diff --git a/src/Makefile b/src/Makefile
index a6a88d5fb680d..574bd407442c9 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -214,13 +214,13 @@ $(BUILDDIR)/jl_internal_funcs.inc: $(SRCDIR)/jl_exported_funcs.inc
 
 # source file rules
 $(BUILDDIR)/%.o: $(SRCDIR)/%.c $(HEADERS) | $(BUILDDIR)
-	@$(call PRINT_CC, $(CC) $(JCPPFLAGS) $(JCFLAGS) $(SHIPFLAGS) $(DISABLE_ASSERTIONS) -c $< -o $@)
+	@$(call PRINT_CC, $(CC) $(JCPPFLAGS) $(JCFLAGS) $(JL_CFLAGS) $(SHIPFLAGS) $(DISABLE_ASSERTIONS) -c $< -o $@)
 $(BUILDDIR)/%.dbg.obj: $(SRCDIR)/%.c $(HEADERS) | $(BUILDDIR)
-	@$(call PRINT_CC, $(CC) $(JCPPFLAGS) $(JCFLAGS) $(DEBUGFLAGS) -c $< -o $@)
+	@$(call PRINT_CC, $(CC) $(JCPPFLAGS) $(JCFLAGS) $(JL_CFLAGS) $(DEBUGFLAGS) -c $< -o $@)
 $(BUILDDIR)/%.o: $(SRCDIR)/%.cpp $(SRCDIR)/llvm-version.h $(HEADERS) $(LLVM_CONFIG_ABSOLUTE) | $(BUILDDIR)
-	@$(call PRINT_CC, $(CXX) $(LLVM_CXXFLAGS) $(JCPPFLAGS) $(JCXXFLAGS) $(SHIPFLAGS) $(CXX_DISABLE_ASSERTION) -c $< -o $@)
+	@$(call PRINT_CC, $(CXX) $(LLVM_CXXFLAGS) $(JCPPFLAGS) $(JCXXFLAGS) $(JL_CXXFLAGS) $(SHIPFLAGS) $(CXX_DISABLE_ASSERTION) -c $< -o $@)
 $(BUILDDIR)/%.dbg.obj: $(SRCDIR)/%.cpp $(SRCDIR)/llvm-version.h $(HEADERS) $(LLVM_CONFIG_ABSOLUTE) | $(BUILDDIR)
-	@$(call PRINT_CC, $(CXX) $(LLVM_CXXFLAGS) $(JCPPFLAGS) $(JCXXFLAGS) $(DEBUGFLAGS) -c $< -o $@)
+	@$(call PRINT_CC, $(CXX) $(LLVM_CXXFLAGS) $(JCPPFLAGS) $(JCXXFLAGS) $(JL_CXXFLAGS) $(DEBUGFLAGS) -c $< -o $@)
 $(BUILDDIR)/%.o : $(SRCDIR)/%.d
 	@$(call PRINT_DTRACE, $(DTRACE) -G -s $< -o $@)
 $(BUILDDIR)/%.dbg.obj : $(SRCDIR)/%.d
@@ -247,7 +247,7 @@ else
 JULIA_SPLITDEBUG := 0
 endif
 $(build_shlibdir)/libccalltest.$(SHLIB_EXT): $(SRCDIR)/ccalltest.c
-	@$(call PRINT_CC, $(CC) $(JCFLAGS) $(JCPPFLAGS) $(FLAGS) -O3 $< $(fPIC) -shared -o $@.tmp $(LDFLAGS))
+	@$(call PRINT_CC, $(CC) $(JCFLAGS) $(JL_CFLAGS) $(JCPPFLAGS) $(FLAGS) -O3 $< $(fPIC) -shared -o $@.tmp $(LDFLAGS))
 	$(INSTALL_NAME_CMD)libccalltest.$(SHLIB_EXT) $@.tmp
 ifeq ($(JULIA_SPLITDEBUG),1)
 	@# Create split debug info file for libccalltest stacktraces test
@@ -352,13 +352,13 @@ $(BUILDDIR)/julia_version.h: $(JULIAHOME)/VERSION
 CXXLD = $(CXX) -shared
 
