#!/bin/csh
#
# On August 14th, 2020 - I mistakenly merged a pull request (PR#44) against Manhattan instead of master.
# I immediately reverted the merge (PR#45) and hoped for the best.
# [Aside: I used a GitHub facility to revert the merge]
# All seemed well - until I wanted to update Manhattan for a new (minor) release.
# 
# git now thinks the merge-base between Manhattan and master is b4ce252
# which was the last commit before the bad merge. This seems like the right commit - however,
# the commits to revert the bad merge (change/add a bunch of files, remove/revert those same files)
# are still intefering with attempts to merge the current master onto Manhattan.
# All attempts to update Manhattan seem to ignore the files from the original
# bad merge - so those files (lots of them) remain unchanged or simply do not exist.
# 
# 6b6c084c70c63ec05ba06a280ecb16e83b1e950d  bad commit (add new files, modify others)
# 72d905da819325bcb8c442f0bdcb6474cf2d32e8  commit to fix (i.e. delete, revert a bunch of files)
# 2a66909778450bcc2f585d20ee84eac944233de7  what I think should be the new merge-base
# 
#-------------------------------------------------------------------------------
# To generate the list of files, do the following from a git repo current with NCAR/DART.git
# git diff --name-status upstream/Manhattan upstream/master | & tee upstream_diff_log.txt

 if ( -d dartdummy ) then
    echo "trying to clone into 'dartdummy', directory exists. Failing."
    exit 1
 endif

 git clone git@github.com:timhoar/DART.git dartdummy
 cd dartdummy

# The upstream version of Manhattan is the one that is corrupt.
# It also has an update we want in the form of filter_mod.f90 - but that's it.
# all other recent changes to upstream/Manhattan are also on upstream/master
# This is done at the end of this script; we want the change that starts:
#         ! CSS added condition
# ultimately, that winds up being about line 1031

 git remote add upstream git@github.com:NCAR/DART.git
 git fetch upstream

 git checkout -b Manhattan44_45 upstream/Manhattan

#-------------------------------------------------------------------------------

 git checkout upstream/master -- .gitignore
 git rm CHANGELOG
 git checkout upstream/master -- CHANGELOG.md
 git checkout upstream/master -- COPYRIGHT.md
 git checkout upstream/master -- README.md
 git checkout upstream/master -- assimilation_code/modules/assimilation/assim_tools_mod.f90

# filter_mod.f90 has changes from CSS and master ... manually merge ... done at end.
# git checkout upstream/master -- assimilation_code/modules/assimilation/filter_mod.f90

 git checkout upstream/master -- assimilation_code/modules/io/direct_netcdf_mod.f90
 git checkout upstream/master -- assimilation_code/modules/io/state_structure_mod.f90
 git checkout upstream/master -- assimilation_code/modules/observations/DEFAULT_obs_kind_mod.F90
 git checkout upstream/master -- assimilation_code/modules/observations/forward_operator_mod.f90
 git checkout upstream/master -- assimilation_code/modules/observations/obs_sequence_mod.f90
 git checkout upstream/master -- assimilation_code/modules/observations/obs_sequence_mod.html
 git checkout upstream/master -- assimilation_code/modules/utilities/ensemble_manager_mod.html
 git checkout upstream/master -- assimilation_code/modules/utilities/mpi_utilities_mod.f90
 git checkout upstream/master -- assimilation_code/modules/utilities/netcdf_utilities_mod.f90
 git checkout upstream/master -- assimilation_code/modules/utilities/null_mpi_utilities_mod.f90
 git checkout upstream/master -- assimilation_code/modules/utilities/utilities_mod.f90
 git checkout upstream/master -- assimilation_code/programs/compare_states/work/mkmf_compare_states
 git checkout upstream/master -- assimilation_code/programs/compare_states/work/quickbuild.csh
 git checkout upstream/master -- assimilation_code/programs/create_obs_sequence/create_obs_sequence.html
 git checkout upstream/master -- assimilation_code/programs/fill_inflation_restart/fill_inflation_restart.f90
 git checkout upstream/master -- assimilation_code/programs/gen_sampling_err_table/work/quickbuild.csh
 git checkout upstream/master -- assimilation_code/programs/obs_assim_count/work/quickbuild.csh
 git checkout upstream/master -- assimilation_code/programs/obs_diag/oned/obs_diag.f90
 git checkout upstream/master -- assimilation_code/programs/obs_diag/threed_cartesian/obs_diag.f90
 git checkout upstream/master -- assimilation_code/programs/obs_diag/threed_sphere/obs_diag.f90
 git checkout upstream/master -- assimilation_code/programs/obs_diag/threed_sphere/streamflow_obs_diag.f90
 git checkout upstream/master -- assimilation_code/programs/obs_loop/obs_loop.f90
 git checkout upstream/master -- assimilation_code/programs/obs_seq_to_netcdf/obs_seq_to_netcdf.f90
 git checkout upstream/master -- assimilation_code/programs/obs_seq_to_netcdf/radiance_obs/obs_seq_to_netcdf.f90
 git checkout upstream/master -- assimilation_code/programs/obs_total_error/work/input.nml
 git checkout upstream/master -- assimilation_code/programs/obs_total_error/work/quickbuild.csh
 git checkout upstream/master -- assimilation_code/programs/obs_utils/create_obs_grid.f90
 git checkout upstream/master -- assimilation_code/programs/obs_utils/obs_assim_count.f90
 git checkout upstream/master -- assimilation_code/programs/obs_utils/obs_assim_count.nml
 git checkout upstream/master -- assimilation_code/programs/obs_utils/obs_info.f90
 git checkout upstream/master -- assimilation_code/programs/obs_utils/obs_info.nml
 git checkout upstream/master -- assimilation_code/programs/perturb_single_instance/perturb_single_instance.f90
 git checkout upstream/master -- assimilation_code/programs/system_simulation/work/quickbuild.csh
 git checkout upstream/master -- assimilation_code/scripts/build_script.csh
 git checkout upstream/master -- assimilation_code/scripts/day_template.csh
 git checkout upstream/master -- assimilation_code/scripts/quickclean.csh
 git checkout upstream/master -- assimilation_code/scripts/split_obs_seq.csh
 git checkout upstream/master -- build_templates/README.md
 git checkout upstream/master -- build_templates/mkmf
 git checkout upstream/master -- build_templates/mkmf.template.absoft.osx
 git checkout upstream/master -- build_templates/mkmf.template.g95
 git checkout upstream/master -- build_templates/mkmf.template.gfortran
 git checkout upstream/master -- build_templates/mkmf.template.intel.linux
 git checkout upstream/master -- build_templates/mkmf.template.intel.osx
 git checkout upstream/master -- build_templates/mkmf.template.lahey.linux
 git checkout upstream/master -- build_templates/mkmf.template.nag.linux
 git checkout upstream/master -- build_templates/mkmf.template.pathscale.linux
 git checkout upstream/master -- build_templates/mkmf.template.pgi.cray
 git checkout upstream/master -- build_templates/mkmf.template.pgi.linux
 git checkout upstream/master -- build_templates/mkmf.template.pgi.osx

# R062  build_templates/mkmf.template build_templates/mkmf.template.rttov.gfortran
 git rm build_templates/mkmf.template
 git checkout upstream/master -- build_templates/mkmf.template.rttov.gfortran

 git checkout upstream/master -- build_templates/mkmf.template.rttov.intel
 git checkout upstream/master -- build_templates/mkmf.template.sgi.altix
 git checkout upstream/master -- build_templates/mkmf.template.xlf.aix
 git checkout upstream/master -- developer_tests/check_tests.csh
 git checkout upstream/master -- developer_tests/compare_two_tests.csh
 git checkout upstream/master -- developer_tests/forward_operators/rttov_test.f90
 git checkout upstream/master -- developer_tests/forward_operators/work/input.nml
 git checkout upstream/master -- developer_tests/forward_operators/work/mkmf_preprocess
 git checkout upstream/master -- developer_tests/forward_operators/work/mkmf_rttov_test

# R050  models/coamps_nest/work/path_names_in_grid developer_tests/forward_operators/work/path_names_preprocess
 git rm models/coamps_nest/work/path_names_in_grid
 git checkout upstream/master -- developer_tests/forward_operators/work/path_names_preprocess

 git checkout upstream/master -- developer_tests/forward_operators/work/path_names_rttov_test
 git checkout upstream/master -- developer_tests/forward_operators/work/quickbuild.csh
 git checkout upstream/master -- developer_tests/io/test_read_write_time.f90
 git checkout upstream/master -- developer_tests/io/work/input.nml
 git checkout upstream/master -- developer_tests/io/work/quickbuild.csh
 git checkout upstream/master -- developer_tests/obs_sequence/work/quickbuild.csh
 git checkout upstream/master -- developer_tests/random_seq/work/quickbuild.csh
 git checkout upstream/master -- developer_tests/test_dart.csh
 git checkout upstream/master -- developer_tests/utilities/file_utils_test.f90
 git checkout upstream/master -- developer_tests/utilities/work/mkmf_file_utils_test
 git checkout upstream/master -- developer_tests/utilities/work/mkmf_find_enclosing_indices_test
 git checkout upstream/master -- developer_tests/utilities/work/mkmf_find_first_occurrence_test
 git checkout upstream/master -- developer_tests/utilities/work/mkmf_sort_test
 git checkout upstream/master -- developer_tests/utilities/work/quickbuild.csh
 git checkout upstream/master -- diagnostics/matlab/plot_evolution.m
 git checkout upstream/master -- diagnostics/matlab/plot_rmse_xxx_evolution.m
 git checkout upstream/master -- diagnostics/matlab/two_experiments_evolution.m
 git checkout upstream/master -- docs/DART_LAB/matlab/private/update_inflate.m
 git checkout upstream/master -- docs/_config.yml
 git checkout upstream/master -- docs/_data/mainmenu.yml
 git checkout upstream/master -- docs/images/MPAS_grid_components.png
 git checkout upstream/master -- docs/images/MPAS_spaghetti_Z500mb_anal.2008090512.png

