diff -up doxygen-1.8.15/src/dirdef.cpp.me doxygen-1.8.15/src/dirdef.cpp

--- doxygen-1.8.15/src/dirdef.cpp.me	2019-02-14 22:57:29.709491363 +0100

+++ doxygen-1.8.15/src/dirdef.cpp	2019-02-14 22:59:10.922169840 +0100

@@ -936,14 +936,14 @@ void buildDirectories()

     for (;(fd=fni.current());++fni)

     {

       //printf("buildDirectories %s\n",fd->name().data());

-      if (fd->getReference().isEmpty())

+      if (fd->getReference().isEmpty() && !fd->isDocumentationFile())

       {

         DirDef *dir;

         if ((dir=Doxygen::directories->find(fd->getPath()))==0) // new directory

         {

           dir = DirDef::mergeDirectoryInTree(fd->getPath());

         }

-        if (dir && !fd->isDocumentationFile()) dir->addFile(fd);

+        if (dir) dir->addFile(fd);

       }

       else

       {