 $(build_shlibdir)/libjulia-internal.$(JL_MAJOR_MINOR_SHLIB_EXT): $(SRCDIR)/julia.expmap $(OBJS) $(BUILDDIR)/flisp/libflisp.a $(BUILDDIR)/support/libsupport.a $(LIBUV)
-	@$(call PRINT_LINK, $(CXXLD) $(call IMPLIB_FLAGS,$@) $(JCXXFLAGS) $(CXXLDFLAGS) $(SHIPFLAGS) $(OBJS) $(RPATH_LIB) -o $@ \
+	@$(call PRINT_LINK, $(CXXLD) $(call IMPLIB_FLAGS,$@) $(JCXXFLAGS) $(JL_CXXFLAGS) $(CXXLDFLAGS) $(SHIPFLAGS) $(OBJS) $(RPATH_LIB) -o $@ \
 		$(JLDFLAGS) $(JLIBLDFLAGS) $(RT_RELEASE_LIBS) $(call SONAME_FLAGS,libjulia-internal.$(JL_MAJOR_SHLIB_EXT)))
 	@$(INSTALL_NAME_CMD)libjulia-internal.$(SHLIB_EXT) $@
 	$(DSYMUTIL) $@
 
 $(build_shlibdir)/libjulia-internal-debug.$(JL_MAJOR_MINOR_SHLIB_EXT): $(SRCDIR)/julia.expmap $(DOBJS) $(BUILDDIR)/flisp/libflisp-debug.a $(BUILDDIR)/support/libsupport-debug.a $(LIBUV)
-	@$(call PRINT_LINK, $(CXXLD) $(call IMPLIB_FLAGS,$@) $(JCXXFLAGS) $(CXXLDFLAGS) $(DEBUGFLAGS) $(DOBJS) $(RPATH_LIB) -o $@ \
+	@$(call PRINT_LINK, $(CXXLD) $(call IMPLIB_FLAGS,$@) $(JCXXFLAGS) $(JL_CXXFLAGS) $(CXXLDFLAGS) $(DEBUGFLAGS) $(DOBJS) $(RPATH_LIB) -o $@ \
 		$(JLDFLAGS) $(JLIBLDFLAGS) $(RT_DEBUG_LIBS) $(call SONAME_FLAGS,libjulia-internal-debug.$(JL_MAJOR_SHLIB_EXT)))
 	@$(INSTALL_NAME_CMD)libjulia-internal-debug.$(SHLIB_EXT) $@
 	$(DSYMUTIL) $@
@@ -378,13 +378,13 @@ libjulia-internal-debug: $(build_shlibdir)/libjulia-internal-debug.$(JL_MAJOR_MI
 libjulia-internal-debug libjulia-internal-release: $(PUBLIC_HEADER_TARGETS)
 
 $(build_shlibdir)/libjulia-codegen.$(JL_MAJOR_MINOR_SHLIB_EXT): $(SRCDIR)/julia.expmap $(CODEGEN_OBJS) $(BUILDDIR)/support/libsupport.a $(build_shlibdir)/libjulia-internal.$(JL_MAJOR_MINOR_SHLIB_EXT)
-	@$(call PRINT_LINK, $(CXXLD) $(call IMPLIB_FLAGS,$@) $(JCXXFLAGS) $(CXXLDFLAGS) $(SHIPFLAGS) $(CODEGEN_OBJS) $(RPATH_LIB) -o $@ \
+	@$(call PRINT_LINK, $(CXXLD) $(call IMPLIB_FLAGS,$@) $(JCXXFLAGS) $(JL_CXXFLAGS) $(CXXLDFLAGS) $(SHIPFLAGS) $(CODEGEN_OBJS) $(RPATH_LIB) -o $@ \
 		$(JLDFLAGS) $(JLIBLDFLAGS) $(CG_RELEASE_LIBS) $(call SONAME_FLAGS,libjulia-codegen.$(JL_MAJOR_SHLIB_EXT)))
 	@$(INSTALL_NAME_CMD)libjulia-codegen.$(SHLIB_EXT) $@
 	$(DSYMUTIL) $@
 