# R100  docs/index.html docs/old_index.html
 git rm docs/index.html
 git checkout upstream/master -- docs/old_index.html

 git checkout upstream/master -- docs/pages/About_Us.md
 git checkout upstream/master -- docs/pages/Getting_Started.md

# R100  docs/pages/DART2_Miscellany.md docs/pages/Miscellany.md
 git rm docs/pages/DART2_Miscellany.md
 git checkout upstream/master -- docs/pages/Miscellany.md

 git checkout upstream/master -- docs/pages/Models.md
 git checkout upstream/master -- docs/pages/Observations.md
 git checkout upstream/master -- docs/pages/Presentations.md
 git checkout upstream/master -- docs/pages/Publications.md
 git checkout upstream/master -- docs/pages/Radiance_support.md
 git checkout upstream/master -- docs/pages/Research.md
 git checkout upstream/master -- docs/pages/random_seq_mod.md
 git checkout upstream/master -- docs/pages/release.md
 git checkout upstream/master -- docs/pages/time_manager_mod.md
 git checkout upstream/master -- models/9var/work/quickbuild.csh
 git checkout upstream/master -- models/9var/work/workshop_setup.csh
 git checkout upstream/master -- models/CESM/shell_scripts/CLM_convert_restarts.csh
 git checkout upstream/master -- models/CESM/shell_scripts/assimilate.csh
 git checkout upstream/master -- models/CESM/shell_scripts/cam_assimilate.csh
 git checkout upstream/master -- models/CESM/shell_scripts/cam_no_assimilate.csh
 git checkout upstream/master -- models/CESM/shell_scripts/cam_perfect_model.csh
 git checkout upstream/master -- models/CESM/shell_scripts/clm_assimilate.csh
 git checkout upstream/master -- models/CESM/shell_scripts/clm_perfect_model.csh
 git checkout upstream/master -- models/CESM/shell_scripts/no_assimilate.csh
 git checkout upstream/master -- models/CESM/shell_scripts/perfect_model.csh
 git checkout upstream/master -- models/CESM/shell_scripts/pop_assimilate.csh
 git checkout upstream/master -- models/CESM/shell_scripts/pop_perfect_model.csh
 git checkout upstream/master -- models/CESM/shell_scripts/run_perfect_model_obs.csh
 git checkout upstream/master -- models/FESOM/README.md
 git checkout upstream/master -- models/FESOM/diagnostics/script/README.md
 git checkout upstream/master -- models/LMDZ/shell_scripts/Control_File.csh
 git checkout upstream/master -- models/LMDZ/shell_scripts/advance_model.csh
 git checkout upstream/master -- models/LMDZ/shell_scripts/job.csh
 git checkout upstream/master -- models/LMDZ/shell_scripts/run_filter.csh
 git checkout upstream/master -- models/LMDZ/shell_scripts/run_lmdz.csh
 git checkout upstream/master -- models/LMDZ/work/quickbuild.csh
 git checkout upstream/master -- models/MITgcm_annulus/shell_scripts/advance_model.csh
 git checkout upstream/master -- models/MITgcm_annulus/work/quickbuild.csh
 git checkout upstream/master -- models/MITgcm_ocean/shell_scripts/MakeInitialEnsemble.csh
 git checkout upstream/master -- models/MITgcm_ocean/shell_scripts/advance_model.csh
 git checkout upstream/master -- models/MITgcm_ocean/shell_scripts/job.simple.csh
 git checkout upstream/master -- models/MITgcm_ocean/work/quickbuild.csh
 git checkout upstream/master -- models/NAAPS/shell_scripts/assimilate.csh
 git checkout upstream/master -- models/NAAPS/work/quickbuild.csh
 git checkout upstream/master -- models/NCOMMAS/shell_scripts/advance_model.csh
 git checkout upstream/master -- models/NCOMMAS/shell_scripts/job.simple.csh
 git checkout upstream/master -- models/NCOMMAS/work/quickbuild.csh
 git checkout upstream/master -- models/POP/dart_pop_mod.f90



# R098 models/POP/shell_scripts/CESM1_1_1_setup_hybrid models/POP/shell_scripts/cesm1_x/CESM1_1_1_setup_hybrid
# R098 models/POP/shell_scripts/CESM1_1_1_setup_pmo models/POP/shell_scripts/cesm1_x/CESM1_1_1_setup_pmo
# R098 models/POP/shell_scripts/CESM1_2_1_setup_hybrid models/POP/shell_scripts/cesm1_x/CESM1_2_1_setup_hybrid
# R098 models/POP/shell_scripts/CESM1_2_1_setup_pmo models/POP/shell_scripts/cesm1_x/CESM1_2_1_setup_pmo
# R098 models/POP/shell_scripts/CESM_DART_config models/POP/shell_scripts/cesm1_x/CESM_DART_config
# R098 models/POP/shell_scripts/MakeInitialEnsemble.csh models/POP/shell_scripts/cesm1_x/MakeInitialEnsemble.csh
# R098 models/POP/shell_scripts/advance_model.csh models/POP/shell_scripts/cesm1_x/advance_model.csh
# R099 models/POP/shell_scripts/assimilate.csh models/POP/shell_scripts/cesm1_x/assimilate.csh
# R098 models/POP/shell_scripts/perfect_model.csh models/POP/shell_scripts/cesm1_x/perfect_model.csh
# R099 models/POP/shell_scripts/run_filter.csh models/POP/shell_scripts/cesm1_x/run_filter.csh
# R098 models/POP/shell_scripts/run_perfect_model_obs.csh models/POP/shell_scripts/cesm1_x/run_perfect_model_obs.csh
# R100 models/POP/shell_scripts/shell_exit.sh models/POP/shell_scripts/cesm1_x/shell_exit.sh
# R100 models/POP/shell_scripts/st_archive.sh models/POP/shell_scripts/cesm1_x/st_archive.sh
# R100 models/POP/shell_scripts/stitch_post.sh models/POP/shell_scripts/cesm1_x/stitch_post.sh
# R100 models/POP/shell_scripts/stitch_prior.sh models/POP/shell_scripts/cesm1_x/stitch_prior.sh
# R100 models/POP/shell_scripts/user_datm.streams.txt.CPLHIST3HrWx.Precip_template models/POP/shell_scripts/cesm1_x/user_datm.streams.txt.CPLHIST3HrWx.Precip_template
# R100 models/POP/shell_scripts/user_datm.streams.txt.CPLHIST3HrWx.Solar_template models/POP/shell_scripts/cesm1_x/user_datm.streams.txt.CPLHIST3HrWx.Solar_template
# R100 models/POP/shell_scripts/user_datm.streams.txt.CPLHIST3HrWx.nonSolarNonPrecip_template models/POP/shell_scripts/cesm1_x/user_datm.streams.txt.CPLHIST3HrWx.nonSolarNonPrecip_template



 git rm                                  models/POP/shell_scripts/CESM1_1_1_setup_hybrid
 git checkout upstream/master -- models/POP/shell_scripts/cesm1_x/CESM1_1_1_setup_hybrid

 git rm                                  models/POP/shell_scripts/CESM1_1_1_setup_pmo
 git checkout upstream/master -- models/POP/shell_scripts/cesm1_x/CESM1_1_1_setup_pmo

 git rm                                  models/POP/shell_scripts/CESM1_2_1_setup_hybrid
 git checkout upstream/master -- models/POP/shell_scripts/cesm1_x/CESM1_2_1_setup_hybrid

 git rm                                  models/POP/shell_scripts/CESM1_2_1_setup_pmo
 git checkout upstream/master -- models/POP/shell_scripts/cesm1_x/CESM1_2_1_setup_pmo

 git rm                                  models/POP/shell_scripts/CESM_DART_config
 git checkout upstream/master -- models/POP/shell_scripts/cesm1_x/CESM_DART_config

 git rm                                  models/POP/shell_scripts/MakeInitialEnsemble.csh
 git checkout upstream/master -- models/POP/shell_scripts/cesm1_x/MakeInitialEnsemble.csh

 git rm                                  models/POP/shell_scripts/advance_model.csh
 git checkout upstream/master -- models/POP/shell_scripts/cesm1_x/advance_model.csh

 git rm                                  models/POP/shell_scripts/assimilate.csh
 git checkout upstream/master -- models/POP/shell_scripts/cesm1_x/assimilate.csh

 git rm                                  models/POP/shell_scripts/perfect_model.csh
 git checkout upstream/master -- models/POP/shell_scripts/cesm1_x/perfect_model.csh

 git rm                                  models/POP/shell_scripts/run_filter.csh
 git checkout upstream/master -- models/POP/shell_scripts/cesm1_x/run_filter.csh

 git rm                                  models/POP/shell_scripts/run_perfect_model_obs.csh
 git checkout upstream/master -- models/POP/shell_scripts/cesm1_x/run_perfect_model_obs.csh

 git rm                                  models/POP/shell_scripts/shell_exit.sh
 git checkout upstream/master -- models/POP/shell_scripts/cesm1_x/shell_exit.sh

 git rm                                  models/POP/shell_scripts/st_archive.sh
 git checkout upstream/master -- models/POP/shell_scripts/cesm1_x/st_archive.sh

 git rm                                  models/POP/shell_scripts/stitch_post.sh
 git checkout upstream/master -- models/POP/shell_scripts/cesm1_x/stitch_post.sh

 git rm                                  models/POP/shell_scripts/stitch_prior.sh
 git checkout upstream/master -- models/POP/shell_scripts/cesm1_x/stitch_prior.sh

 git rm                                  models/POP/shell_scripts/user_datm.streams.txt.CPLHIST3HrWx.Precip_template
 git checkout upstream/master -- models/POP/shell_scripts/cesm1_x/user_datm.streams.txt.CPLHIST3HrWx.Precip_template

