diff --git a/.testing/Makefile b/.testing/Makefile
index 7f52d2a47a..64686c0727 100644
--- a/.testing/Makefile
+++ b/.testing/Makefile
@@ -324,7 +324,7 @@ $(TARGET_CODEBASE):
 # FMS
 
 # Set up the FMS build environment variables
-FMS_ENV = PATH="${PATH}:$(realpath ../ac)" FCFLAGS="$(FCFLAGS_DEBUG)"
+FMS_ENV = PATH="${PATH}:../../bin" FCFLAGS="$(FCFLAGS_DEBUG)"
 
 # TODO: *.mod dependencies?
 $(DEPS)/lib/libFMS.a: $(DEPS)/fms/build/libFMS.a
@@ -335,6 +335,7 @@ $(DEPS)/fms/build/libFMS.a: $(DEPS)/fms/build/Makefile
 
 $(DEPS)/fms/build/Makefile: $(DEPS)/fms/src/configure $(DEPS)/Makefile.fms.in
 	$(FMS_ENV) $(MAKE) -C $(DEPS) fms/build/Makefile
+	$(MAKE) -C $(DEPS) fms/build/Makefile
 
 $(DEPS)/Makefile.fms.in: ../ac/deps/Makefile.fms.in $(DEPS)/Makefile
 	cp $< $(DEPS)
diff --git a/ac/Makefile.in b/ac/Makefile.in
index 2e482ab0c5..711fab1f6f 100644
--- a/ac/Makefile.in
+++ b/ac/Makefile.in
@@ -2,34 +2,65 @@
 #
 # Compiler flags are configured by autoconf's configure script.
 #
-# Source code dependencies are configured by makedep and saved to Makefile.dep.
+# Source code dependencies are configured by mkmf and list_paths, specified in
+# the `Makefile.mkmf` file.
+#
+# mkmf conventions are close, but not identical, to autoconf.  We attempt to
+# map the autoconf variables to the mkmf variables.
+#
+# The following variables are used by Makefiles generated by mkmf.
+#
+#   CC      C compiler
+#   CXX     C++ compiler
+#   FC      Fortran compiler (f77 and f90)
+#   LD      Linker
+#   AR      Archiver
+#
+#   CPPDEFS     Preprocessor macros
+#   CPPFLAGS    C preprocessing flags
+#   CXXFLAGS    C++ preprocessing flags
+#   FPPFLAGS    Fortran preprocessing flags
+#
+#   CFLAGS      C compiler flags
+#   FFLAGS      Fortran compiler flags
+#   LDFLAGS     Linker flags + libraries
+#   ARFLAGS     Archiver flags
+#
+#   OTHERFLAGS      Additional flags for all languages (C, C++, Fortran)
+#   OTHER_CFLAGS    Optional C flags
+#   OTHER_CXXFLAGS  Optional C++ flags
+#   OTHER_FFLAGS    Optional Fortran flags
+#   TMPFILES        Placeholder for `make clean` deletion (as `make neat`).
+#
+#
+#   NOTES:
+#    - FPPFLAGS and FFLAGS always appear as a pair, and autoconf does not use
+#      FPPFLAGS, so FPPFLAGS does not serve much purpose.
+#
+#    - mkmf's FFLAGS does not distinguish between autoconf's fixed-format
+#      FFLAGS and free-format FCFLAGS.
+#
+#    - LDFLAGS does not distinguish between autoconf's LDFLAGS and LIBS.
+#      It also places both after the executable rather than just LIBS.
 
 FC = @FC@
 LD = @FC@
-MAKEDEP = @MAKEDEP@
 
-DEFS = @DEFS@
+CPPDEFS = @DEFS@
 CPPFLAGS = @CPPFLAGS@
-FCFLAGS = @FCFLAGS@
-LDFLAGS = @LDFLAGS@
-LIBS = @LIBS@
+FFLAGS = @FCFLAGS@
+LDFLAGS = @LDFLAGS@ @LIBS@
+
 SRC_DIRS = @SRC_DIRS@
 
+# Gather modulefiles
+TMPFILES = $(wildcard *.mod)
 
