diff --git a/Make.inc b/Make.inc
index e9cb241198..66f3e6afd7 100644
--- a/Make.inc
+++ b/Make.inc
@@ -185,7 +185,7 @@ USE_GPL_LIBS ?= 1
 # Directories where said libraries get installed to
 prefix ?= $(BUILDROOT)/julia-$(JULIA_COMMIT)
 bindir := $(prefix)/bin
-libdir := $(prefix)/lib
+libdir := $(prefix)/GENTOOLIBDIR
 libexecdir := $(prefix)/libexec
 datarootdir := $(prefix)/share
 docdir := $(datarootdir)/doc/julia
@@ -416,7 +416,7 @@ ifneq ($(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)
@@ -427,7 +427,7 @@ 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
@@ -456,7 +456,7 @@ 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/base/Makefile b/base/Makefile
index acdd4bb9f8..4483149b2b 100644
--- a/base/Makefile
+++ b/base/Makefile
@@ -216,7 +216,6 @@ $(build_private_libdir)/libLLVM.dylib:
 	ln -sf "$$REALPATH" "$@"
 ifneq ($(USE_SYSTEM_LLVM),0)
 ifneq ($(USE_LLVM_SHLIB),0)
-SYMLINK_SYSTEM_LIBRARIES += symlink_libLLVM
 endif
 endif
 
diff --git a/doc/Makefile b/doc/Makefile
index 99e60ee665..2027fb5952 100644
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -30,7 +30,7 @@ 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 e4da8c6357..85a411d9b7 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -50,33 +50,7 @@ ifeq ($(USEMSVC), 1)
 SRCS += getopt
 endif
 
-LLVMLINK :=
-
-ifeq ($(JULIACODEGEN),LLVM)
-SRCS += codegen jitlayers disasm debuginfo llvm-simdloop llvm-ptls llvm-muladd \
-	llvm-late-gc-lowering llvm-lower-handlers llvm-gc-invariant-verifier \
-	llvm-propagate-addrspaces llvm-multiversioning llvm-alloc-opt cgmemmgr \
-	llvm-api
-FLAGS += -I$(shell $(LLVM_CONFIG_HOST) --includedir)
-LLVM_LIBS := all
-ifeq ($(USE_POLLY),1)
-LLVMLINK += -lPolly -lPollyISL
-FLAGS += -I$(shell $(LLVM_CONFIG_HOST) --src-root)/tools/polly/include
-FLAGS += -I$(shell $(LLVM_CONFIG_HOST) --obj-root)/tools/polly/include
-FLAGS += -DUSE_POLLY
-ifeq ($(USE_POLLY_OPENMP),1)
-FLAGS += -fopenmp
-endif
-ifeq ($(USE_POLLY_ACC),1)
-LLVMLINK += -lPollyPPCG -lGPURuntime
-FLAGS += -DUSE_POLLY_ACC
-FLAGS += -I$(shell $(LLVM_CONFIG_HOST) --src-root)/tools/polly/tools # Required to find GPURuntime/GPUJIT.h
-endif
-endif
-else
-SRCS += anticodegen
-LLVM_LIBS := support
-endif
+LLVMLINK = $(call exec,$(LLVM_CONFIG) --ldflags) $(call exec,$(LLVM_CONFIG) --libs) $(call exec,$(LLVM_CONFIG) --ldflags) $(call exec,$(LLVM_CONFIG) --system-libs)
 
 # headers are used for dependency tracking, while public headers will be part of the dist
 UV_HEADERS :=