 git rm                                  models/POP/shell_scripts/user_datm.streams.txt.CPLHIST3HrWx.Solar_template
 git checkout upstream/master -- models/POP/shell_scripts/cesm1_x/user_datm.streams.txt.CPLHIST3HrWx.Solar_template

 git rm                                  models/POP/shell_scripts/user_datm.streams.txt.CPLHIST3HrWx.nonSolarNonPrecip_template
 git checkout upstream/master -- models/POP/shell_scripts/cesm1_x/user_datm.streams.txt.CPLHIST3HrWx.nonSolarNonPrecip_template



 git checkout upstream/master -- models/POP/shell_scripts/cesm2_1/CESM2_1_setup_hybrid
 git checkout upstream/master -- models/POP/shell_scripts/cesm2_1/CESM2_1_setup_pmo
 git checkout upstream/master -- models/POP/shell_scripts/cesm2_1/CESM_DART_config
 git checkout upstream/master -- models/POP/shell_scripts/cesm2_1/DART_params.csh
 git checkout upstream/master -- models/POP/shell_scripts/cesm2_1/HPSS_get_ensemble
 git checkout upstream/master -- models/POP/shell_scripts/cesm2_1/assimilate.csh
 git checkout upstream/master -- models/POP/shell_scripts/cesm2_1/perfect_model.csh
 git checkout upstream/master -- models/POP/shell_scripts/cesm2_1/user_datm.streams.txt.CPLHISTForcing.Solar_template
 git checkout upstream/master -- models/POP/shell_scripts/cesm2_1/user_datm.streams.txt.CPLHISTForcing.State1hr_template
 git checkout upstream/master -- models/POP/shell_scripts/cesm2_1/user_datm.streams.txt.CPLHISTForcing.State3hr_template
 git checkout upstream/master -- models/POP/shell_scripts/cesm2_1/user_datm.streams.txt.CPLHISTForcing.nonSolarFlux_template
 git checkout upstream/master -- models/POP/work/input.nml
 git checkout upstream/master -- models/POP/work/mkmf_create_fixed_network_seq
 git checkout upstream/master -- models/POP/work/mkmf_create_obs_sequence
 git checkout upstream/master -- models/POP/work/mkmf_fill_inflation_restart
 git checkout upstream/master -- models/POP/work/mkmf_filter
 git checkout upstream/master -- models/POP/work/mkmf_model_mod_check
 git checkout upstream/master -- models/POP/work/mkmf_obs_diag
 git checkout upstream/master -- models/POP/work/mkmf_obs_seq_to_netcdf
 git checkout upstream/master -- models/POP/work/mkmf_obs_sequence_tool
 git checkout upstream/master -- models/POP/work/mkmf_perfect_model_obs
 git checkout upstream/master -- models/POP/work/mkmf_preprocess
 git checkout upstream/master -- models/POP/work/path_names_fill_inflation_restart
 git checkout upstream/master -- models/POP/work/quickbuild.csh
 git checkout upstream/master -- models/README.md
 git checkout upstream/master -- models/ROMS/shell_scripts/get_ocean_time.csh
 git checkout upstream/master -- models/ROMS/shell_scripts/stage_experiment.csh
 git checkout upstream/master -- models/ROMS/shell_scripts/submit_multiple_cycles_lsf.csh
 git checkout upstream/master -- models/ROMS/shell_scripts/submit_multiple_jobs_slurm.csh
 git checkout upstream/master -- models/ROMS/work/quickbuild.csh
 git checkout upstream/master -- models/am2/work/quickbuild.csh
 git checkout upstream/master -- models/bgrid_solo/shell_scripts/Convert_Diags_to_restarts.csh
 git checkout upstream/master -- models/bgrid_solo/shell_scripts/advance_model.csh
 git checkout upstream/master -- models/bgrid_solo/shell_scripts/run_filter.csh
 git checkout upstream/master -- models/bgrid_solo/work/mkmf_column_rand
 git checkout upstream/master -- models/bgrid_solo/work/mkmf_create_fixed_network_seq
 git checkout upstream/master -- models/bgrid_solo/work/mkmf_create_obs_sequence
 git checkout upstream/master -- models/bgrid_solo/work/mkmf_filter
 git checkout upstream/master -- models/bgrid_solo/work/mkmf_id_set_def_stdin
 git checkout upstream/master -- models/bgrid_solo/work/mkmf_integrate_model
 git checkout upstream/master -- models/bgrid_solo/work/mkmf_model_mod_check
 git checkout upstream/master -- models/bgrid_solo/work/mkmf_obs_diag
 git checkout upstream/master -- models/bgrid_solo/work/mkmf_obs_sequence_tool
 git checkout upstream/master -- models/bgrid_solo/work/mkmf_perfect_model_obs
 git checkout upstream/master -- models/bgrid_solo/work/mkmf_preprocess
 git checkout upstream/master -- models/bgrid_solo/work/mkmf_ps_rand_local
 git checkout upstream/master -- models/bgrid_solo/work/quickbuild.csh
 git checkout upstream/master -- models/bgrid_solo/work/workshop_setup.csh
 git checkout upstream/master -- models/cam-fv/model_mod.f90
 git checkout upstream/master -- models/cam-fv/shell_scripts/cesm1_5/assimilate.csh
 git checkout upstream/master -- models/cam-fv/shell_scripts/cesm2_0/assimilate.csh.template
 git checkout upstream/master -- models/cam-fv/shell_scripts/cesm2_0/setup_advanced
 git checkout upstream/master -- models/cam-fv/shell_scripts/cesm2_0/spinup_single
 git checkout upstream/master -- models/cam-fv/shell_scripts/cesm2_0/spinup_single_sst.25
 git checkout upstream/master -- models/cam-fv/shell_scripts/cesm2_0_beta05/assimilate.csh
 git checkout upstream/master -- models/cam-fv/shell_scripts/cesm2_1/compress.csh
 git checkout upstream/master -- models/cam-fv/shell_scripts/cesm2_1/mv_to_campaign.csh
 git checkout upstream/master -- models/cam-fv/shell_scripts/cesm2_1/test_assimilate.csh
 git checkout upstream/master -- models/cam-fv/work/minimal_build.csh
 git checkout upstream/master -- models/cam-fv/work/mkmf_perturb_single_instance
 git checkout upstream/master -- models/cam-fv/work/quickbuild.csh
 git checkout upstream/master -- models/cam-old/deprecated/advance_model.csh
 git checkout upstream/master -- models/cam-old/deprecated/advance_model.retry.csh
 git checkout upstream/master -- models/cam-old/deprecated/check_model.csh
 git checkout upstream/master -- models/cam-old/deprecated/job.simple.csh
 git checkout upstream/master -- models/cam-old/deprecated/monthlydiags.csh
 git checkout upstream/master -- models/cam-old/deprecated/run-cam.csh
 git checkout upstream/master -- models/cam-old/deprecated/run-pc.csh
 git checkout upstream/master -- models/cam-old/full_experiment/analyses2initial.csh
 git checkout upstream/master -- models/cam-old/full_experiment/auto_ICs2hpss.csh
 git checkout upstream/master -- models/cam-old/full_experiment/auto_diag2hpss_LSF.csh
 git checkout upstream/master -- models/cam-old/full_experiment/auto_re2hpss_LSF.csh
 git checkout upstream/master -- models/cam-old/full_experiment/diags.csh
 git checkout upstream/master -- models/cam-old/full_experiment/hpss2restart.csh
 git checkout upstream/master -- models/cam-old/full_experiment/job_mpi.csh
 git checkout upstream/master -- models/cam-old/full_experiment/mean2cam_init.csh
 git checkout upstream/master -- models/cam-old/full_experiment/obs_seq2hpss.csh
 git checkout upstream/master -- models/cam-old/matlab/err_cam-se.csh
 git checkout upstream/master -- models/cam-old/matlab/project_cells_make_array.csh
 git checkout upstream/master -- models/cam-old/matlab/se_plot_prep.csh
 git checkout upstream/master -- models/cam-old/perfect_model/pmo.csh
 git checkout upstream/master -- models/cam-old/shell_scripts/archive_cycles.csh
 git checkout upstream/master -- models/cam-old/shell_scripts/assimilate.csh
 git checkout upstream/master -- models/cam-old/shell_scripts/no_assimilate.csh
 git checkout upstream/master -- models/cam-old/shell_scripts/perfect_model.csh
 git checkout upstream/master -- models/cam-old/shell_scripts/submit_cycles.csh
 git checkout upstream/master -- models/cam-old/work/input.nml
 git checkout upstream/master -- models/cam-old/work/quickbuild.csh
 git checkout upstream/master -- models/cice/cice_to_dart.f90
 git checkout upstream/master -- models/cice/shell_scripts/assimilate1_5.csh
 git checkout upstream/master -- models/cice/shell_scripts/assimilate2_0.csh
 git checkout upstream/master -- models/cice/shell_scripts/loop_obs_common_subset.csh
 git checkout upstream/master -- models/cice/shell_scripts/loop_obs_seq_tool.csh
 git checkout upstream/master -- models/cice/shell_scripts/run_ens.csh
 git checkout upstream/master -- models/cice/shell_scripts/run_single.csh
 git checkout upstream/master -- models/cice/work/loop_obs_seq_tool.csh
 git checkout upstream/master -- models/cice/work/quickbuild.csh
 git checkout upstream/master -- models/clm/datm/AppendMonths.csh
 git checkout upstream/master -- models/clm/datm/Process6hrlyCPLHIST.csh
 git checkout upstream/master -- models/clm/model_mod.f90
 git checkout upstream/master -- models/clm/model_mod.html
