diff --git a/.testing/Makefile b/.testing/Makefile
index a1461fe7ab..8ca3fe21eb 100644
--- a/.testing/Makefile
+++ b/.testing/Makefile
@@ -133,9 +133,6 @@ TIME ?= time
 WORKSPACE ?= .
 
 # Set directories for build/ and work/
-#BUILD ?= $(WORKSPACE)build
-#DEPS ?= $(BUILD)/deps
-#WORK ?= $(WORKSPACE)work
 BUILD ?= $(WORKSPACE)/build
 DEPS ?= $(BUILD)/deps
 WORK ?= $(WORKSPACE)/work
@@ -207,34 +204,6 @@ else
 endif
 
 
-# List of source files to link this Makefile's dependencies to model Makefiles
-# Assumes a depth of two, and the following extensions: F90 inc c h
-# (1): Root directory
-# NOTE: extensions could be a second variable
-SOURCE = \
-  $(foreach ext,F90 inc c h,$(wildcard $(1)/*/*.$(ext) $(1)/*/*/*.$(ext)))
-
-MOM_SOURCE = \
-  $(call SOURCE,../src) \
-  $(wildcard ../config_src/drivers/solo_driver/*.F90) \
-  $(wildcard ../config_src/ext*/*/*.F90)
-
-TARGET_SOURCE = \
-  $(call SOURCE,$(BUILD)/target_codebase/src) \
-  $(wildcard $(BUILD)/target_codebase/config_src/drivers/solo_driver/*.F90) \
-  $(wildcard $(BUILD)target_codebase/config_src/ext*/*.F90)
-
-ifeq ($(FRAMEWORK), fms1)
-  MOM_SOURCE += $(wildcard ../config_src/infra/FMS1/*.F90)
-  TARGET_SOURCE += $(wildcard $(BUILD)/target_codebase/config_src/infra/FMS1/*.F90)
-else
-  MOM_SOURCE +=$(wildcard ../config_src/infra/FMS2/*.F90)
-  TARGET_SOURCE += $(wildcard $(BUILD)/target_codebase/config_src/infra/FMS2/*.F90)
-endif
-
-FMS_SOURCE = $(call SOURCE,$(DEPS)/fms/src)
-
-
 ## Rules
 
 .PHONY: all build.regressions build.prof
@@ -286,7 +255,6 @@ $(BUILD)/unit/Makefile: MOM_ENV += $(COV_FCFLAGS) $(COV_LDFLAGS)
 $(BUILD)/timing/Makefile: MOM_ENV += $(OPT_FCFLAGS) $(MOM_LDFLAGS)
 
 # Configure script flags
-MOM_ACFLAGS := --with-framework=$(FRAMEWORK)
 $(BUILD)/openmp/Makefile: MOM_ACFLAGS += --enable-openmp
 $(BUILD)/coupled/Makefile: MOM_ACFLAGS += --with-driver=FMS_cap
 $(BUILD)/nuopc/Makefile: MOM_ACFLAGS += --with-driver=nuopc_cap
@@ -298,11 +266,21 @@ $(BUILD)/timing/Makefile: MOM_ACFLAGS += --with-driver=timing_tests
 $(BUILD)/unit/test_%: $(BUILD)/unit/Makefile FORCE
 	cd $(@D) && $(TIME) $(MAKE) $(@F) -j
 $(BUILD)/unit/Makefile: $(foreach e,$(UNIT_EXECS),../config_src/drivers/unit_tests/$(e).F90)
+
 $(BUILD)/timing/time_%: $(BUILD)/timing/Makefile FORCE
 	cd $(@D) && $(TIME) $(MAKE) $(@F) -j
 $(BUILD)/timing/Makefile: $(foreach e,$(TIMING_EXECS),../config_src/drivers/timing_tests/$(e).F90)
+
 $(BUILD)/%/MOM6: $(BUILD)/%/Makefile FORCE
 	cd $(@D) && $(TIME) $(MAKE) $(@F) -j
+
+# Target codebase should use its own build system
+$(BUILD)/target/MOM6: $(BUILD)/target FORCE | $(TARGET_CODEBASE)
+	$(MAKE) -C $(TARGET_CODEBASE)/.testing build/symmetric/MOM6
+
+$(BUILD)/target: | $(TARGET_CODEBASE)
+	ln -s $(abspath $(TARGET_CODEBASE))/.testing/build/symmetric $@
+
 FORCE:
 
