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You depend on message_generation, but message_generation is not in your custom rosdistro and therefore bloom cannot figure out how to transform message_generation into a OS specific key like ros-hydro-message-generation.

This happens even if I am in a shell that freshly sourced /opt/ros/hydro/setup.bash; i.e. ROSDISTRO_INDEX is not set.

I don't see how this is possible unless you have changed your ROSDISTRO_INDEX_URL, did you rosdep update after unsetting ROSDISTRO_INDEX_URL?