 git checkout upstream/master -- models/clm/shell_scripts/GenerateEnsemble.csh
 git checkout upstream/master -- models/clm/shell_scripts/GetCleanStarts.csh
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 git checkout upstream/master -- models/cm1/shell_scripts/unfinished/advance_model.csh
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 git checkout upstream/master -- models/coamps/shell_scripts/advance_group.csh
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 git checkout upstream/master -- models/coamps/shell_scripts/advance_wrapper.csh
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 git checkout upstream/master -- models/coamps/templates/EXAMPLE.input.nml
 git checkout upstream/master -- models/coamps_nest/shell_scripts/COAMPS_RESTART_SCRIPTS/advance_group.csh
 git checkout upstream/master -- models/coamps_nest/shell_scripts/COAMPS_RESTART_SCRIPTS/advance_model.csh
 git checkout upstream/master -- models/coamps_nest/shell_scripts/COAMPS_RESTART_SCRIPTS/advance_wrapper.csh
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 git checkout upstream/master -- models/coamps_nest/shell_scripts/COAMPS_RESTART_SCRIPTS/run_pmo.csh
 git checkout upstream/master -- models/coamps_nest/shell_scripts/quickbuild.csh
 git checkout upstream/master -- models/coamps_nest/templates/EXAMPLE.input.nml
 git rm models/coamps_nest/work/path_names_coamps_to_dart
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 git checkout upstream/master -- models/coamps_nest/work/quickbuild.csh
 git checkout upstream/master -- models/dynamo/work/adv_model_par.csh
 git checkout upstream/master -- models/dynamo/work/quickbuild.csh
 git checkout upstream/master -- models/forced_barot/work/quickbuild.csh
 git checkout upstream/master -- models/forced_lorenz_96/shell_scripts/advance_model.csh
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 git checkout upstream/master -- models/forced_lorenz_96/work/workshop_setup.csh
 git checkout upstream/master -- models/gitm/GITM2/src/ModConstants.f90
 git checkout upstream/master -- models/gitm/GITM2/src/ModEarth.f90
 git checkout upstream/master -- models/gitm/GITM2/src/ModOrbital.f90
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 git checkout upstream/master -- models/gitm/GITM2/src/ModTime.f90
 git checkout upstream/master -- models/gitm/dart_gitm_mod.f90
 git checkout upstream/master -- models/gitm/gitm_blocks_to_netcdf.f90
 git checkout upstream/master -- models/gitm/gitm_to_netcdf.f90
 git checkout upstream/master -- models/gitm/model_mod.f90
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 git checkout upstream/master -- models/gitm/shell_scripts/advance_model.csh
 git checkout upstream/master -- models/gitm/testdata2/2DTEC_t110311_204500.bin
 git checkout upstream/master -- models/gitm/testdata2/3DUSR_t110311_204500.bin
 git checkout upstream/master -- models/gitm/testdata2/README
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 git checkout upstream/master -- models/gitm/work/mkmf_gitm_to_netcdf
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 git checkout upstream/master -- models/gitm/work/path_names_gitm_to_netcdf
 git checkout upstream/master -- models/gitm/work/path_names_model_mod_check
 git checkout upstream/master -- models/gitm/work/path_names_netcdf_to_gitm_blocks
 git checkout upstream/master -- models/gitm/work/path_names_obs_diag
 git checkout upstream/master -- models/gitm/work/path_names_obs_seq_to_netcdf
 git checkout upstream/master -- models/gitm/work/path_names_obs_sequence_tool
 git checkout upstream/master -- models/gitm/work/path_names_perfect_model_obs
 git checkout upstream/master -- models/gitm/work/quickbuild.csh
 git checkout upstream/master -- models/ikeda/work/quickbuild.csh
 git checkout upstream/master -- models/lorenz_04/work/quickbuild.csh
 git checkout upstream/master -- models/lorenz_04/work/workshop_setup.csh
 git checkout upstream/master -- models/lorenz_63/model_mod.f90
 git checkout upstream/master -- models/lorenz_63/work/quickbuild.csh
 git checkout upstream/master -- models/lorenz_63/work/workshop_setup.csh
 git checkout upstream/master -- models/lorenz_84/work/quickbuild.csh
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 git checkout upstream/master -- models/lorenz_96/shell_scripts/advance_model.csh
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 git checkout upstream/master -- models/lorenz_96/shell_scripts/run_filter_async4.csh
 git checkout upstream/master -- models/lorenz_96/shell_scripts/run_filter_nonpipe.csh
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 git checkout upstream/master -- models/lorenz_96_2scale/work/quickbuild.csh
 git checkout upstream/master -- models/lorenz_96_2scale/work/workshop_setup.csh
 git checkout upstream/master -- models/model_mod_tools/work/mkmf_preprocess
 git checkout upstream/master -- models/model_mod_tools/work/mkmf_test_quad_irreg_interp
 git checkout upstream/master -- models/model_mod_tools/work/mkmf_test_quad_reg_interp
 git checkout upstream/master -- models/model_mod_tools/work/quickbuild.csh
 git checkout upstream/master -- models/mpas_atm/data/boundary_inout.txt
 git checkout upstream/master -- models/mpas_atm/data/filter_in.txt
 git checkout upstream/master -- models/mpas_atm/data/filter_out.txt
 git checkout upstream/master -- models/mpas_atm/data/input.nml
 git checkout upstream/master -- models/mpas_atm/data/namelist.atmosphere.global
 git checkout upstream/master -- models/mpas_atm/data/namelist.atmosphere.regional
 git checkout upstream/master -- models/mpas_atm/data/namelist.init_atmosphere
 git checkout upstream/master -- models/mpas_atm/data/obs_seq1.out
 git checkout upstream/master -- models/mpas_atm/data/points.txt
 git checkout upstream/master -- models/mpas_atm/data/streams.atmosphere
 git checkout upstream/master -- models/mpas_atm/data/streams.init_atmosphere
 git checkout upstream/master -- models/mpas_atm/model_mod.f90
 git checkout upstream/master -- models/mpas_atm/mpas_dart_obs_preprocess.f90
 git checkout upstream/master -- models/mpas_atm/shell_scripts/README
 git checkout upstream/master -- models/mpas_atm/shell_scripts/README.init_ensemble
 git checkout upstream/master -- models/mpas_atm/shell_scripts/README.regional
 git checkout upstream/master -- models/mpas_atm/shell_scripts/advance_model.csh
 git checkout upstream/master -- models/mpas_atm/shell_scripts/advance_model.template
 git checkout upstream/master -- models/mpas_atm/shell_scripts/driver_initial_ens.csh
 git checkout upstream/master -- models/mpas_atm/shell_scripts/driver_mpas_dart.csh
 git checkout upstream/master -- models/mpas_atm/shell_scripts/setup.csh
 git checkout upstream/master -- models/mpas_atm/shell_scripts/setup_params.csh
 git checkout upstream/master -- models/mpas_atm/update_bc.f90
 git checkout upstream/master -- models/mpas_atm/update_mpas_states.f90
 git checkout upstream/master -- models/mpas_atm/work/input.nml
 git checkout upstream/master -- models/mpas_atm/work/mkmf_update_bc
 git checkout upstream/master -- models/mpas_atm/work/path_names_update_bc
 git checkout upstream/master -- models/mpas_atm/work/quickbuild.csh
 git checkout upstream/master -- models/mpas_ocn/shell_scripts/advance_model.csh
 git checkout upstream/master -- models/mpas_ocn/shell_scripts/run_filter.csh
 git checkout upstream/master -- models/mpas_ocn/shell_scripts/run_filter_mpas.csh
 git checkout upstream/master -- models/mpas_ocn/work/quickbuild.csh
 git rm models/noah/dart_to_noah.html
 git checkout upstream/master -- models/noah/model_mod.f90
 git checkout upstream/master -- models/noah/shell_scripts/advance_model.csh
 git checkout upstream/master -- models/noah/shell_scripts/compile_noah.csh
 git checkout upstream/master -- models/noah/shell_scripts/run_filter.csh
 git checkout upstream/master -- models/noah/shell_scripts/run_pmo.csh
 git checkout upstream/master -- models/noah/shell_scripts/setup_filter.csh
 git checkout upstream/master -- models/noah/shell_scripts/setup_pmo.csh
 git checkout upstream/master -- models/noah/work/input.nml
 git rm models/noah/work/obs_seq.in
 git checkout upstream/master -- models/noah/work/path_names_obs_common_subset
 git checkout upstream/master -- models/noah/work/quickbuild.csh
 git checkout upstream/master -- models/noah/work/set_def.out
 git checkout upstream/master -- models/null_model/work/quickbuild.csh
