Index: lib/libnv/Makefile
===================================================================
--- lib/libnv/Makefile
+++ lib/libnv/Makefile
@@ -9,7 +9,10 @@
 SHLIB_MAJOR= 0
 
 .PATH: ${SRCTOP}/sys/contrib/libnv ${SRCTOP}/sys/sys
-CFLAGS+=-I${SRCTOP}/sys -I${.CURDIR}
+.ifndef BOOTSTRAPPING
+CFLAGS+=-I${SRCTOP}/sys
+.endif
+CFLAGS+=-I${.CURDIR}
 
 SRCS=	cnvlist.c
 SRCS+=	dnvlist.c
Index: tools/build/mk/Makefile.boot
===================================================================
--- tools/build/mk/Makefile.boot
+++ tools/build/mk/Makefile.boot
@@ -7,3 +7,15 @@
 
 # we do not want to capture dependencies referring to the above
 UPDATE_DEPENDFILE= no
+
+.if !empty(CFLAGS:M*${SRCTOP}/sys*)
+.error Do not include $${SRCTOP}/sys when building bootstrap tools. \
+    Copy the header to ${WORLDTMP}/legacy in tools/build/Makefile instead. \
+    Error was caused by Makefile in ${.PARSEDIR}
+.endif
+
+.if !empty(CFLAGS:M*${SRCTOP}/include*)
+.error Do not include $${SRCTOP}/include when building bootstrap tools. \
+    Copy the header to ${WORLDTMP}/legacy in tools/build/Makefile instead. \
+    Error was caused by Makefile in ${.PARSEDIR}
+.endif