'pthread.h' is not the only file that needs to be symlinked. When NPTL gets merged, you will need to do 'semaphore.h' and 'bits/pthreadtypes.h'. I think I have been a good little boy and keeping my NPTL changes out of mainline, so I'm going to go ahead and cross the line this once to get this change in.

Makefile

@@ -350,6 +350,7 @@ clean:
 	$(MAKE) -C libc/sysdeps/linux/common clean
 	$(MAKE) -C extra/locale clean
 	$(MAKE) -C utils clean
+	$(MAKE) -C libpthread clean
 	@set -e; \
 	for i in `(cd $(TOPDIR)/libc/sysdeps/linux/common/sys; ls *.h)` ; do \
 		$(RM) include/sys/$$i; \

libpthread/Makefile

@@ -49,7 +49,18 @@ LIBTHREAD_DB_LDFLAGS := $(subst -z defs,,$(LDFLAGS))
 all: $(LIBPTHREAD) $(LIBTHREAD_DB)
 
 headers:
-	$(LN) -sf $(TOPDIR)libpthread/linuxthreads/sysdeps/pthread/pthread.h $(TOPDIR)include/pthread.h
+ifeq ($(strip $(UCLIBC_HAS_THREADS_NATIVE)),y)
+	$(LN) -sf $(TOPDIR)libpthread/nptl/sysdeps/pthread/pthread.h $(TOPDIR)include
+	$(LN) -sf $(TOPDIR)libpthread/nptl/semaphore.h $(TOPDIR)include
+	$(LN) -sf ../$(TOPDIR)libpthread/nptl/sysdeps/unix/sysv/linux/$(TARGET_ARCH)/bits/semaphore.h $(TOPDIR)include/bits
+	$(LN) -sf ../$(TOPDIR)libpthread/nptl/sysdeps/unix/sysv/linux/$(TARGET_ARCH)/bits/pthreadtypes.h $(TOPDIR)include/bits
+	$(LN) -sf ../$(TOPDIR)libpthread/nptl/sysdeps/pthread/bits/libc-lock.h $(TOPDIR)include/bits
+	$(LN) -sf ../$(TOPDIR)libpthread/nptl/sysdeps/pthread/bits/stdio-lock.h $(TOPDIR)include/bits
+else
+	$(LN) -sf $(TOPDIR)libpthread/linuxthreads/sysdeps/pthread/pthread.h $(TOPDIR)include
+	$(LN) -sf $(TOPDIR)libpthread/linuxthreads/semaphore.h $(TOPDIR)include
+	$(LN) -sf ../$(TOPDIR)libpthread/linuxthreads/sysdeps/pthread/bits/pthreadtypes.h $(TOPDIR)include/bits
+endif
 
 $(LIBPTHREAD): subdirs
 ifeq ($(strip $(UCLIBC_HAS_THREADS)),y)
@@ -117,6 +128,7 @@ $(patsubst %, _dirclean_%, $(ALL_SUBDIRS)) : dummy
 
 clean: subdirs_clean
 	$(RM) *.[oa] *~ core $(LIBPTHREAD) $(LIBPTHREAD_SHARED_FULLNAME) \
-		$(LIBTHREAD_DB) $(LIBTHREAD_DB_SHARED_FULLNAME)
+		$(LIBTHREAD_DB) $(LIBTHREAD_DB_SHARED_FULLNAME)		 \
+		$(RM) $(TOPDIR)include/pthread.h $(TOPDIR)include/semaphore.h
 
 .PHONY: dummy