 git checkout upstream/master -- models/pe2lyr/work/quickbuild.csh
 git checkout upstream/master -- models/rose/shell_scripts/advance_model.csh
 git checkout upstream/master -- models/rose/shell_scripts/run_perfect_model_obs.csh
 git checkout upstream/master -- models/rose/work/quickbuild.csh
 git checkout upstream/master -- models/simple_advection/work/quickbuild.csh
 git checkout upstream/master -- models/simple_advection/work/workshop_setup.csh
 git checkout upstream/master -- models/sqg/work/quickbuild.csh
 git checkout upstream/master -- models/template/shell_scripts/advance_model.csh
 git checkout upstream/master -- models/template/shell_scripts/run_filter.csh
 git checkout upstream/master -- models/template/work/quickbuild.csh
 git checkout upstream/master -- models/tiegcm/shell_scripts/advance_model.csh
 git checkout upstream/master -- models/tiegcm/shell_scripts/run_filter.csh
 git checkout upstream/master -- models/tiegcm/shell_scripts/run_filter_async4.csh
 git checkout upstream/master -- models/tiegcm/shell_scripts/run_perfect_model_obs.csh
 git checkout upstream/master -- models/tiegcm/work/quickbuild.csh
 git checkout upstream/master -- models/wrf/PERTURB/3DVAR-COVAR/3dvar-covar.csh
 git checkout upstream/master -- models/wrf/experiments/Radar/IC/prep_IC_pertsounding.csh
 git checkout upstream/master -- models/wrf/experiments/Radar/IC/sounding_perturbation/compile_pert_sounding.csh
 git checkout upstream/master -- models/wrf/experiments/Radar/start_over.csh
 git checkout upstream/master -- models/wrf/model_mod.f90
 git checkout upstream/master -- models/wrf/regression/CONUS-V2/gen_ic_files.csh
 git checkout upstream/master -- models/wrf/regression/CONUS-V3/icbc_real.ksh
 git checkout upstream/master -- models/wrf/shell_scripts/assim_advance.csh
 git checkout upstream/master -- models/wrf/shell_scripts/assimilate.csh
 git checkout upstream/master -- models/wrf/shell_scripts/diagnostics_obs.csh
 git checkout upstream/master -- models/wrf/shell_scripts/driver.csh
 git checkout upstream/master -- models/wrf/shell_scripts/first_advance.csh
 git checkout upstream/master -- models/wrf/shell_scripts/gen_pert_bank.csh
 git checkout upstream/master -- models/wrf/shell_scripts/gen_retro_icbc.csh
 git checkout upstream/master -- models/wrf/shell_scripts/init_ensemble_var.csh
 git checkout upstream/master -- models/wrf/shell_scripts/new_advance_model.csh
 git checkout upstream/master -- models/wrf/shell_scripts/param.csh
 git checkout upstream/master -- models/wrf/shell_scripts/prep_ic.csh
 git checkout upstream/master -- models/wrf/shell_scripts/setup.csh
 git rm models/wrf/tutorial/README
 git checkout upstream/master -- models/wrf/tutorial/README.md
 git rm models/wrf/tutorial/index.html
 git checkout upstream/master -- models/wrf/work/mkmf_perturb_single_instance
 git checkout upstream/master -- models/wrf/work/mkmf_radiance_obs_to_netcdf
 git checkout upstream/master -- models/wrf/work/path_names_radiance_obs_to_netcdf
 git checkout upstream/master -- models/wrf/work/quickbuild.csh
 git checkout upstream/master -- models/wrf_hydro/R/PlotEnsTimeSeries.R
 git checkout upstream/master -- models/wrf_hydro/R/plot_gages.R
 git checkout upstream/master -- models/wrf_hydro/README.md
 git checkout upstream/master -- models/wrf_hydro/create_identity_streamflow_obs.f90
 git checkout upstream/master -- models/wrf_hydro/ensemble_config_files/ens_setup_NWM_channel-only.py
 git checkout upstream/master -- models/wrf_hydro/ensemble_config_files/ens_setup_croton_gridded.py
 git checkout upstream/master -- models/wrf_hydro/ensemble_config_files/ens_setup_exp_1.py
 git checkout upstream/master -- models/wrf_hydro/ensemble_config_files/ensemble_config-multiphysics-channel-only.py
 git checkout upstream/master -- models/wrf_hydro/ensemble_forecasts/example_ens_forecast.py
 git checkout upstream/master -- models/wrf_hydro/ensemble_open_loop_runs/florence_cutout_bucket_expon_ensemble.ipynb
 git checkout upstream/master -- models/wrf_hydro/ensemble_open_loop_runs/florence_cutout_mannings_ensemble.ipynb
 git checkout upstream/master -- models/wrf_hydro/experiment_config_files/OSSE_cutout_MP.yaml
 git checkout upstream/master -- models/wrf_hydro/experiment_config_files/cheyenne_croton_gridded.yaml
 git checkout upstream/master -- models/wrf_hydro/experiment_config_files/cheyenne_sixmile.yaml
 git checkout upstream/master -- models/wrf_hydro/experiment_config_files/cheyenne_sixmile_moha.yaml
 git checkout upstream/master -- models/wrf_hydro/experiment_config_files/docker_sixmile.yaml
 git checkout upstream/master -- models/wrf_hydro/experiment_config_files/docker_sixmile_setup.sh
 git checkout upstream/master -- models/wrf_hydro/experiment_config_files/hydro_dart_config.cheyenne.croton_gridded.yaml
 git checkout upstream/master -- models/wrf_hydro/experiment_config_files/test_exp.yaml
 git checkout upstream/master -- models/wrf_hydro/hydro_dart_py/README.md
 git checkout upstream/master -- models/wrf_hydro/hydro_dart_py/hydrodartpy/__init__.py
 git checkout upstream/master -- models/wrf_hydro/hydro_dart_py/hydrodartpy/core/__init__.py
 git checkout upstream/master -- models/wrf_hydro/hydro_dart_py/hydrodartpy/core/advance_ensemble.py
 git checkout upstream/master -- models/wrf_hydro/hydro_dart_py/hydrodartpy/core/collect_run_output.py
 git checkout upstream/master -- models/wrf_hydro/hydro_dart_py/hydrodartpy/core/create_parameter_restart_file.py
 git checkout upstream/master -- models/wrf_hydro/hydro_dart_py/hydrodartpy/core/create_usgs_daily_obs_seq.py
 git checkout upstream/master -- models/wrf_hydro/hydro_dart_py/hydrodartpy/core/dartclasses.py
 git checkout upstream/master -- models/wrf_hydro/hydro_dart_py/hydrodartpy/core/get_ensemble_time.py
 git checkout upstream/master -- models/wrf_hydro/hydro_dart_py/hydrodartpy/core/gregorian.py
 git checkout upstream/master -- models/wrf_hydro/hydro_dart_py/hydrodartpy/core/obs_seq_dummy.py
 git checkout upstream/master -- models/wrf_hydro/hydro_dart_py/hydrodartpy/core/run_filter_experiment.py
 git checkout upstream/master -- models/wrf_hydro/hydro_dart_py/hydrodartpy/core/set_obs_seq_times.py
 git checkout upstream/master -- models/wrf_hydro/hydro_dart_py/hydrodartpy/core/setup_dart.py
 git checkout upstream/master -- models/wrf_hydro/hydro_dart_py/hydrodartpy/core/setup_experiment.py
 git checkout upstream/master -- models/wrf_hydro/hydro_dart_py/hydrodartpy/core/setup_experiment_tools.py
 git checkout upstream/master -- models/wrf_hydro/hydro_dart_py/hydrodartpy/core/setup_initial_ens.py
 git checkout upstream/master -- models/wrf_hydro/hydro_dart_py/hydrodartpy/core/setup_obs_prep.py
 git checkout upstream/master -- models/wrf_hydro/hydro_dart_py/hydrodartpy/core/setup_usgs_daily.py
 git checkout upstream/master -- models/wrf_hydro/hydro_dart_py/hydrodartpy/core/setup_wrf_hydro.py
 git checkout upstream/master -- models/wrf_hydro/hydro_dart_py/hydrodartpy/core/setup_wrf_hydro_ens.py
 git checkout upstream/master -- models/wrf_hydro/hydro_dart_py/hydrodartpy/core/setup_wrf_hydro_ens_job.py
 git checkout upstream/master -- models/wrf_hydro/hydro_dart_py/hydrodartpy/core/submission_scripts/submit_filter_experiment.sh
 git checkout upstream/master -- models/wrf_hydro/hydro_dart_py/hydrodartpy/core/submission_scripts/submit_usgs_daily_obs_converter.sh
 git checkout upstream/master -- models/wrf_hydro/hydro_dart_py/hydrodartpy/tests/__init__.py
 git checkout upstream/master -- models/wrf_hydro/hydro_dart_py/hydrodartpy/tests/conftest.py
 git checkout upstream/master -- models/wrf_hydro/hydro_dart_py/hydrodartpy/tests/experiment_config_files/docker_testing_sixmile.yaml
 git checkout upstream/master -- models/wrf_hydro/hydro_dart_py/hydrodartpy/tests/local/run_tests.py
 git checkout upstream/master -- models/wrf_hydro/hydro_dart_py/hydrodartpy/tests/test_1_fundamental.py
 git checkout upstream/master -- models/wrf_hydro/hydro_dart_py/setup.py
 git checkout upstream/master -- models/wrf_hydro/matlab/disp_ATS_localization.m
 git checkout upstream/master -- models/wrf_hydro/matlab/gauges_2_indices.m
 git checkout upstream/master -- models/wrf_hydro/matlab/norm_taylor_diag.m
 git checkout upstream/master -- models/wrf_hydro/matlab/plot_connections.m
 git checkout upstream/master -- models/wrf_hydro/matlab/stream_diags.m
 git checkout upstream/master -- models/wrf_hydro/model_mod.f90

