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How, you are dealing with your CmakeLists.txt ?

you should have fields below, in order to create header file of your custom message

find_package(catkin REQUIRED COMPONENTS
  message_generation
  std_msgs
)

add_message_files(
  FILES
  YourCustomMessage.msg
)

generate_messages(
  DEPENDENCIES
  std_msgs
)

catkin_package(
  CATKIN_DEPENDS message_runtime std_msgs
)

in your package.xml you need to depend on correct packages;

  <build_depend>message_generation</build_depend>
  <exec_depend>message_runtime</exec_depend>
  <depend>std_msgs</depend>

and finally, your .msg file should be under msg folder in the project root directory