 
@@ -334,27 +312,12 @@ $(BUILD)/%/configure.ac: ../ac/configure.ac | $(BUILD)/%/
 $(BUILD)/%/m4/: ../ac/m4/ | $(BUILD)/%/
 	cp -r ../ac/m4 $(@D)
 
-ALL_EXECS = symmetric asymmetric repro openmp target opt opt_target coupled \
-  nuopc cov unit timing
+ALL_EXECS = symmetric asymmetric repro openmp opt opt_target coupled nuopc \
+  cov unit timing
 $(foreach b,$(ALL_EXECS),$(BUILD)/$(b)/):
 	mkdir -p $@
 
 # Fetch the regression target codebase
-
-$(BUILD)/target/config.status: $(BUILD)/target/configure $(DEPS)/lib/libFMS.a
-	cd $(@D) && $(MOM_ENV) ./configure -n \
-	  --srcdir=$(abspath $(BUILD))/target_codebase/ac $(MOM_ACFLAGS) \
-	|| (cat config.log && false)
-
-$(BUILD)/target/Makefile.in: | $(TARGET_CODEBASE) $(BUILD)/target/
-	cp $(TARGET_CODEBASE)/ac/Makefile.in $(@D)
-
-$(BUILD)/target/configure.ac: | $(TARGET_CODEBASE) $(BUILD)/target/
-	cp $(TARGET_CODEBASE)/ac/configure.ac $(@D)
-
-$(BUILD)/target/m4/: | $(TARGET_CODEBASE) $(BUILD)/target/
-	cp -r $(TARGET_CODEBASE)/ac/m4 $(@D)
-
 $(TARGET_CODEBASE):
 	git clone --recursive $(MOM_TARGET_URL) $@
 	cd $@ && git checkout --recurse-submodules $(MOM_TARGET_BRANCH)
diff --git a/ac/configure.ac b/ac/configure.ac
index c774c39129..8196e2eb01 100644
--- a/ac/configure.ac
+++ b/ac/configure.ac
@@ -79,18 +79,6 @@ AS_IF([test "x$with_driver" != "x"],
 # used to configure a header based on a template.
 #AC_CONFIG_HEADERS(["$MEM_LAYOUT/MOM_memory.h"])
 
-# Select the model framework (default: FMS1)
-# NOTE: We can phase this out after the FMS1 I/O has been removed from FMS and
-#   replace with a detection test.  For now, it is a user-defined switch.
-MODEL_FRAMEWORK=${srcdir}/config_src/infra/FMS2
-AC_ARG_WITH([framework],
-  AS_HELP_STRING([--with-framework=fms1|fms2], [Select the model framework]))
-AS_CASE(["$with_framework"],
-  [fms1], [MODEL_FRAMEWORK=${srcdir}/config_src/infra/FMS1],
-  [fms2], [MODEL_FRAMEWORK=${srcdir}/config_src/infra/FMS2],
-  [MODEL_FRAMEWORK=${srcdir}/config_src/infra/FMS2]
-)
-
 
 # Explicitly assume free-form Fortran
 AC_LANG(Fortran)
@@ -220,7 +208,6 @@ AX_FC_CHECK_LIB([FMS], [fms_init], [fms_mod],
   ]
 )
 
-
 # Verify that FMS is at least 2019.01.02
 # NOTE: 2019.01.02 introduced two changes:
 #   - diag_axis_init supports an optional domain_position argument
@@ -236,6 +223,14 @@ AC_COMPILE_IFELSE(
   ]
 )
 
+# Determine the FMS IO implementation.
+AX_FC_CHECK_MODULE([fms2_io_mod], [
+  MODEL_FRAMEWORK=${srcdir}/config_src/infra/FMS2
+],[
+  MODEL_FRAMEWORK=${srcdir}/config_src/infra/FMS1
+])
+
+
 # Python interpreter test
 
 # Declare the Python interpreter variable