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
       {