In my project, I do most of my coding in headers files.
However, the include directory is not bolded like the cpp directory and things like code intentions/intellisense don't work in these files (they work fine in .cpp files). It's as if CLion thinks my headers are external source. Classes defined in the headers also do not show up in searches unless I do Cmd-Shift-N a few times (I'm on mac).
I also have another project where this sort of structure is fine, I'm not sure what the magic setting/cmake configuration is required to make this work.