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While knowing more specifics about which package you're looking at would help give a more confident answer, I think the following may help:

  1. Add a new top-level CMakeLists.txt file in the location catkin is expecting
  2. Fill it with the basics (cmake_mininum_required(..), project(...), etc.)
  3. Use add_subdirectory(cmake) to tell catkin to look in the 'cmake' directory for another CMakeLists.txt file