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Most likely the problem is that the folder in which the generated header file is stored is not being added as an include directory to be searched.
The recommended practice when creating custom messages is to create a new package just for the messages. Then you can depend on that from the package that wants to use the messages, and by the time it gets compiled the custom messages' header files have been installed into the correct location to be found by the include file search.
Take a look at the example_interfaces
package to see what a messages-only package looks like.