diff --git a/coupled_AM2_LM3_SIS2/Makefile b/coupled_AM2_LM3_SIS2/Makefile
index b0871f6abc..7f6ec559e3 100644
--- a/coupled_AM2_LM3_SIS2/Makefile
+++ b/coupled_AM2_LM3_SIS2/Makefile
@@ -4,10 +4,11 @@ MOM_MEMORY ?=
 SIS_MEMORY ?=
 
 # Dependencies
-FMS_BUILD ?= ../shared/fms/build
+FMS_CODEBASE ?= ../src/FMS1
+FMS_BUILD ?= ../shared/fms/build_fms1
 AM2_BUILD ?= ../shared/AM2/build
-ICEBERGS_BUILD ?= ../shared/icebergs/build
-ICE_PARAM_BUILD ?= ../shared/ice_param/build
+ICEBERGS_BUILD ?= ../shared/icebergs/build_fms1
+ICE_PARAM_BUILD ?= ../shared/ice_param/build_fms1
 LM3_BUILD ?= ../shared/LM3/build
 
 # Autoconf configuration
@@ -32,6 +33,7 @@ EXTRA_SRC_DIRS = \
 CONFIG_FLAGS := --config-cache
 CONFIG_FLAGS += --srcdir=$(abspath $(MOM_CODEBASE))
 CONFIG_FLAGS += --with-driver=FMS_cap
+CONFIG_FLAGS += --with-framework=fms1
 ifdef MOM_MEMORY
   CONFIG_FLAGS += MOM_MEMORY=$(abspath $(MOM_MEMORY))
 endif
@@ -46,7 +48,7 @@ FCFLAGS ?= -g -O2
 # Path to fms_platform.h
 # NOTE: Most libraries need an explicit path to this file.  Someday, this could
 #   be handled by library-specific autoconf tests.
-FCFLAGS += -I$(abspath ../src/FMS/include)
+FCFLAGS += -I$(abspath $(FMS_CODEBASE)/include)
 
 MOM_FCFLAGS = $(FCFLAGS) \
   -I$(abspath $(FMS_BUILD)) \
@@ -170,7 +172,8 @@ $(ICEBERGS_BUILD)/libicebergs.a: FORCE $(FMS_BUILD)/libFMS.a
 
 $(FMS_BUILD)/libFMS.a: FORCE
 	$(MAKE) -C ../shared/fms \
-	  BUILD=$(abspath $(FMS_BUILD))
+	  BUILD=$(abspath $(FMS_BUILD)) \
+	  CODEBASE=$(abspath $(FMS_CODEBASE))
 
 FORCE:
 
@@ -230,11 +233,16 @@ $(foreach expt,$(EXPTS),$(eval $(call EXPT_RULE,$(expt))))
 .PHONY: clean
 clean:
 	rm -rf $(BUILD)
-	$(MAKE) -C ../shared/AM2 clean
+	$(MAKE) -C ../shared/AM2 clean \
+	  BUILD=$(abspath $(AM2_BUILD))
 	$(MAKE) -C ../shared/LM3 clean
-	$(MAKE) -C ../shared/ice_param clean
-	$(MAKE) -C ../shared/icebergs clean
-	$(MAKE) -C ../shared/fms clean
+	  BUILD=$(abspath $(LM3_BUILD))
+	$(MAKE) -C ../shared/ice_param clean \
+	  BUILD=$(abspath $(ICE_PARAM_BUILD))
+	$(MAKE) -C ../shared/icebergs clean \
+	  BUILD=$(abspath $(ICEBERGS_BUILD))
+	$(MAKE) -C ../shared/fms clean \
+	  BUILD=$(abspath $(FMS_BUILD))
 
 .PHONY: clean.runs
 clean.runs: $(foreach e,$(EXPTS),clean.$(e))
diff --git a/ice_ocean_SIS2/Makefile b/ice_ocean_SIS2/Makefile
index 69ea3b7629..bfd1020c40 100644
--- a/ice_ocean_SIS2/Makefile
+++ b/ice_ocean_SIS2/Makefile
@@ -4,6 +4,7 @@ MOM_MEMORY ?=
 SIS_MEMORY ?=
 
