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/opt/ros/indigo is managed by the package manager, and it may overwrite files and directories there at any time, so I don't recommend installing packages into /opt/ros/indigo. (conversely, if the package manager finds files there that it isn't managing, it may fail to install future packages.)

As an alternative, you can create a global overlay that isn't managed by the package manager, and install packages from source there. /opt/ros/indigo_overlay or /opt/ros/indigo_local might be a good choices.