 -include Makefile.dep
 
-
-# Generate Makefile from template
-Makefile: @srcdir@/ac/Makefile.in config.status
-	./config.status
-
-
-# Generate dependencies
 .PHONY: depend
-depend: Makefile.dep
-Makefile.dep:
-	$(MAKEDEP) -o Makefile.dep $(SRC_DIRS)
-
+depend:
+	../../../ac/makedep -o Makefile.dep $(SRC_DIRS)
 
 # Delete any files associated with configuration (including the Makefile).
 .PHONY: distclean
diff --git a/ac/configure.ac b/ac/configure.ac
index 15a14708e0..02e39c63a0 100644
--- a/ac/configure.ac
+++ b/ac/configure.ac
@@ -223,20 +223,13 @@ AC_COMPILE_IFELSE(
   ]
 )
 
-
-# Verify that makedep is available
-AC_PATH_PROG([MAKEDEP], [makedep], [${srcdir}/ac/makedep])
-AC_SUBST([MAKEDEP])
-
-
-# Generate source list and configure dependency command
-AC_SUBST([SRC_DIRS],
-    ["${srcdir}/src ${MODEL_FRAMEWORK} ${srcdir}/config_src/external ${DRIVER_DIR} ${MEM_LAYOUT}"]
-)
-AC_CONFIG_COMMANDS([Makefile.dep], [make depend])
+SRC_DIRS="${srcdir}/src ${MODEL_FRAMEWORK} ${srcdir}/config_src/external ${DRIVER_DIR} ${MEM_LAYOUT}"
+AC_CONFIG_COMMANDS([Makefile.dep],
+  [make depend])
 
 # Prepare output
-AC_SUBST([CPPFLAGS])
+AC_SUBST(CPPFLAGS)
+AC_SUBST(SRC_DIRS)
 AC_CONFIG_FILES([Makefile:${srcdir}/ac/Makefile.in])
 AC_OUTPUT
 
diff --git a/ac/deps/Makefile b/ac/deps/Makefile
index af567f6a72..f56b762883 100644
--- a/ac/deps/Makefile
+++ b/ac/deps/Makefile
@@ -6,6 +6,7 @@ SHELL = bash
 # Disable implicit variables
 MAKEFLAGS += -R
 
+
 # FMS framework
 FMS_URL ?= https://github.com/NOAA-GFDL/FMS.git
 FMS_COMMIT ?= 2019.01.03
@@ -25,8 +26,14 @@ FMS_SOURCE = $(call SOURCE,fms/src)
 # Rules
 
 .PHONY: all
-all: lib/libFMS.a
+all: bin/makedep lib/libFMS.a
+
+#---
+# makedep script
 
+bin/makedep: ../../ac/makedep
+	mkdir -p $(@D)
+	cp $^ $@
 
 #---
 # FMS build
@@ -38,7 +45,7 @@ all: lib/libFMS.a
 
 
 # TODO: track *.mod copy?
-lib/libFMS.a: fms/build/libFMS.a
+lib/libFMS.a: fms/build/libFMS.a fms/build/Makefile
 	mkdir -p {lib,include}
 	cp fms/build/libFMS.a lib/libFMS.a
 	cp fms/build/*.mod include
@@ -48,7 +55,7 @@ fms/build/libFMS.a: fms/build/Makefile
 	make -C fms/build libFMS.a
 
 
-fms/build/Makefile: Makefile.fms.in fms/src/configure
+fms/build/Makefile: Makefile.fms.in fms/src/configure bin/makedep
 	mkdir -p fms/build
 	cp Makefile.fms.in fms/src/Makefile.in
 	cd $(@D) && ../src/configure --srcdir=../src
@@ -60,7 +67,6 @@ fms/src/configure: configure.fms.ac $(FMS_SOURCE) | fms/src
 	cp -r m4 $(@D)
 	cd $(@D) && autoreconf -i
 
-
 fms/src:
 	git clone $(FMS_URL) $@
 	git -C $@ checkout $(FMS_COMMIT)
@@ -68,7 +74,7 @@ fms/src:
 
 .PHONY: clean
 clean:
-	rm -rf fms/build lib include
+	rm -rf fms/build lib include bin
 