 # Dependencies
+FMS_CODEBASE ?= ../src/FMS2
 FMS_BUILD ?= ../shared/fms/build
 ICEBERGS_BUILD ?= ../shared/icebergs/build
 ICE_PARAM_BUILD ?= ../shared/ice_param/build
@@ -172,7 +173,8 @@ $(ICEBERGS_BUILD)/libicebergs.a: FORCE $(FMS_BUILD)/libFMS.a
 
 $(FMS_BUILD)/libFMS.a: FORCE
 	$(MAKE) -C ../shared/fms \
-	  BUILD=$(abspath $(FMS_BUILD))
+	  BUILD=$(abspath $(FMS_BUILD)) \
+	  CODEBASE=$(abspath $(FMS_CODEBASE))
 
 FORCE:
 
diff --git a/ocean_only/Makefile b/ocean_only/Makefile
index b3e72cf679..5ca3e909cb 100644
--- a/ocean_only/Makefile
+++ b/ocean_only/Makefile
@@ -3,6 +3,7 @@ BUILD ?= build
 MOM_MEMORY ?=
 
 # Dependencies
+FMS_CODEBASE ?= ../src/FMS2
 FMS_BUILD ?= ../shared/fms/build
 
 # Autoconf configuration
@@ -104,7 +105,9 @@ $(BUILD):
 # Dependencies
 
 $(FMS_BUILD)/libFMS.a: FORCE
-	$(MAKE) -C ../shared/fms BUILD=$(abspath $(FMS_BUILD))
+	$(MAKE) -C ../shared/fms \
+	  BUILD=$(abspath $(FMS_BUILD)) \
+	  CODEBASE=$(abspath $(FMS_CODEBASE))
 
 FORCE:
 
diff --git a/shared/AM2/Makefile b/shared/AM2/Makefile
index 8540b8c7e5..a82c314215 100644
--- a/shared/AM2/Makefile
+++ b/shared/AM2/Makefile
@@ -1,6 +1,7 @@
 # Configuration
 BUILD ?= build
 FMS_BUILD ?= ../fms/build
+FMS_CODEBASE ?= ../../src/FMS1
 
 TARGET = libAM2.a
 CODEBASE = ../../src/AM2
@@ -13,7 +14,7 @@ SRCDIRS = $(addprefix $(abspath $(CODEBASE))/, \
   atmos_param_am3)
 
 FCFLAGS += -I$(abspath $(FMS_BUILD))
-FCFLAGS += -I$(abspath ../../src/FMS/include)
+FCFLAGS += -I$(abspath $(FMS_CODEBASE)/include)
 
 LDFLAGS += -L$(abspath $(FMS_BUILD))
 
diff --git a/shared/config/Libs.mk b/shared/config/Libs.mk
index d9d8c677c1..0d0cc354ca 100644
--- a/shared/config/Libs.mk
+++ b/shared/config/Libs.mk
@@ -10,6 +10,10 @@ MAKEPATH = $(realpath $(dir $(abspath $(lastword $(MAKEFILE_LIST)))))
 M4DIR ?= $(MAKEPATH)/../../src/MOM6/ac/m4
 MAKEDEP = $(MAKEPATH)/../../src/MOM6/ac/makedep
 
+# `export` disables autoconf defaults; this restores them
+CFLAGS ?= -g -O2
+FCFLAGS ?= -g -O2
+
 # Autoconf configuration
 export CPPFLAGS
 export CC
diff --git a/shared/fms/Makefile b/shared/fms/Makefile
index e626737fd0..43f7ab7103 100644
--- a/shared/fms/Makefile
+++ b/shared/fms/Makefile
@@ -1,7 +1,7 @@
 # Configuration
 BUILD ?= build
+CODEBASE ?= ../../src/FMS2
 
-CODEBASE = ../../src/FMS
 TARGET = libFMS.a
 MAKEFILE_IN = ../../src/MOM6/ac/deps/Makefile.fms.in
 CONFIGURE_AC = ../../src/MOM6/ac/deps/configure.fms.ac
diff --git a/src/MOM6 b/src/MOM6
index 5137442fc9..714d2da17e 160000
--- a/src/MOM6
+++ b/src/MOM6
@@ -1 +1 @@
-Subproject commit 5137442fc91aced5162e00f5b8d2a1b5906b8e32
+Subproject commit 714d2da17ed29d34f73e88513192acb9439e1061