thisi is what worked for me:

  1. download, cmake, make and make install PCL from github
  2. download perception_pcl from github and put it into catkin_ws/src
  3. edit CMakeLists.txt of both pcl_ros and pcl_conversions packages (inside perception_pcl folder) and add version of your PCL package into find_package command

find_package(PCL 1.8 REQUIRED COMPONENTS core ...)

This makes ROS look for your customized pcl_ros package instead of the one installed via package manager, which consequently looks for PCL built from source instead of the old version installed via package manager.