Fixes for acme_cime_split based on initial full tryout

.github/PULL_REQUEST_TEMPLATE

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+[ Description of the changes in this Pull Request. It should be enough
+information for someone not following this development to understand.
+Lines should be wrapped at about 72 characters. Please also update
+the CIME documentation, if necessary, in doc/source/rst and indicate
+below if you need to have the gh-pages html regenerated.]
+
+Test suite: 
+Test baseline: 
+Test namelist changes: 
+Test status: [bit for bit, roundoff, climate changing]
+
+Fixes [CIME Github issue #]
+
+User interface changes?: 
+
+Update gh-pages html (Y/N)?:
+
+Code review: 

.gitignore

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+# Ignore python bytecode files
+*.pyc
+buildnmlc
+
+# Ignore emacs backup files
+*~
+
+# Ignore doc/build/doctrees
+##doc/build/doctrees 
+# ignore for the merge to master and orphaning of the gh-pages branch
+doc/build
+

CMakeLists.txt

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+cmake_minimum_required(VERSION 2.8)
+include(ExternalProject)
+set(CIME_ROOT "${CMAKE_CURRENT_SOURCE_DIR}")
+
+list(APPEND CMAKE_MODULE_PATH ${CIME_CMAKE_MODULE_DIRECTORY})
+include(CIME_initial_setup)
+
+project(cime_tests Fortran C)
+
+# We rely on pio for cmake utilities like findnetcdf.cmake, so that we don't
+# need to duplicate this cmake code
+list(APPEND CMAKE_MODULE_PATH "${CIME_ROOT}/src/externals/pio2/cmake")
+
+include(CIME_utils)
+find_package(NetCDF COMPONENTS C Fortran)
+include_directories(${NetCDF_C_INCLUDE_DIRS} ${NetCDF_Fortran_INCLUDE_DIRS})
+
+# TODO: Some of the below should be done in the relevant directories, not in
+# this top level CMakeLists.
+
+# ------------------------------------------------------------------------
+# Build mct
+# ------------------------------------------------------------------------
+set(MCT_ROOT "${CIME_ROOT}/src/externals/mct")
+
+if (USE_MPI_SERIAL)
+  set(ENABLE_MPI_SERIAL "--enable-mpiserial")
+else()
+  set(ENABLE_MPI_SERIAL "")
+endif()
+
+ExternalProject_add(mct_project
+  PREFIX ${CMAKE_CURRENT_BINARY_DIR}
+  SOURCE_DIR ${MCT_ROOT}
+  BINARY_DIR ${CMAKE_CURRENT_BINARY_DIR}/mct
+  CONFIGURE_COMMAND ${MCT_ROOT}/configure ${ENABLE_MPI_SERIAL} --enable-debugging --prefix=${CMAKE_CURRENT_BINARY_DIR} CC=${CMAKE_C_COMPILER} FC=${CMAKE_Fortran_COMPILER} CFLAGS=${CFLAGS} FCFLAGS=${FFLAGS} SRCDIR=${MCT_ROOT} DEBUG="-g"
+  BUILD_COMMAND $(MAKE) SRCDIR=${MCT_ROOT}
+  # Leave things in <BINARY_DIR> rather than "installing", because we have
+  # no need to move things around inside of the CMake binary directory. Also,
+  # mpi-serial doesn't install properly in the out-of-source build
+  INSTALL_COMMAND :
+  )
+# This copy_makefiles step is needed because mct currently doesn't support an
+# out-of-source build. I am replicating what is done for the CIME system build.
+ExternalProject_add_step(mct_project copy_makefiles
+  DEPENDEES configure
+  DEPENDERS build
+  WORKING_DIRECTORY <BINARY_DIR>
+  COMMAND cp -p <SOURCE_DIR>/Makefile .
+  COMMAND mkdir -p mct
+  COMMAND cp -p <SOURCE_DIR>/mct/Makefile mct/
+  COMMAND mkdir -p mpeu
+  COMMAND cp -p <SOURCE_DIR>/mpeu/Makefile mpeu/
+  )
+if (USE_MPI_SERIAL)
+  ExternalProject_add_step(mct_project copy_mpi_serial_files
+    DEPENDEES configure
+    DEPENDERS build
+    WORKING_DIRECTORY <BINARY_DIR>
+    COMMAND mkdir -p mpi-serial
+    COMMAND cp -p <SOURCE_DIR>/mpi-serial/Makefile mpi-serial/
+    COMMAND cp <SOURCE_DIR>/mpi-serial/mpif.h mpi-serial/
+    COMMAND cp <SOURCE_DIR>/mpi-serial/mpi.h mpi-serial/
+    )
+endif()
+
+# Tell cmake to look for libraries & mod files here, because this is where we built libraries
+include_directories(${CMAKE_CURRENT_BINARY_DIR}/mct/mct)
+include_directories(${CMAKE_CURRENT_BINARY_DIR}/mct/mpeu)
+link_directories(${CMAKE_CURRENT_BINARY_DIR}/mct/mct)
+link_directories(${CMAKE_CURRENT_BINARY_DIR}/mct/mpeu)
+if (USE_MPI_SERIAL)
+  include_directories(${CMAKE_CURRENT_BINARY_DIR}/mct/mpi-serial)
+  link_directories(${CMAKE_CURRENT_BINARY_DIR}/mct/mpi-serial)
+endif()
+
+# ------------------------------------------------------------------------
+# Done MCT build
+# ------------------------------------------------------------------------
+
+# Now a bunch of includes for share code.
+
+# csm_share (we don't build it here because it seems to be built differently
+# by different tests?)
+set(SHARE_ROOT "${CIME_ROOT}/src/share")
+add_subdirectory(${SHARE_ROOT}/util csm_share)
+add_subdirectory(${SHARE_ROOT}/unit_test_stubs/util csm_share_stubs)
+include_directories(${SHARE_ROOT}/include)
+
+# esmf_wrf_timemgr not built here because it depends on csm_share.
+add_subdirectory(${SHARE_ROOT}/esmf_wrf_timemgr esmf_wrf_timemgr)
+include_directories(${SHARE_ROOT}/esmf_wrf_timemgr)
+
+# Now the actual test directories.
+add_subdirectory(${CIME_ROOT}/src/drivers/mct/unit_test)
+add_subdirectory(${SHARE_ROOT}/test/unit)