# R095  models/noah/model_mod.html models/wrf_hydro/model_mod.html
 git rm models/noah/model_mod.html
 git checkout upstream/master -- models/wrf_hydro/model_mod.html

 git checkout upstream/master -- models/wrf_hydro/model_mod.nml
 git checkout upstream/master -- models/wrf_hydro/noah_hydro_mod.f90
 git checkout upstream/master -- models/wrf_hydro/obs_config_files/florence_obs_ex.yaml
 git checkout upstream/master -- models/wrf_hydro/python/.gitignore
 git checkout upstream/master -- models/wrf_hydro/python/analysis/get_nwm_chrtout_postgres.py
 git checkout upstream/master -- models/wrf_hydro/python/analysis/matthew_daily_variance.ipy
 git checkout upstream/master -- models/wrf_hydro/python/analysis/matthew_error_cov.ipy
 git checkout upstream/master -- models/wrf_hydro/python/analysis/sixmile_plot_domain.py
 git checkout upstream/master -- models/wrf_hydro/python/diagnostic/plot_channel_network.py
 git checkout upstream/master -- models/wrf_hydro/python/experiment/README.md
 git checkout upstream/master -- models/wrf_hydro/python/experiment/setup_filter_experiment.py
 git checkout upstream/master -- models/wrf_hydro/python/perturb/noise_qBtmVertRunoff_additive_fraction04.py
 git checkout upstream/master -- models/wrf_hydro/python/perturb/noise_qBucket_additive.py
 git checkout upstream/master -- models/wrf_hydro/python/perturb/noise_qSfcLatRunoff_additive.py
 git checkout upstream/master -- models/wrf_hydro/python/perturb/noise_qSfcLatRunoff_additive_fraction.py
 git checkout upstream/master -- models/wrf_hydro/python/perturb/noise_qSfcLatRunoff_additive_fraction04.py
 git checkout upstream/master -- models/wrf_hydro/python/perturb/perturb_channel_bucket_only_forcing.py
 git checkout upstream/master -- models/wrf_hydro/python/perturb/perturb_channel_only_forcing.py
 git checkout upstream/master -- models/wrf_hydro/python/perturb/test_perturb.py
 git checkout upstream/master -- models/wrf_hydro/shell_scripts/DART_cleanup.csh
 git checkout upstream/master -- models/wrf_hydro/shell_scripts/DART_cleanup_add_time.csh
 git checkout upstream/master -- models/wrf_hydro/shell_scripts/DART_cleanup_pack_members.csh
 git checkout upstream/master -- models/wrf_hydro/shell_scripts/run_filter_experiment.csh.template
 git checkout upstream/master -- models/wrf_hydro/shell_scripts/setup_experiment_example.cheyenne.sixmile.sh
 git checkout upstream/master -- models/wrf_hydro/shell_scripts/setup_experiment_example.docker.sixmile.sh
 git checkout upstream/master -- models/wrf_hydro/shell_scripts/templates/advance_ensemble.csh.template
 git checkout upstream/master -- models/wrf_hydro/shell_scripts/templates/advance_model.csh
 git checkout upstream/master -- models/wrf_hydro/shell_scripts/templates/batch_job_resource_explanation.txt
 git checkout upstream/master -- models/wrf_hydro/shell_scripts/templates/run_filter.csh.template
 git checkout upstream/master -- models/wrf_hydro/shell_scripts/templates/run_multiple_cycles.csh
 git checkout upstream/master -- models/wrf_hydro/shell_scripts/templates/setup_experiment.csh
 git checkout upstream/master -- models/wrf_hydro/shell_scripts/templates/submit_multiple_jobs_slurm.csh
 git checkout upstream/master -- models/wrf_hydro/shell_scripts/wrf_hydro_cleanup.csh
 git checkout upstream/master -- models/wrf_hydro/shell_scripts/wrf_hydro_cleanup_worker.csh
 git checkout upstream/master -- models/wrf_hydro/templates/README
 git checkout upstream/master -- models/wrf_hydro/templates/RESTART.YYYYMMDDHH_DOMAIN1.template.ascii
 git checkout upstream/master -- models/wrf_hydro/templates/namelist.hrldas.template

# R100  models/noah/templates/wrfinput.template.ascii models/wrf_hydro/templates/wrfinput.template.ascii
 git rm models/noah/templates/wrfinput.template.ascii
 git checkout upstream/master -- models/wrf_hydro/templates/wrfinput.template.ascii

 git checkout upstream/master -- models/wrf_hydro/work/cleanup.csh
 git checkout upstream/master -- models/wrf_hydro/work/hydro.namelist
 git checkout upstream/master -- models/wrf_hydro/work/input.nml
 git checkout upstream/master -- models/wrf_hydro/work/list_of_obs_files.txt

# R070  models/coamps_nest/work/mkmf_in_grid models/wrf_hydro/work/mkmf_advance_time
 git rm models/coamps_nest/work/mkmf_in_grid
 git checkout upstream/master -- models/wrf_hydro/work/mkmf_advance_time

 git checkout upstream/master -- models/wrf_hydro/work/mkmf_create_fixed_network_seq

# R065  models/coamps_nest/work/mkmf_coamps_to_dart models/wrf_hydro/work/mkmf_create_identity_streamflow_obs
 git rm models/coamps_nest/work/mkmf_coamps_to_dart
 git checkout upstream/master -- models/wrf_hydro/work/mkmf_create_identity_streamflow_obs

 git checkout upstream/master -- models/wrf_hydro/work/mkmf_create_obs_sequence
 git checkout upstream/master -- models/wrf_hydro/work/mkmf_filter
 git checkout upstream/master -- models/wrf_hydro/work/mkmf_model_mod_check

# R072  models/mpas_atm/work/broken_mkmf_integrate_model models/wrf_hydro/work/mkmf_obs_diag
 git rm models/mpas_atm/work/broken_mkmf_integrate_model
 git checkout upstream/master -- models/wrf_hydro/work/mkmf_obs_diag

# R069  models/coamps_nest/work/mkmf_dart_to_coamps models/wrf_hydro/work/mkmf_obs_seq_to_netcdf
 git rm models/coamps_nest/work/mkmf_dart_to_coamps
 git checkout upstream/master -- models/wrf_hydro/work/mkmf_obs_seq_to_netcdf

 git checkout upstream/master -- models/wrf_hydro/work/mkmf_obs_sequence_tool
 git checkout upstream/master -- models/wrf_hydro/work/mkmf_perfect_model_obs

# R071  models/mpas_atm/work/broken_mkmf_model_mod_check models/wrf_hydro/work/mkmf_preprocess
 git rm models/mpas_atm/work/broken_mkmf_model_mod_check
 git checkout upstream/master -- models/wrf_hydro/work/mkmf_preprocess

