diff --git a/.circleci/checkout.sh b/.circleci/checkout.sh
index daae362417f8..579832db643f 100755
--- a/.circleci/checkout.sh
+++ b/.circleci/checkout.sh
@@ -3,6 +3,3 @@
 # Replace all ssh URLs to submodules with HTTP URLs
 sed -i 's/git@github.com:/https:\/\/github.com\//' .gitmodules
 git submodule update --init
-cd components/mpas-source
-sed -i 's/git@github.com:/https:\/\/github.com\//' .gitmodules
-git submodule update --init --recursive
diff --git a/.travis.yml b/.travis.yml
index b920febedd12..df1e63022b34 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -35,10 +35,6 @@ before_install:
     # Replace all ssh URLs to submodules with HTTP URLs
     - sed -i 's/git@github.com:/https:\/\/github.com\//' .gitmodules
     - git submodule update --init
-    - cd components/mpas-source
-    - sed -i 's/git@github.com:/https:\/\/github.com\//' .gitmodules
-    - git submodule update --init --recursive
-    - cd ../..
     # Download the E3SM Singularity container
     - wget https://dabdceba-6d04-11e5-ba46-22000b92c6ec.e.globus.org/containers/public/e3sm.sif
     # Install Singularity
diff --git a/components/cmake/build_model.cmake b/components/cmake/build_model.cmake
index c5e49dd819e6..17c02ebb4094 100644
--- a/components/cmake/build_model.cmake
+++ b/components/cmake/build_model.cmake
@@ -26,7 +26,7 @@ function(build_model COMP_CLASS COMP_NAME)
   endif()
 
   if (COMP_NAME STREQUAL "cpl")
-    list(APPEND INCLDIR "${EXEROOT}/cmake-bld/mpas-source/src")
+    list(APPEND INCLDIR "${EXEROOT}/cmake-bld/mpas-framework/src")
     foreach(ITEM IN LISTS COMP_CLASSES)
       list(APPEND INCLDIR "${EXEROOT}/cmake-bld/cmake/${ITEM}")
     endforeach()
diff --git a/components/cmake/build_mpas_model.cmake b/components/cmake/build_mpas_model.cmake
index 53d6e388eee3..9201a07d7b74 100644
--- a/components/cmake/build_mpas_model.cmake
+++ b/components/cmake/build_mpas_model.cmake
@@ -33,7 +33,7 @@ function(build_mpas_models)
   set(CIMESRC_PATH "../cime/src")
 
   if (CORES)
-    add_subdirectory("mpas-source/src")
+    add_subdirectory("mpas-framework/src")
   endif()
 
 endfunction(build_mpas_models)
diff --git a/components/mpas-albany-landice/src/Makefile b/components/mpas-albany-landice/src/Makefile
index d7dc35bd0a92..b622a1757d0c 100644
--- a/components/mpas-albany-landice/src/Makefile
+++ b/components/mpas-albany-landice/src/Makefile
@@ -2,7 +2,8 @@
 .SUFFIXES: .F .o .cpp
 .PHONY: mode_forward shared analysis_members
 
-SHARED_INCLUDES  = -I$(PWD)/../framework -I$(PWD)/../external/esmf_time_f90 -I$(PWD)/../operators
+FW = ../../../mpas-framework/src
+SHARED_INCLUDES  = -I$(FW)/framework -I$(FW)/external/esmf_time_f90 -I$(FW)/operators
 SHARED_INCLUDES += -I$(PWD)/shared -I$(PWD)/analysis_members -I$(PWD)/mode_forward
 
 all: core_landice
diff --git a/components/mpas-framework/src/build_core.cmake b/components/mpas-framework/src/build_core.cmake
index c2c36464cbb8..cc2739837269 100644
--- a/components/mpas-framework/src/build_core.cmake
+++ b/components/mpas-framework/src/build_core.cmake
@@ -47,7 +47,7 @@ function(build_core CORE)
 
   add_custom_command(
     OUTPUT ${INC_DIR}/core_variables.inc
-    COMMAND ${CMAKE_BINARY_DIR}/mpas-source/src/tools/parse < ${CORE_BLDDIR}/Registry_processed.xml
+    COMMAND ${CMAKE_BINARY_DIR}/mpas-framework/src/tools/parse < ${CORE_BLDDIR}/Registry_processed.xml
     DEPENDS parse ${CORE_BLDDIR}/Registry_processed.xml
     WORKING_DIRECTORY ${INC_DIR}
   )
diff --git a/components/mpas-ocean/src/Makefile b/components/mpas-ocean/src/Makefile
index 4f6eff7fdfdf..a37742cd7c44 100644
--- a/components/mpas-ocean/src/Makefile
+++ b/components/mpas-ocean/src/Makefile
@@ -5,11 +5,13 @@ CPPLOCALFLAGS = -DEXCLUDE_INIT_MODE
 $(info "EXCLUDE_INIT_MODE found")
 endif
 
