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I don't see it in the tutorials anymore, but there's a command (at least there was in groovy) called catkin_init_workspace that I was under the impression needed to be run in the overall catkin workspace (not the src folder) before catkin_make was run. Things might have changed, but it's worth looking into.

$ catkin_init_workspace -h
usage: catkin_init_workspace [-h] [workspace]

Initializes a catkin workspace by creating a top-level CMakeLists.txt.

positional arguments:
  workspace   The path to an existing folder (default: .)

optional arguments:
  -h, --help  show this help message and exit