 $(build_shlibdir)/libjulia-codegen-debug.$(JL_MAJOR_MINOR_SHLIB_EXT): $(SRCDIR)/julia.expmap $(CODEGEN_DOBJS) $(BUILDDIR)/support/libsupport-debug.a $(build_shlibdir)/libjulia-internal-debug.$(JL_MAJOR_MINOR_SHLIB_EXT)
-	@$(call PRINT_LINK, $(CXXLD) $(call IMPLIB_FLAGS,$@) $(JCXXFLAGS) $(CXXLDFLAGS) $(DEBUGFLAGS) $(CODEGEN_DOBJS) $(RPATH_LIB) -o $@ \
+	@$(call PRINT_LINK, $(CXXLD) $(call IMPLIB_FLAGS,$@) $(JCXXFLAGS) $(JL_CXXFLAGS) $(CXXLDFLAGS) $(DEBUGFLAGS) $(CODEGEN_DOBJS) $(RPATH_LIB) -o $@ \
 		$(JLDFLAGS) $(JLIBLDFLAGS) $(CG_DEBUG_LIBS) $(call SONAME_FLAGS,libjulia-codegen-debug.$(JL_MAJOR_SHLIB_EXT)))
 	@$(INSTALL_NAME_CMD)libjulia-codegen-debug.$(SHLIB_EXT) $@
 	$(DSYMUTIL) $@
@@ -443,11 +443,11 @@ clangsa: $(build_shlibdir)/libImplicitAtomicsPlugin.$(SHLIB_EXT)
 clang-sagc-%: $(SRCDIR)/%.c $(build_shlibdir)/libGCCheckerPlugin.$(SHLIB_EXT) .FORCE | analyzegc-deps-check
 	@$(call PRINT_ANALYZE, $(build_depsbindir)/clang -D__clang_gcanalyzer__ --analyze -Xanalyzer -analyzer-werror -Xanalyzer -analyzer-output=text --analyzer-no-default-checks \
 		-Xclang -load -Xclang $(build_shlibdir)/libGCCheckerPlugin.$(SHLIB_EXT) -Xclang -analyzer-checker=core$(COMMA)julia.GCChecker \
-		$(CLANGSA_FLAGS) $(JCPPFLAGS) $(JCFLAGS) $(DEBUGFLAGS) -fcolor-diagnostics -x c $<)
+		$(CLANGSA_FLAGS) $(JCPPFLAGS) $(JCFLAGS) $(JL_CFLAGS) $(DEBUGFLAGS) -fcolor-diagnostics -x c $<)
 clang-sagc-%: $(SRCDIR)/%.cpp $(build_shlibdir)/libGCCheckerPlugin.$(SHLIB_EXT) .FORCE | analyzegc-deps-check
 	@$(call PRINT_ANALYZE, $(build_depsbindir)/clang -D__clang_gcanalyzer__ --analyze -Xanalyzer -analyzer-werror -Xanalyzer -analyzer-output=text --analyzer-no-default-checks \
 		-Xclang -load -Xclang $(build_shlibdir)/libGCCheckerPlugin.$(SHLIB_EXT) -Xclang -analyzer-checker=core$(COMMA)julia.GCChecker \
-		$(CLANGSA_FLAGS) $(CLANGSA_CXXFLAGS) $(LLVM_CXXFLAGS) $(JCPPFLAGS) $(JCXXFLAGS) $(DEBUGFLAGS) -fcolor-diagnostics -x c++ $<)
+		$(CLANGSA_FLAGS) $(CLANGSA_CXXFLAGS) $(LLVM_CXXFLAGS) $(JCPPFLAGS) $(JCXXFLAGS) $(JL_CXXFLAGS) $(DEBUGFLAGS) -fcolor-diagnostics -x c++ $<)
 