 git checkout upstream/master -- models/wrf_hydro/work/namelist.hrldas
 git checkout upstream/master -- models/wrf_hydro/work/obs_seq.in
 git checkout upstream/master -- models/wrf_hydro/work/path_names_advance_time
 git checkout upstream/master -- models/wrf_hydro/work/path_names_create_fixed_network_seq
 git checkout upstream/master -- models/wrf_hydro/work/path_names_create_identity_streamflow_obs
 git checkout upstream/master -- models/wrf_hydro/work/path_names_create_obs_sequence
 git checkout upstream/master -- models/wrf_hydro/work/path_names_filter
 git checkout upstream/master -- models/wrf_hydro/work/path_names_model_mod_check
 git checkout upstream/master -- models/wrf_hydro/work/path_names_obs_diag
 git checkout upstream/master -- models/wrf_hydro/work/path_names_obs_seq_to_netcdf
 git checkout upstream/master -- models/wrf_hydro/work/path_names_obs_sequence_tool
 git checkout upstream/master -- models/wrf_hydro/work/path_names_perfect_model_obs
 git checkout upstream/master -- models/wrf_hydro/work/path_names_preprocess
 git checkout upstream/master -- models/wrf_hydro/work/quickbuild.csh
 git checkout upstream/master -- models/wrf_hydro/work/wanted_gages_list.txt
 git checkout upstream/master -- observations/forward_operators/DEFAULT_obs_def_mod.F90
 git checkout upstream/master -- observations/forward_operators/obs_def_GRACE_mod.f90
 git checkout upstream/master -- observations/forward_operators/obs_def_abs_humidity_mod.f90
 git checkout upstream/master -- observations/forward_operators/obs_def_altimeter_mod.f90
 git rm observations/forward_operators/obs_def_chem_units_mod.f90
 git checkout upstream/master -- observations/forward_operators/obs_def_land_mod.f90
 git checkout upstream/master -- observations/forward_operators/obs_def_mesonet_mod.f90
 git rm observations/forward_operators/obs_def_mod.CAM.f90
 git checkout upstream/master -- observations/forward_operators/obs_def_oxygen_ion_density_mod.f90
 git checkout upstream/master -- observations/forward_operators/obs_def_reanalysis_bufr_mod.f90
 git checkout upstream/master -- observations/forward_operators/obs_def_rel_humidity_mod.f90
 git checkout upstream/master -- observations/forward_operators/obs_def_rttov_mod.f90
 git checkout upstream/master -- observations/forward_operators/obs_def_rttov_mod.html
 git checkout upstream/master -- observations/forward_operators/obs_def_rttov_mod.nml
 git checkout upstream/master -- observations/forward_operators/obs_def_streamflow_mod.f90
 git checkout upstream/master -- observations/forward_operators/obs_def_tower_mod.f90
 git checkout upstream/master -- observations/forward_operators/obs_def_upper_atm_mod.f90
 git checkout upstream/master -- observations/forward_operators/rttov_sensor_db.csv
 git checkout upstream/master -- observations/obs_converters/AIRS/BUILDME
 git checkout upstream/master -- observations/obs_converters/AIRS/airs_JPL_mod.f90
 git checkout upstream/master -- observations/obs_converters/AIRS/airs_obs_mod.f90
 git checkout upstream/master -- observations/obs_converters/AIRS/convert_airs_L2.f90
 git rm observations/obs_converters/AIRS/data/AIRS.2007.11.01.001.L2.RetStd.v5.2.2.0.G08078150655.hdf
 git checkout upstream/master -- observations/obs_converters/AIRS/work/input.nml
 git checkout upstream/master -- observations/obs_converters/AIRS/work/mkmf_convert_airs_L2
 git checkout upstream/master -- observations/obs_converters/AIRS/work/quickbuild.csh
 git checkout upstream/master -- observations/obs_converters/AURA/work/input.nml
 git checkout upstream/master -- observations/obs_converters/AURA/work/quickbuild.csh
 git checkout upstream/master -- observations/obs_converters/AURA/work/run_sept.csh
 git checkout upstream/master -- observations/obs_converters/AVISO/work/quickbuild.csh
 git checkout upstream/master -- observations/obs_converters/Ameriflux/level4_to_obs.f90
 git checkout upstream/master -- observations/obs_converters/Ameriflux/level4_to_obs.html
 git checkout upstream/master -- observations/obs_converters/Ameriflux/shell_scripts/CreateObs.csh
 git checkout upstream/master -- observations/obs_converters/Ameriflux/work/quickbuild.csh
 git checkout upstream/master -- observations/obs_converters/CHAMP/work/quickbuild.csh
 git checkout upstream/master -- observations/obs_converters/CNOFS/work/quickbuild.csh
 git checkout upstream/master -- observations/obs_converters/CONAGUA/CONAGUA_convert_streamflow.f90
 git checkout upstream/master -- observations/obs_converters/CONAGUA/CONAGUA_convert_streamflow.nml
 git checkout upstream/master -- observations/obs_converters/CONAGUA/README
 git checkout upstream/master -- observations/obs_converters/CONAGUA/work/input.nml
 git checkout upstream/master -- observations/obs_converters/CONAGUA/work/mkmf_CONAGUA_convert_streamflow
 git checkout upstream/master -- observations/obs_converters/CONAGUA/work/mkmf_advance_time
 git checkout upstream/master -- observations/obs_converters/CONAGUA/work/mkmf_obs_seq_to_netcdf
 git checkout upstream/master -- observations/obs_converters/CONAGUA/work/mkmf_obs_sequence_tool
 git checkout upstream/master -- observations/obs_converters/CONAGUA/work/mkmf_preprocess
 git checkout upstream/master -- observations/obs_converters/CONAGUA/work/path_names_CONAGUA_convert_streamflow
 git checkout upstream/master -- observations/obs_converters/CONAGUA/work/path_names_advance_time
 git checkout upstream/master -- observations/obs_converters/CONAGUA/work/path_names_obs_seq_to_netcdf
 git checkout upstream/master -- observations/obs_converters/CONAGUA/work/path_names_obs_sequence_tool
 git checkout upstream/master -- observations/obs_converters/CONAGUA/work/path_names_preprocess
 git checkout upstream/master -- observations/obs_converters/CONAGUA/work/quickbuild.csh
 git checkout upstream/master -- observations/obs_converters/COSMOS/COSMOS_development.html
 git checkout upstream/master -- observations/obs_converters/COSMOS/COSMOS_to_obs.html
 git checkout upstream/master -- observations/obs_converters/COSMOS/work/input.nml
 git checkout upstream/master -- observations/obs_converters/COSMOS/work/quickbuild.csh
 git checkout upstream/master -- observations/obs_converters/DWL/shell_scripts/hour_time_loop.csh
 git checkout upstream/master -- observations/obs_converters/DWL/work/quickbuild.csh
 git checkout upstream/master -- observations/obs_converters/GMI/README.md
 git checkout upstream/master -- observations/obs_converters/GMI/convert_gmi_L1.f90
 git checkout upstream/master -- observations/obs_converters/GMI/gmi_L1_mod.f90
 git checkout upstream/master -- observations/obs_converters/GMI/work/input.nml
 git checkout upstream/master -- observations/obs_converters/GMI/work/mkmf_convert_gmi_L1
 git checkout upstream/master -- observations/obs_converters/GMI/work/mkmf_preprocess
 git checkout upstream/master -- observations/obs_converters/GMI/work/path_names_convert_gmi_L1
 git checkout upstream/master -- observations/obs_converters/GMI/work/path_names_preprocess
 git checkout upstream/master -- observations/obs_converters/GMI/work/quickbuild.csh
 git checkout upstream/master -- observations/obs_converters/GOES/work/mkmf_convert_goes_ABI_L1b
 git checkout upstream/master -- observations/obs_converters/GOES/work/mkmf_preprocess
 git checkout upstream/master -- observations/obs_converters/GOES/work/path_names_convert_goes_ABI_L1b
 git checkout upstream/master -- observations/obs_converters/GOES/work/path_names_preprocess
 git checkout upstream/master -- observations/obs_converters/GOES/work/quickbuild.csh
 git checkout upstream/master -- observations/obs_converters/GPSPW/shell_scripts/get_gpspwv.csh
 git checkout upstream/master -- observations/obs_converters/GPSPW/shell_scripts/run_convert_gpspw.csh
 git checkout upstream/master -- observations/obs_converters/GPSPW/shell_scripts/run_convert_gpspw_conus.csh
 git checkout upstream/master -- observations/obs_converters/GPSPW/shell_scripts/run_obs_seq_tool_gpspw.csh
 git checkout upstream/master -- observations/obs_converters/GPSPW/work/input.nml
 git checkout upstream/master -- observations/obs_converters/GPSPW/work/quickbuild.csh
 git checkout upstream/master -- observations/obs_converters/GRACE/convert_daily_grace.f90
 git checkout upstream/master -- observations/obs_converters/GRACE/shell_scripts/get_grace_obsseq.csh
 git checkout upstream/master -- observations/obs_converters/GRACE/work/input.nml
 git checkout upstream/master -- observations/obs_converters/GRACE/work/mkmf_convert_daily_grace
 git checkout upstream/master -- observations/obs_converters/GRACE/work/mkmf_obs_seq_to_netcdf
 git checkout upstream/master -- observations/obs_converters/GRACE/work/mkmf_obs_sequence_tool
 git checkout upstream/master -- observations/obs_converters/GRACE/work/mkmf_preprocess
 git checkout upstream/master -- observations/obs_converters/GRACE/work/path_names_convert_daily_grace
 git checkout upstream/master -- observations/obs_converters/GRACE/work/path_names_obs_seq_to_netcdf
 git checkout upstream/master -- observations/obs_converters/GRACE/work/path_names_obs_sequence_tool
 git checkout upstream/master -- observations/obs_converters/GRACE/work/path_names_preprocess
 git checkout upstream/master -- observations/obs_converters/GRACE/work/quickbuild.csh
 git rm observations/obs_converters/GSI2DART/README
 git checkout upstream/master -- observations/obs_converters/GSI2DART/README.rst
 git checkout upstream/master -- observations/obs_converters/GSI2DART/dart_obs_seq_mod.f90
 git checkout upstream/master -- observations/obs_converters/GSI2DART/enkf/README
 git checkout upstream/master -- observations/obs_converters/GSI2DART/enkf/read_diag.f90
 git checkout upstream/master -- observations/obs_converters/GSI2DART/enkf/readconvobs.f90
 git checkout upstream/master -- observations/obs_converters/GSI2DART/enkf/readozobs.f90
 git checkout upstream/master -- observations/obs_converters/GSI2DART/enkf/readsatobs.f90
 git checkout upstream/master -- observations/obs_converters/GSI2DART/gsi_to_dart.f90
 git checkout upstream/master -- observations/obs_converters/GSI2DART/gsi_to_dart.nml
 git checkout upstream/master -- observations/obs_converters/GSI2DART/mpisetup.f90
 git checkout upstream/master -- observations/obs_converters/GSI2DART/params.f90
 git checkout upstream/master -- observations/obs_converters/GSI2DART/radinfo.f90
 git rm observations/obs_converters/GSI2DART/work/fnames.txt
 git checkout upstream/master -- observations/obs_converters/GSI2DART/work/input.nml
 git checkout upstream/master -- observations/obs_converters/GSI2DART/work/mkmf_gsi_to_dart
 git checkout upstream/master -- observations/obs_converters/GSI2DART/work/path_names_gsi_to_dart
 git checkout upstream/master -- observations/obs_converters/GSI2DART/work/submit.csh
 git checkout upstream/master -- observations/obs_converters/GTSPP/work/input.nml
 git checkout upstream/master -- observations/obs_converters/GTSPP/work/quickbuild.csh
 git checkout upstream/master -- observations/obs_converters/MADIS/convert_madis_rawin.f90
 git rm observations/obs_converters/MADIS/data/2011060311_profiler.nc
 git checkout upstream/master -- observations/obs_converters/MADIS/data/2011060311_profiler.nc.gz
 git checkout upstream/master -- observations/obs_converters/MADIS/shell_scripts/madis_archive.csh
 git checkout upstream/master -- observations/obs_converters/MADIS/shell_scripts/madis_conv.csh
 git checkout upstream/master -- observations/obs_converters/MADIS/shell_scripts/windowing.csh
 git checkout upstream/master -- observations/obs_converters/MADIS/work/quickbuild.csh