 .PHONY: distclean
 distclean: clean
diff --git a/ac/deps/Makefile.fms.in b/ac/deps/Makefile.fms.in
index fc580a8c9e..499a1a6a72 100644
--- a/ac/deps/Makefile.fms.in
+++ b/ac/deps/Makefile.fms.in
@@ -1,25 +1,66 @@
-# Makefile template for FMS
+# Makefile template for autoconf builds using mkmf
 #
 # Compiler flags are configured by autoconf's configure script.
 #
-# Source code dependencies are configured by makedep and saved to Makefile.dep.
+# Source code dependencies are configured by mkmf and list_paths, specified in
+# the `Makefile.mkmf` file.
+#
+# mkmf conventions are close, but not identical, to autoconf.  We attempt to
+# map the autoconf variables to the mkmf variables.
+#
+# The following variables are used by Makefiles generated by mkmf.
+#
+#   CC      C compiler
+#   CXX     C++ compiler
+#   FC      Fortran compiler (f77 and f90)
+#   LD      Linker
+#   AR      Archiver
+#
+#   CPPDEFS     Preprocessor macros
+#   CPPFLAGS    C preprocessing flags
+#   CXXFLAGS    C++ preprocessing flags
+#   FPPFLAGS    Fortran preprocessing flags
+#
+#   CFLAGS      C compiler flags
+#   FFLAGS      Fortran compiler flags
+#   LDFLAGS     Linker flags + libraries
+#   ARFLAGS     Archiver flags
+#
+#   OTHERFLAGS      Additional flags for all languages (C, C++, Fortran)
+#   OTHER_CFLAGS    Optional C flags
+#   OTHER_CXXFLAGS  Optional C++ flags
+#   OTHER_FFLAGS    Optional Fortran flags
+#   TMPFILES        Placeholder for `make clean` deletion (as `make neat`).
+#
+#
+#   NOTES:
+#    - FPPFLAGS and FFLAGS always appear as a pair, and autoconf does not use
+#      FPPFLAGS, so FPPFLAGS does not serve much purpose.
+#
+#    - mkmf's FFLAGS does not distinguish between autoconf's fixed-format
+#      FFLAGS and free-format FCFLAGS.
+#
+#    - LDFLAGS does not distinguish between autoconf's LDFLAGS and LIBS.
+#      It also places both after the executable rather than just LIBS.
 
 CC = @CC@
 FC = @FC@
 LD = @FC@
 AR = @AR@
-MAKEDEP = @MAKEDEP@
 
-DEFS = @DEFS@
+CPPDEFS = @DEFS@
 CPPFLAGS = @CPPFLAGS@
-FCFLAGS = @FCFLAGS@
+FFLAGS = @FCFLAGS@
 LDFLAGS = @LDFLAGS@
-LIBS = @LIBS@
 ARFLAGS = @ARFLAGS@
 
+SRC_DIRS = @SRC_DIRS@
+
+# Gather modulefiles
+TMPFILES = $(wildcard *.mod)
+
 -include Makefile.dep
 
 .PHONY: depend
-depend: Makefile.dep
-Makefile.dep:
-	$(MAKEDEP) -o Makefile.dep -x libFMS.a @srcdir@
+depend:
+	../../bin/makedep -o Makefile.dep -f '$$(FC) $$(CPPFLAGS) $$(CPPDEFS) $$(FFLAGS) -c $$<' -x libFMS.a -d $(SRC_DIRS)
diff --git a/ac/deps/configure.fms.ac b/ac/deps/configure.fms.ac
index 4e0c0f1390..4dc1a6614f 100644
--- a/ac/deps/configure.fms.ac
+++ b/ac/deps/configure.fms.ac
@@ -158,26 +158,20 @@ AX_FC_ALLOW_ARG_MISMATCH
 FCFLAGS="$FCFLAGS $ALLOW_ARG_MISMATCH_FCFLAGS"
 
 
-# Verify makedep
-AC_PATH_PROGS([MAKEDEP], [makedep], [], ["${PATH}:${srcdir}/../../.."])
-AS_IF([test -n "${MAKEDEP}"], [
-  AC_SUBST([MAKEDEP])
-], [
-  AC_MSG_ERROR(["Could not find makedep."])
-])
-
 
 # Autoconf does not configure the archiver (ar), as it is handled by Automake.
 # TODO: Properly configure this tool.  For now, we hard-set this to `ar`.
 AR=ar
 ARFLAGS=rv
-AC_SUBST([AR])
-AC_SUBST([ARFLAGS])
-
-AC_CONFIG_COMMANDS([Makefile.dep], [make depend])
+AC_SUBST(AR)
+AC_SUBST(ARFLAGS)
 
