It looks straightforward to fix this for posix builds. There is a small binary called makeHeader which does the necessary work of concatenating and cleaning the header files. It is just a question of adding jrd/ntrace.h to the list of files to process.
It is also necessary to comment out the line '//#include "firebird/Interface.h"' in ntrace.h otherwise empbuild doesn't build.
It is more difficult on windows because we do not have a good way to generate header files. There is one version in make_all.bat which just concatenates them. The result is that all the license templates are repeated. BuildExecutableInstall.bat removes all the license templates apart from the first, but also removes all the comments. This was OK a long time ago when I first wrote that script. It is not OK now as some of the comments are the only documentation.
The order of concatenation in all three instances is different, too.
The ideal solution for windows would be to incorporate makeHeader into the windows build process but in the meantime I shall modify the existing windows batch files.