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Try the following and see if it improves your situation:

  1. remove all source .. lines that you added from your .bashrc
  2. delete the build and devel folder from your first workspace (ignore your second one for now)
  3. in a new terminal, source /opt/ros/indigo/setup.bash
  4. run catkin_make (or catkin build, whichever you prefer)
  5. source devel/setup.bash

Now see whether you end up in the correct location.

The setup files are not magic, they basically just set some environment variables, and depending on what you sourced before, those variables could / may include additional paths.

By rebuilding your workspace you regenerate a fresh set of setup.* files, which, if you followed the proper procedure, should work correctly.