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I think I found the answer by myself: For ROS electric and upwards, only the rosinstall files in the rosdistro repository at github (https://github.com/ros/rosdistro) are used by the rosdoc_lite indexer running on Willow Garage's build farm to decide which packages and stacks have to be documented and from which source URL and branch. rosdoc_lite also generates and uploads yaml files with meta information to http://www.ros.org/doc/distro/api, which in turn are parsed by the wiki macros PackageHeader, StackHeader and MsgSrvDoc to create the package/stack meta information on http://www.ros.org/wiki/. http://www.ros.org/doc/api is a symlink to the API documentation for the current ROS distro.

All this is pretty well documented at the wiki page of rosdoc_lite and in the "Get Involved" instructions on how to submit new repositories.

The confusion regarding our stacks from the tu-darmstadt-ros-pkg came from the fact that there have been two different rosinstall files present with inconsistent source URLs in the rosdistro/doc/furte folder, one for the whole repository created by ourselves, and others for each of the released stacks that have been copied over from the old documentation system during the migration to rosdoc_lite.

Please add comments or edit this post directly if I missed some details.