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In a new terminal you need to run

source /opt/ros/indigo/setup.bash

That will set your current terminal to use Indigo. Be careful that you don't source any other Hydro setup.bash files in your ~/.bashrc file or you might start overlaying packages, which is probably not what you want to do.

To switch back to Hydro, you need to open a new terminal and run

source /opt/ros/hydro/setup.bash