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It seems like your workspace is setting the PATH environment variable incorrectly. Sourcing one workspace overrides and previous workspace or other setup.bash, so it doesn't matter if you've sourced the setup.bash for the system install of ROS or not.
I would look at the PATH after you've sourced the setup.bash for your workspace, to see if it's including a path to a previous version of ROS or a workspace that's been deleted.
You can re-create the setup.bash in your workspace by deleting the devel folder, sourcing your system install and rebuilding the workspace:
cd /home/user/repo/workspace
rm -rf build devel
source /opt/ros/include/setup.bash
catkin_make
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