diff --git a/Makefile.in b/Makefile.in
index af21ab4fac2..05b62157de9 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -206,9 +206,6 @@ endef
 $(foreach target,$(CFG_TARGET),\
   $(eval $(call DEF_X,$(target))))
 
-# Look in doc and src dirs.
-VPATH := $(S)doc $(S)src
-
 # "Source" files we generate in builddir along the way.
 GENERATED :=
 
diff --git a/mk/rt.mk b/mk/rt.mk
index 269491649bb..f2226b1ae3e 100644
--- a/mk/rt.mk
+++ b/mk/rt.mk
@@ -67,13 +67,14 @@ NATIVE_DEPS_morestack_$(1) := arch/$$(HOST_$(1))/morestack.S
 
 RT_OUTPUT_DIR_$(1) := $(1)/rt
 
-$$(RT_OUTPUT_DIR_$(1))/%.o: rt/%.ll $$(MKFILE_DEPS) $$(LLVM_CONFIG_$$(CFG_BUILD))
+$$(RT_OUTPUT_DIR_$(1))/%.o: $(S)src/rt/%.ll $$(MKFILE_DEPS) \
+	    $$(LLVM_CONFIG_$$(CFG_BUILD))
 	@mkdir -p $$(@D)
 	@$$(call E, compile: $$@)
 	$$(Q)$$(LLC_$$(CFG_BUILD)) $$(CFG_LLC_FLAGS_$(1)) \
 	    -filetype=obj -mtriple=$(1) -relocation-model=pic -o $$@ $$<
 
-$$(RT_OUTPUT_DIR_$(1))/%.o: rt/%.c $$(MKFILE_DEPS)
+$$(RT_OUTPUT_DIR_$(1))/%.o: $(S)src/rt/%.c $$(MKFILE_DEPS)
 	@mkdir -p $$(@D)
 	@$$(call E, compile: $$@)
 	$$(Q)$$(call CFG_COMPILE_C_$(1), $$@, \
@@ -81,7 +82,8 @@ $$(RT_OUTPUT_DIR_$(1))/%.o: rt/%.c $$(MKFILE_DEPS)
 		-I $$(S)src/libuv/include -I $$(S)src/rt \
                  $$(RUNTIME_CFLAGS_$(1))) $$<
 
-$$(RT_OUTPUT_DIR_$(1))/%.o: rt/%.S $$(MKFILE_DEPS) $$(LLVM_CONFIG_$$(CFG_BUILD))
+$$(RT_OUTPUT_DIR_$(1))/%.o: $(S)src/rt/%.S $$(MKFILE_DEPS) \
+	    $$(LLVM_CONFIG_$$(CFG_BUILD))
 	@mkdir -p $$(@D)
 	@$$(call E, compile: $$@)
 	$$(Q)$$(call CFG_ASSEMBLE_$(1),$$@,$$<)
diff --git a/mk/rustllvm.mk b/mk/rustllvm.mk
index 8d7abc020cc..a62386818c1 100644
--- a/mk/rustllvm.mk
+++ b/mk/rustllvm.mk
@@ -37,7 +37,7 @@ $$(RT_OUTPUT_DIR_$(1))/$$(call CFG_STATIC_LIB_NAME_$(1),rustllvm): \
 	@$$(call E, link: $$@)
 	$$(Q)$$(AR_$(1)) rcs $$@ $$(RUSTLLVM_OBJS_OBJS_$(1))
 
-$(1)/rustllvm/%.o: rustllvm/%.cpp $$(MKFILE_DEPS) $$(LLVM_CONFIG_$(1))
+$(1)/rustllvm/%.o: $(S)src/rustllvm/%.cpp $$(MKFILE_DEPS) $$(LLVM_CONFIG_$(1))
 	@$$(call E, compile: $$@)
 	$$(Q)$$(call CFG_COMPILE_CXX_$(1), $$@, $$(LLVM_CXXFLAGS_$(1)) $$(RUSTLLVM_INCS_$(1))) $$<
 endef