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It's not entirely clear exactly what you've done to get here, but it's clear that your workspace is kind of messed up.
catkin_EXTRAS_DIR is one of the variables used internally by catkin during the build process; if it's not set it means that some file for catkin is corrupt or empty.
The first steps at troubleshooting would be to remove the build and devel directories in your workspace, and since the CMakeLists.txt link at the root of your workspace seems messed up, you should remove that too. A fresh build will re-create all of these.
After that, next steps will depend on how you installed ROS. If you did a binary install, you should reinstall any apt packages you suspect are damaged with apt-get install --reinstall <package>. If you did a source install, you should make sure that the source files are still intact, and then run the build steps (catkin_make_isolated, etc) again.
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