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Repositories might not have branches for each an every ROS version. Sometimes the same code is being used for different ROS distributions and then only a single branch (commonly with the name of the older ROS distro) exists.

You can find the information you are looking for by look into the rosdistro database. In the Indigo distribution file you will find an entry for rqt which specifies the URL and branch name to be used in that ROS distro: https://github.com/ros/rosdistro/blob/df65c25ff7445aa818953c1e778fffabedb4f3d6/indigo/distribution.yaml#L13013-L13033

So the branch you are looking for is groovy-devel:

rqt:
  doc:
    type: git
    url: https://github.com/ros-visualization/rqt.git
    version: groovy-devel
  release:
    packages:
    - rqt
    - rqt_gui
    - rqt_gui_cpp
    - rqt_gui_py
    - rqt_py_common
    tags:
      release: release/indigo/{package}/{version}
    url: https://github.com/ros-gbp/rqt-release.git
    version: 0.4.8-0
  source:
    type: git
    url: https://github.com/ros-visualization/rqt.git
    version: groovy-devel
  status: maintained

As an alternative you could also use rosinstall_generator to fetch the information for you:

rosinstall_generator --rosdistro indigo rqt --upstream-development

- git:
    local-name: rqt
    uri: https://github.com/ros-visualization/rqt.git
    version: groovy-devel