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Includes should be relative to Mapfile #44
As per http://mapserver.org/mapfile/include.html "File location can be given as a full path to the file, or (in MapServer >= 4.10.1) as a path relative to the mapfile".
Currently includes are relative to their parent file. This should be changed to the parent Mapfile (when not passing a string in directly) to be consistent with MapServer.