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The problem only arises with catkin_make which builds all packages in a single CMake context.

The package A needs to add the target(s) which generate the files to the following variable which will be exported through the CMake config file of the package:

list(APPEND ${PROJECT_NAME}_EXPORTED_TARGETS <your-target-name(s)-here>)

And package B needs to add a proper target dependency onto the value of the exported variable for all target which need the generated files:

add_dependency(<your-library-or-executable-target> ${a_exported_targets})