-OCEAN_SHARED_INCLUDES = -I$(PWD)/../framework -I$(PWD)/../external/esmf_time_f90 -I$(PWD)/../operators
-OCEAN_SHARED_INCLUDES += -I$(PWD)/shared -I$(PWD)/analysis_members -I$(PWD)/mode_forward -I$(PWD)/mode_analysis
-OCEAN_SHARED_INCLUDES += -I$(PWD)/BGC -I$(PWD)/cvmix/src/shared -I$(PWD)/gotm/build -I$(PWD)/gotm/build/modules
+FRAMEWORK_DIR = ../../../mpas-framework/src
+UP = ..
+OCEAN_SHARED_INCLUDES = -I$(FRAMEWORK_DIR)/framework -I$(FRAMEWORK_DIR)/external/esmf_time_f90 -I$(FRAMEWORK_DIR)/operators
+OCEAN_SHARED_INCLUDES += -I$(UP)/shared -I$(UP)/analysis_members -I$(UP)/mode_forward -I$(UP)/mode_analysis
+OCEAN_SHARED_INCLUDES += -I$(UP)/BGC -I$(UP)/cvmix/src/shared -I$(UP)/gotm/build -I$(UP)/gotm/build/modules
 ifneq "$(EXCLUDE_INIT_MODE)" "true"
-	OCEAN_SHARED_INCLUDES += -I$(PWD)/mode_init
+	OCEAN_SHARED_INCLUDES += -I$(UP)/mode_init
 endif
 
 GOTM_CMAKE_FLAGS = -DGOTM_BUILD_LIBRARIES_ONLY=true -DGOTM_USE_FABM=false -DGOTM_USE_NetCDF=false -DCMAKE_Fortran_COMPILER="$(FC)" -DCMAKE_Fortran_FLAGS="$(FFLAGS)"
@@ -68,14 +70,14 @@ libcvmix:
 	if [ -e cvmix/.git ]; then \
 		(cd cvmix/src/shared; make all FC="$(FC)" FCFLAGS="$(FFLAGS)" FINCLUDES="$(FINCLUDES)") \
 	else \
-		(pwd ; echo "Missing core_ocean/cvmix/.git, did you forget to 'git submodule update --init --recursive' ?"; exit 1) \
+		(pwd ; echo "Missing mpas-ocean/src/cvmix/.git, did you forget to 'git submodule update --init --recursive' ?"; exit 1) \
 	fi
 
 libBGC:
 	if [ -e BGC/.git ]; then \
 		(cd BGC; make all FC="$(FC)" FCFLAGS="$(FFLAGS)" FINCLUDES="$(FINCLUDES)") \
 	else \
-		(echo "Missing core_ocean/BGC/.git, did you forget to 'git submodule update --init --recursive' ?"; exit 1) \
+		(echo "Missing mpas-ocean/src/BGC/.git, did you forget to 'git submodule update --init --recursive' ?"; exit 1) \
 	fi
 
 libgotm:
diff --git a/components/mpas-ocean/src/build_options.mk b/components/mpas-ocean/src/build_options.mk
index e979a3b0a33e..cea9e4665ae4 100644
--- a/components/mpas-ocean/src/build_options.mk
+++ b/components/mpas-ocean/src/build_options.mk
@@ -8,7 +8,7 @@ FCINCLUDES += -I$(ROOT_DIR)/core_ocean/mode_forward -I$(ROOT_DIR)/core_ocean/mod
 FCINCLUDES += -I$(ROOT_DIR)/core_ocean/shared -I$(ROOT_DIR)/core_ocean/analysis_members
 FCINCLUDES += -I$(ROOT_DIR)/core_ocean/cvmix/src/shared
 FCINCLUDES += -I$(ROOT_DIR)/core_ocean/BGC
-FCINCLUDES += -I$(ROOT_DIR)/core_ocean/gotm/include
+FCINCLUDES += -I$(ROOT_DIR)/core_ocean/gotm/build/modules
 override CPPFLAGS += -DCORE_OCEAN
 
 report_builds:
diff --git a/components/mpas-seaice/src/analysis_members/Makefile b/components/mpas-seaice/src/analysis_members/Makefile
index 4999f0382a78..da2f7e44ccab 100644
--- a/components/mpas-seaice/src/analysis_members/Makefile
+++ b/components/mpas-seaice/src/analysis_members/Makefile
@@ -15,14 +15,16 @@ mpas_seaice_analysis_driver.o: $(MEMBERS)
 clean:
 	$(RM) *.o *.i *.mod *.f90
 