  # optarg is a required_argument for these
 SA_EXCEPTIONS-jloptions.c                   := -Xanalyzer -analyzer-disable-checker=core.NonNullParamChecker,unix.cstring.NullArg
@@ -462,23 +462,23 @@ clang-sa-%: $(SRCDIR)/%.c $(build_shlibdir)/libImplicitAtomicsPlugin.$(SHLIB_EXT
 		-Xanalyzer -analyzer-disable-checker=deadcode.DeadStores \
 		 --analyzer-no-default-checks  \
 		$(SA_EXCEPTIONS-$(notdir $<)) \
-		$(CLANGSA_FLAGS) $(JCPPFLAGS) $(JCFLAGS) $(DEBUGFLAGS) -fcolor-diagnostics -Werror -x c $<)
+		$(CLANGSA_FLAGS) $(JCPPFLAGS) $(JCFLAGS) $(JL_CFLAGS) $(DEBUGFLAGS) -fcolor-diagnostics -Werror -x c $<)
 clang-sa-%: $(SRCDIR)/%.cpp $(build_shlibdir)/libImplicitAtomicsPlugin.$(SHLIB_EXT) .FORCE | analyzegc-deps-check
 	@$(call PRINT_ANALYZE, $(build_depsbindir)/clang --analyze -Xanalyzer -analyzer-werror -Xanalyzer -analyzer-output=text \
 		$(if $(findstring $(notdir $<),$(SKIP_IMPLICIT_ATOMICS)),,-Xclang -load -Xclang $(build_shlibdir)/libImplicitAtomicsPlugin.$(SHLIB_EXT) -Xclang -analyzer-checker=julia.ImplicitAtomics) \
 		-Xanalyzer -analyzer-disable-checker=deadcode.DeadStores \
 		 --analyzer-no-default-checks  \
 		$(SA_EXCEPTIONS-$(notdir $<)) \
-		$(CLANGSA_FLAGS) $(CLANGSA_CXXFLAGS) $(LLVM_CXXFLAGS) $(JCPPFLAGS) $(JCXXFLAGS) $(DEBUGFLAGS) -fcolor-diagnostics -Werror -x c++ $<)
+		$(CLANGSA_FLAGS) $(CLANGSA_CXXFLAGS) $(LLVM_CXXFLAGS) $(JCPPFLAGS) $(JCXXFLAGS) $(JL_CXXFLAGS) $(DEBUGFLAGS) -fcolor-diagnostics -Werror -x c++ $<)
 
 clang-tidy-%: $(SRCDIR)/%.c $(build_shlibdir)/libImplicitAtomics2Plugin.$(SHLIB_EXT) .FORCE | analyzegc-deps-check
 	@$(call PRINT_ANALYZE, $(build_depsbindir)/clang-tidy $< -header-filter='.*' --quiet \
 		-load $(build_shlibdir)/libImplicitAtomics2Plugin.$(SHLIB_EXT) --checks='-clang-analyzer-*$(COMMA)-clang-diagnostic-*$(COMMA)concurrency-implicit-atomics' --warnings-as-errors='*' \
-		-- $(CLANGSA_FLAGS) $(JCPPFLAGS) $(JCFLAGS) $(DEBUGFLAGS) -fcolor-diagnostics -fno-caret-diagnostics -x c)
+		-- $(CLANGSA_FLAGS) $(JCPPFLAGS) $(JCFLAGS) $(JL_CFLAGS) $(DEBUGFLAGS) -fcolor-diagnostics -fno-caret-diagnostics -x c)
 clang-tidy-%: $(SRCDIR)/%.cpp $(build_shlibdir)/libImplicitAtomics2Plugin.$(SHLIB_EXT) .FORCE | analyzegc-deps-check
 	@$(call PRINT_ANALYZE, $(build_depsbindir)/clang-tidy $< -header-filter='.*' --quiet \
 		-load $(build_shlibdir)/libImplicitAtomics2Plugin.$(SHLIB_EXT) --checks='-clang-analyzer-*$(COMMA)-clang-diagnostic-*$(COMMA)concurrency-implicit-atomics' --warnings-as-errors='*' \
-		-- $(CLANGSA_FLAGS) $(CLANGSA_CXXFLAGS) $(LLVM_CXXFLAGS) $(JCPPFLAGS) $(JCXXFLAGS) $(DEBUGFLAGS) -fcolor-diagnostics --system-header-prefix=llvm -Wno-deprecated-declarations -fno-caret-diagnostics -x c++)
+		-- $(CLANGSA_FLAGS) $(CLANGSA_CXXFLAGS) $(LLVM_CXXFLAGS) $(JCPPFLAGS) $(JCXXFLAGS) $(JL_CXXFLAGS) $(DEBUGFLAGS) -fcolor-diagnostics --system-header-prefix=llvm -Wno-deprecated-declarations -fno-caret-diagnostics -x c++)
 
 
 # Add C files as a target of `analyzesrc` and `analyzegc` and `tidysrc`