 git checkout upstream/master -- observations/obs_converters/MIDAS/work/input.nml
 git checkout upstream/master -- observations/obs_converters/MIDAS/work/quickbuild.csh
 git checkout upstream/master -- observations/obs_converters/MODIS/MOD15A2_to_obs.html
 git checkout upstream/master -- observations/obs_converters/MODIS/work/input.nml
 git checkout upstream/master -- observations/obs_converters/MODIS/work/input.nml.template
 git checkout upstream/master -- observations/obs_converters/MODIS/work/quickbuild.csh
 git checkout upstream/master -- observations/obs_converters/MPD/MPD_text_to_obs.f90
 git checkout upstream/master -- observations/obs_converters/MPD/README.md
 git checkout upstream/master -- observations/obs_converters/MPD/work/.gitignore
 git checkout upstream/master -- observations/obs_converters/MPD/work/convert_to_text.py
 git checkout upstream/master -- observations/obs_converters/MPD/work/input.nml
 git checkout upstream/master -- observations/obs_converters/MPD/work/mkmf_MPD_text_to_obs
 git checkout upstream/master -- observations/obs_converters/MPD/work/mkmf_preprocess
 git checkout upstream/master -- observations/obs_converters/MPD/work/path_names_MPD_text_to_obs
 git checkout upstream/master -- observations/obs_converters/MPD/work/path_names_preprocess
 git checkout upstream/master -- observations/obs_converters/MPD/work/quickbuild.csh
 git checkout upstream/master -- observations/obs_converters/MPD/work/text.txt
 git checkout upstream/master -- observations/obs_converters/NCEP/ascii_to_obs/shell_scripts/create_obs_seq.csh
 git checkout upstream/master -- observations/obs_converters/NCEP/ascii_to_obs/shell_scripts/multi_create.csh
 git checkout upstream/master -- observations/obs_converters/NCEP/ascii_to_obs/work/quickbuild.csh
 git checkout upstream/master -- observations/obs_converters/NCEP/netcdf/work/quickbuild.csh
 git checkout upstream/master -- observations/obs_converters/NCEP/prep_bufr/convert_bufr/convert_bufr.csh
 git checkout upstream/master -- observations/obs_converters/NCEP/prep_bufr/exe/.empty_for_a_reason
 git checkout upstream/master -- observations/obs_converters/NCEP/prep_bufr/install.sh
 git checkout upstream/master -- observations/obs_converters/NCEP/prep_bufr/src/prepbufr.f
 git checkout upstream/master -- observations/obs_converters/NCEP/prep_bufr/work/prepbufr.csh
 git checkout upstream/master -- observations/obs_converters/NCEP/prep_bufr/work/quickbuild.csh
 git checkout upstream/master -- observations/obs_converters/NCEP/prep_bufr/work/run_one_prepbufr.csh
 git checkout upstream/master -- observations/obs_converters/NCEP/prep_bufr/work/run_some_prepbufr.csh
 git rm observations/obs_converters/README
 git checkout upstream/master -- observations/obs_converters/README.md
 git checkout upstream/master -- observations/obs_converters/ROMS/shell_scripts/Edit_Attributes.csh
 git checkout upstream/master -- observations/obs_converters/ROMS/work/quickbuild.csh
 git checkout upstream/master -- observations/obs_converters/SABER/work/input.nml
 git checkout upstream/master -- observations/obs_converters/SABER/work/quickbuild.csh
 git checkout upstream/master -- observations/obs_converters/SSEC/work/quickbuild.csh
 git checkout upstream/master -- observations/obs_converters/SST/SST.html
 git checkout upstream/master -- observations/obs_converters/SST/work/quickbuild.csh
 git checkout upstream/master -- observations/obs_converters/SSUSI/shell_scripts/netcdf_manip.csh
 git checkout upstream/master -- observations/obs_converters/SSUSI/work/input.nml
 git checkout upstream/master -- observations/obs_converters/SSUSI/work/quickbuild.csh
 git checkout upstream/master -- observations/obs_converters/USGS/convert_streamflow.f90
 git checkout upstream/master -- observations/obs_converters/USGS/scripts/makedaily.TEMPLATE.csh
 git checkout upstream/master -- observations/obs_converters/USGS/scripts/makedaily.csh
 git checkout upstream/master -- observations/obs_converters/USGS/scripts/parallel_daily.batch.TEMPLATE.csh
 git checkout upstream/master -- observations/obs_converters/USGS/scripts/parallel_daily.batch.csh
 git checkout upstream/master -- observations/obs_converters/USGS/work/input.nml
 git checkout upstream/master -- observations/obs_converters/USGS/work/list_of_obs_files.txt
 git checkout upstream/master -- observations/obs_converters/USGS/work/mkmf_advance_time
 git checkout upstream/master -- observations/obs_converters/USGS/work/mkmf_convert_streamflow
 git checkout upstream/master -- observations/obs_converters/USGS/work/mkmf_obs_seq_to_netcdf
 git checkout upstream/master -- observations/obs_converters/USGS/work/mkmf_obs_sequence_tool
 git checkout upstream/master -- observations/obs_converters/USGS/work/mkmf_preprocess
 git checkout upstream/master -- observations/obs_converters/USGS/work/path_names_advance_time
 git checkout upstream/master -- observations/obs_converters/USGS/work/path_names_convert_streamflow
 git checkout upstream/master -- observations/obs_converters/USGS/work/path_names_obs_seq_to_netcdf
 git checkout upstream/master -- observations/obs_converters/USGS/work/path_names_obs_sequence_tool
 git checkout upstream/master -- observations/obs_converters/USGS/work/path_names_preprocess
 git checkout upstream/master -- observations/obs_converters/USGS/work/quickbuild.csh
 git checkout upstream/master -- observations/obs_converters/USGS/work/wanted_gages_list.txt
 git checkout upstream/master -- observations/obs_converters/WOD/shell_scripts/runyear.sh
 git checkout upstream/master -- observations/obs_converters/WOD/work/input.nml
 git checkout upstream/master -- observations/obs_converters/WOD/work/quickbuild.csh
 git checkout upstream/master -- observations/obs_converters/cice/shell_scripts/day_time_loop_aggre.csh
 git checkout upstream/master -- observations/obs_converters/cice/shell_scripts/day_time_loop_modis_ist.csh
 git checkout upstream/master -- observations/obs_converters/cice/shell_scripts/hour_time_loop.csh
 git checkout upstream/master -- observations/obs_converters/cice/work/quickbuild.csh
 git checkout upstream/master -- observations/obs_converters/even_sphere/run_fixed_network_daily.csh
 git checkout upstream/master -- observations/obs_converters/even_sphere/run_fixed_network_seq.csh
 git checkout upstream/master -- observations/obs_converters/gnd_gps_vtec/work/quickbuild.csh
 git checkout upstream/master -- observations/obs_converters/gps/shell_scripts/README
 git checkout upstream/master -- observations/obs_converters/gps/shell_scripts/README.iono_example_files
 git checkout upstream/master -- observations/obs_converters/gps/shell_scripts/convert_afew_gpsro.csh
 git checkout upstream/master -- observations/obs_converters/gps/shell_scripts/convert_many_gpsro.csh
 git checkout upstream/master -- observations/obs_converters/gps/shell_scripts/gpsro_to_obsseq.csh
 git checkout upstream/master -- observations/obs_converters/gps/shell_scripts/iono_to_obsseq.csh
 git checkout upstream/master -- observations/obs_converters/gps/shell_scripts/multi_parallel.batch
 git checkout upstream/master -- observations/obs_converters/gps/shell_scripts/my_convert_many_gpsro.csh
 git checkout upstream/master -- observations/obs_converters/gps/shell_scripts/my_gpsro_to_obsseq.csh
 git checkout upstream/master -- observations/obs_converters/gps/shell_scripts/split_obs_seq.csh
 git checkout upstream/master -- observations/obs_converters/gps/work/input.nml
 git checkout upstream/master -- observations/obs_converters/gps/work/quickbuild.csh
 git checkout upstream/master -- observations/obs_converters/ok_mesonet/work/quickbuild.csh
 git checkout upstream/master -- observations/obs_converters/quikscat/work/ConvertMany.csh
 git checkout upstream/master -- observations/obs_converters/quikscat/work/quickbuild.csh
 git checkout upstream/master -- observations/obs_converters/radar/work/quickbuild.csh
 git checkout upstream/master -- observations/obs_converters/snow/shell_scripts/hour_time_loop.csh
 git checkout upstream/master -- observations/obs_converters/snow/work/input.nml
 git checkout upstream/master -- observations/obs_converters/snow/work/quickbuild.csh
 git checkout upstream/master -- observations/obs_converters/tec/README
 git checkout upstream/master -- observations/obs_converters/tec/tec_to_obs.f90
 git checkout upstream/master -- observations/obs_converters/tec/work/input.nml
 git checkout upstream/master -- observations/obs_converters/tec/work/mkmf_advance_time
 git checkout upstream/master -- observations/obs_converters/tec/work/mkmf_obs_sequence_tool
 git checkout upstream/master -- observations/obs_converters/tec/work/mkmf_preprocess
 git checkout upstream/master -- observations/obs_converters/tec/work/mkmf_tec_to_obs
 git checkout upstream/master -- observations/obs_converters/tec/work/path_names_advance_time
 git checkout upstream/master -- observations/obs_converters/tec/work/path_names_obs_sequence_tool
 git checkout upstream/master -- observations/obs_converters/tec/work/path_names_preprocess
 git checkout upstream/master -- observations/obs_converters/tec/work/path_names_tec_to_obs
 git checkout upstream/master -- observations/obs_converters/tec/work/quickbuild.csh
 git checkout upstream/master -- observations/obs_converters/text/shell_scripts/hour_time_loop.csh
 git checkout upstream/master -- observations/obs_converters/text/text_to_obs.html
 git checkout upstream/master -- observations/obs_converters/text/work/quickbuild.csh
 git checkout upstream/master -- observations/obs_converters/text_GITM/work/quickbuild.csh
 git checkout upstream/master -- observations/obs_converters/tpw/convert_gpspw.nml
 git checkout upstream/master -- observations/obs_converters/tpw/work/input.nml
 git checkout upstream/master -- observations/obs_converters/tpw/work/quickbuild.csh
 git checkout upstream/master -- observations/obs_converters/tropical_cyclone/work/quickbuild.csh
 git checkout upstream/master -- observations/obs_converters/utilities/obs_utilities_mod.f90
 git checkout upstream/master -- observations/obs_converters/utilities/threed_sphere/quickbuild.csh
 git checkout upstream/master -- observations/obs_converters/var/work/input.nml
 git checkout upstream/master -- observations/obs_converters/var/work/quickbuild.csh
 git checkout upstream/master -- observations/utilities/oned/input.nml
 git checkout upstream/master -- observations/utilities/oned/quickbuild.csh
 git checkout upstream/master -- observations/utilities/threed_sphere/input.nml
 git checkout upstream/master -- observations/utilities/threed_sphere/mkmf_obs_remove_dups
 git checkout upstream/master -- observations/utilities/threed_sphere/quickbuild.csh

# filter_mod.f90 has changes from CSS and master ... manually merge
 git checkout upstream/master -- assimilation_code/modules/assimilation/filter_mod.f90
 gitdiff   upstream/Manhattan -- assimilation_code/modules/assimilation/filter_mod.f90
 git add                         assimilation_code/modules/assimilation/filter_mod.f90

 echo "manually updating to master ... use git log --follow"            >  commit.msg
 echo                                                                   >> commit.msg
 echo "Updating Manhattan to correct the PR44/45 debacle now that the"  >> commit.msg
 echo "master branch is ready to be released as 9.9.0"                  >> commit.msg

 echo 
 echo "The commit message is"
 cat commit.msg
 echo 

 echo 
 echo "If you like that, you can "
 echo 
 echo "git commit -F commit.msg"
 echo 