-AC_SUBST([CPPFLAGS])
+SRC_DIRS="../src"
+AC_CONFIG_COMMANDS([Makefile.dep],
+  [make depend])
 
 # Prepare output
-AC_CONFIG_FILES([Makefile])
+AC_SUBST(CPPFLAGS)
+AC_SUBST(SRC_DIRS)
+AC_CONFIG_FILES(Makefile)
 AC_OUTPUT
diff --git a/ac/makedep b/ac/makedep
index 74d9200ce8..cb0a8896e3 100755
--- a/ac/makedep
+++ b/ac/makedep
@@ -16,7 +16,7 @@ usage() {
     echo "  -x EXEC  Name of executable to build. Fails if more than one"
     echo "           is found. If EXEC ends in .a then a library is built."
     echo "  -f CMD   String to use in compile rule. Default is:"
-    echo "             '$(FC) $(DEFS) $(FCFLAGS) $(CPPFLAGS) -c $<'"
+    echo "             '$(FC) $(FFLAGS) $(CPPFLAGS) -c $<'"
 }
 
 # Defaults
@@ -24,7 +24,7 @@ makefile=Makefile.dep
 debug=0
 executable=""
 librarymode=0
-compile_line='$(FC) $(DEFS) $(FCFLAGS) $(CPPFLAGS) -c $<'
+compile_line='$(FC) $(FFLAGS) $(CPPFLAGS) -c $<'
 
 while getopts dho:x:f: option
 do
@@ -61,7 +61,7 @@ for F in ${A}; do # F is the relative path to source file
         u=`echo $u | sed s:$m::g`
     fi
     if [ ${#u} -ne 0 ]; then o2use["$o"]=$u; fi
-    H=$(cpp -E -MM $I $F | tr -d '\n' | sed 's:\\::g') # line of form a.o: a.F b.h c.h ...
+    H=$(/lib/cpp -E -MM $I $F | tr -d '\n' | sed 's:\\::g') # line of form a.o: a.F b.h c.h ...
     o2H["$o"]=$H
     h=`echo ${H} | cut -d\  -f3- ` # header files
     if [ ${#h} -ne 0 ]; then o2head["$o"]=$h; fi
@@ -91,7 +91,7 @@ for F in ${A}; do # F is the relative path to source file
     f=`basename $F` # file name stripped of path
     o=${f/.c/}.o # object file name
     o2c["$o"]=$F
-    H=$(cpp -E -MM $I $F | tr -d '\n' | sed 's:\\::g') # line of form a.o: a.F b.h c.h ...
+    H=$(/lib/cpp -E -MM $I $F | tr -d '\n' | sed 's:\\::g') # line of form a.o: a.F b.h c.h ...
     o2H["$o"]=$H
     h=`echo ${H} | cut -d\  -f3- ` # header files
     if [ ${#h} -ne 0 ]; then o2head["$o"]=$h; fi
@@ -189,7 +189,7 @@ for o in ${OC[@]}; do
         echo "#   incpath:" $i >> ${makefile}
     fi
     echo $H ${U[@]} >> ${makefile} # a.mod a.o: a.F b.mod
-    echo -e '\t$(CC) $(DEFS) $(CPPFLAGS) $(CFLAGS) -c $<' ${i} >> ${makefile} # compile rule
+    echo -e '\t$(CC) $(CPPDEFS) $(CPPFLAGS) $(CFLAGS) -c $<' ${i} >> ${makefile} # compile rule
 done
 
 if [ ${#lib} -ne 0 ]; then # rule to build library
@@ -207,7 +207,7 @@ if [ ${#p2o[@]} -ne 0 ]; then # write rules for linking executables
         o=${p2o[$p]}
         l=$(make -f ${makefile} -B -n -t $o | egrep "\.o$" | sed 's:touch ::' | sort)
         echo $p: $l ${externals[@]} >> ${makefile}
-        echo -e '\t$(LD) $(LDFLAGS) -o $@ $^ $(LIBS)' >> ${makefile} # link rule
+        echo -e '\t$(LD) -o $@ $^ $(LDFLAGS)' >> ${makefile} # link rule
     done
 elif [ -z "$lib" ]; then
     echo "Warning: no library target specified (with -x) and no programs found!"