diff --git a/Make.inc b/Make.inc
index e77681669..bc17c6fd0 100644
--- a/Make.inc
+++ b/Make.inc
@@ -399,7 +399,7 @@ ifneq ($(OS), WINNT)
 JCXXFLAGS += -pedantic
 endif
 DEBUGFLAGS := -O0 -ggdb2 -DJL_DEBUG_BUILD -fstack-protector-all
-SHIPFLAGS := -O3 -ggdb2 -falign-functions
+SHIPFLAGS := GENTOOCFLAGS
 endif
 
 ifeq ($(USECLANG),1)
@@ -410,7 +410,7 @@ JCFLAGS := -pipe $(fPIC) -fno-strict-aliasing -D_FILE_OFFSET_BITS=64
 JCPPFLAGS := -fasynchronous-unwind-tables
 JCXXFLAGS := -pipe $(fPIC) -fno-rtti -pedantic
 DEBUGFLAGS := -O0 -g -DJL_DEBUG_BUILD -fstack-protector-all
-SHIPFLAGS := -O3 -g
+SHIPFLAGS := GENTOOCFLAGS
 ifeq ($(OS), Darwin)
 ifeq ($(USE_LIBCPP), 1)
 MACOSX_VERSION_MIN := 10.8
@@ -439,7 +439,7 @@ JCFLAGS := -std=gnu11 -pipe $(fPIC) -fno-strict-aliasing -D_FILE_OFFSET_BITS=64
 JCPPFLAGS :=
 JCXXFLAGS := -pipe $(fPIC) -fno-rtti
 DEBUGFLAGS := -O0 -g -DJL_DEBUG_BUILD -fstack-protector-all
-SHIPFLAGS := -O3 -g -falign-functions
+SHIPFLAGS := GENTOOCFLAGS
 endif
 
 ifeq ($(USECCACHE), 1)
diff --git a/doc/Makefile b/doc/Makefile
index 743804d8b..e06dde030 100644
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -25,7 +25,7 @@ deps: UnicodeData.txt
 	$(JLCHECKSUM) UnicodeData.txt
 
 clean:
-	-rm -rf _build/* deps/* docbuild.log UnicodeData.txt
+	@echo "Do not clean doc/_build/html. Just use it..."
 
 cleanall: clean
 
diff --git a/src/Makefile b/src/Makefile
index d3ff98900..9c4d889b4 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -87,14 +87,7 @@ PUBLIC_HEADERS += $(LIBUV_INC)/uv*
 endif
 PUBLIC_HEADER_TARGETS := $(addprefix $(build_includedir)/julia/,$(notdir $(PUBLIC_HEADERS)))
 
-# In LLVM < 3.4, --ldflags includes both options and libraries, so use it both before and after --libs
-# In LLVM >= 3.4, --ldflags has only options, and --system-libs has the libraries.
-ifneq ($(USE_LLVM_SHLIB),1)
-LLVMLINK += $(shell $(LLVM_CONFIG_HOST) --ldflags) $(shell $(LLVM_CONFIG_HOST) --libs $(LLVM_LIBS)) $(shell $(LLVM_CONFIG_HOST) --ldflags) $(shell $(LLVM_CONFIG_HOST) --system-libs 2> /dev/null)
-else
-LLVMLINK += $(shell $(LLVM_CONFIG_HOST) --ldflags) -lLLVM
-FLAGS += -DLLVM_SHLIB
-endif # USE_LLVM_SHLIB == 1
+LLVMLINK = $(call exec,$(LLVM_CONFIG) --ldflags) $(call exec,$(LLVM_CONFIG) --libs) $(call exec,$(LLVM_CONFIG) --ldflags) $(call exec,$(LLVM_CONFIG) --system-libs)
 
 COMMON_LIBS := -L$(build_shlibdir) -L$(build_libdir) $(LIBUV) $(LIBUTF8PROC) $(NO_WHOLE_ARCHIVE) $(LLVMLINK) $(OSLIBS)
 DEBUG_LIBS := $(WHOLE_ARCHIVE) $(BUILDDIR)/flisp/libflisp-debug.a $(WHOLE_ARCHIVE) $(BUILDDIR)/support/libsupport-debug.a $(COMMON_LIBS)