+FW = ../../../mpas-framework/src
+
 .F.o:
 	$(RM) $@ $*.mod
 ifeq "$(GEN_F90)" "true"
 	$(CPP) $(CPPFLAGS) $(CPPINCLUDES) $< > $*.f90
-	$(FC) $(FFLAGS) -c $*.f90 -I../../external/esmf_time_f90 -I../../framework -I../../operators -I../column -I../shared -I../model_forward $(FCINCLUDES) 
+	$(FC) $(FFLAGS) -c $*.f90 -I$(FW)/external/esmf_time_f90 -I$(FW)/framework -I$(FW)/operators -I../column -I../shared -I../model_forward $(FCINCLUDES)
 else
-	$(FC) $(CPPFLAGS) $(FFLAGS) -c $*.F -I../../external/esmf_time_f90 -I../../framework -I../../operators -I../column -I../shared -I../model_forward $(CPPINCLUDES) $(FCINCLUDES) 
+	$(FC) $(CPPFLAGS) $(FFLAGS) -c $*.F -I$(FW)/external/esmf_time_f90 -I$(FW)/framework -I$(FW)/operators -I../column -I../shared -I../model_forward $(CPPINCLUDES) $(FCINCLUDES)
 endif
 
 .c.o:
-	$(CC) $(CPPFLAGS) $(CFLAGS) $(CINCLUDES) -I../../external/esmf_time_f90 -I../../framework -I../../operators -I../column -I../shared -I../model_forward -c $<
+	$(CC) $(CPPFLAGS) $(CFLAGS) $(CINCLUDES) -I$(FW)/external/esmf_time_f90 -I$(FW)/framework -I$(FW)/operators -I../column -I../shared -I../model_forward -c $<
diff --git a/components/mpas-seaice/src/model_forward/Makefile b/components/mpas-seaice/src/model_forward/Makefile
index 523922976e65..cc97d64aa6bd 100644
--- a/components/mpas-seaice/src/model_forward/Makefile
+++ b/components/mpas-seaice/src/model_forward/Makefile
@@ -18,12 +18,14 @@ else
 FFLAGS_noSMP := $(FFLAGS)
 endif
 
+FW = ../../../mpas-framework/src
+
 .F.o:
 	$(RM) $@ $*.mod
 ifeq "$(GEN_F90)" "true"
 	$(CPP) $(CPPFLAGS) $(CPPINCLUDES) $< > $*.f90
 
-	$(FC) $(FFLAGS_noSMP) -c $*.f90 $(FCINCLUDES) -I../../framework -I../../operators -I../../external/esmf_time_f90 -I../column -I../shared
+	$(FC) $(FFLAGS_noSMP) -c $*.f90 $(FCINCLUDES) -I$(FW)/framework -I$(FW)/operators -I$(FW)/external/esmf_time_f90 -I../column -I../shared
 else
-	$(FC) $(CPPFLAGS) $(FFLAGS_noSMP) -c $*.F $(CPPINCLUDES) $(FCINCLUDES) -I../../framework -I../../operators -I../../external/esmf_time_f90 -I../column -I../shared
+	$(FC) $(CPPFLAGS) $(FFLAGS_noSMP) -c $*.F $(CPPINCLUDES) $(FCINCLUDES) -I$(FW)/framework -I$(FW)/operators -I$(FW)/external/esmf_time_f90 -I../column -I../shared
 endif
diff --git a/components/mpas-seaice/src/shared/Makefile b/components/mpas-seaice/src/shared/Makefile
index 52bcb7571039..06c417313202 100644
--- a/components/mpas-seaice/src/shared/Makefile
+++ b/components/mpas-seaice/src/shared/Makefile
@@ -81,12 +81,14 @@ mpas_seaice_core_interface.o: mpas_seaice_core.o
 clean:
 	$(RM) *.o *.i *.mod *.f90
 
+FW = ../../../mpas-framework/src
+
 .F.o:
 	$(RM) $@ $*.mod
 ifeq "$(GEN_F90)" "true"
 	$(CPP) $(CPPFLAGS) $(CPPINCLUDES) $< > $*.f90
 
-	$(FC) $(FFLAGS) -c $*.f90 $(FCINCLUDES) -I../../framework -I../../operators -I../../external/esmf_time_f90 -I../column
+	$(FC) $(FFLAGS) -c $*.f90 $(FCINCLUDES) -I$(FW)/framework -I$(FW)/operators -I$(FW)/external/esmf_time_f90 -I../column
 else
-	$(FC) $(CPPFLAGS) $(FFLAGS) -c $*.F $(CPPINCLUDES) $(FCINCLUDES) -I../../framework -I../../operators -I../../external/esmf_time_f90 -I../column
+	$(FC) $(CPPFLAGS) $(FFLAGS) -c $*.F $(CPPINCLUDES) $(FCINCLUDES) -I$(FW)/framework -I$(FW)/operators -I$(FW)/external/esmf_time_f90 -I../column
 endif