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We just ran into the same problem. From what we found, you need to use the rosisntall_generator and wstool commands. Specifically:

rosinstall_generator sensor_msgs --rosdistro indigo --deps -wet-only --tar > indigo-sensor_msgs-wet.rosinstall
wstool init src indigo-sensor_msgs-wet.rosinstall

This worked for us using indigo and for installing the image_transport and cv_bridge packages as well. As a note, we had to delete the previous .rosinstall file in the src directory for these commands to work. Don't know if there's a better solution.