diff --git a/tests/integration/generated/test_debug_chrysalis.cfg b/tests/integration/generated/test_debug_chrysalis.cfg
new file mode 100644
index 00000000..957651d1
--- /dev/null
+++ b/tests/integration/generated/test_debug_chrysalis.cfg
@@ -0,0 +1,149 @@
+[default]
+case = v2.LR.historical_0201
+constraint = ""
+dry_run = "False"
+environment_commands = ""
+input = "/lcrc/group/e3sm/ac.forsyth2//E3SMv2/v2.LR.historical_0201"
+input_subdir = archive/atm/hist
+mapping_file = "map_ne30pg2_to_cmip6_180x360_aave.20200201.nc"
+# To run this test, edit `output` and `www` in this file, along with `actual_images_dir` in test_debug.py
+output = "/lcrc/group/e3sm/ac.forsyth2/zppy_test_debug_output/unique_id/v2.LR.historical_0201"
+partition = "debug"
+qos = "regular"
+www = "/lcrc/group/e3sm/public_html/diagnostic_output/ac.forsyth2/zppy_test_debug_www/unique_id"
+
+[climo]
+active = True
+walltime = "00:30:00"
+years = "1850:1854:2", "1850:1854:4",
+
+  [[ atm_monthly_180x360_aave ]]
+  frequency = "monthly"
+  input_files = "eam.h0"
+  input_subdir = "archive/atm/hist"
+  vars = ""
+
+  [[ atm_monthly_diurnal_8xdaily_180x360_aave ]]
+  frequency = "diurnal_8xdaily"
+  input_files = "eam.h4"
+  input_subdir = "archive/atm/hist"
+  vars = "PRECT"
+
+  [[ land_monthly_climo ]]
+  frequency = "monthly"
+  input_files = "elm.h0"
+  input_subdir = "archive/lnd/hist"
+  vars = ""
+
+[ts]
+active = True
+e3sm_to_cmip_environment_commands = ""
+walltime = "00:30:00"
+years = "1850:1854:2",
+
+  [[ atm_monthly_180x360_aave ]]
+  frequency = "monthly"
+  input_files = "eam.h0"
+  input_subdir = "archive/atm/hist"
+  ts_fmt = "cmip"
+
+  [[ atm_daily_180x360_aave ]]
+  frequency = "daily"
+  input_files = "eam.h1"
+  input_subdir = "archive/atm/hist"
+  vars = "PRECT"
+
+  [[ atm_monthly_glb ]]
+  # Note global average won't work for 3D variables.
+  frequency = "monthly"
+  input_files = "eam.h0"
+  input_subdir = "archive/atm/hist"
+  mapping_file = "glb"
+  years = "1850:1860:5",
+
+  [[ land_monthly ]]
+  e3sm_to_cmip_environment_commands = ""
+  extra_vars = "landfrac"
+  frequency = "monthly"
+  input_files = "elm.h0"
+  input_subdir = "archive/lnd/hist"
+  vars = "LAISHA,LAISUN"
+  ts_fmt = "cmip"
+
+  [[ lnd_monthly_glb ]]
+  frequency = "monthly"
+  input_files = "elm.h0"
+  input_subdir = "archive/lnd/hist"
+  mapping_file = "glb"
+  vars = "LAISHA,LAISUN"
+  years = "1850:1860:5",
+
+  [[ rof_monthly ]]
+  extra_vars = 'areatotal2'
+  frequency = "monthly"
+  input_files = "mosart.h0"
+  input_subdir = "archive/rof/hist"
+  mapping_file = ""
+  vars = "RIVER_DISCHARGE_OVER_LAND_LIQ"
+
+[e3sm_diags]
+active = True
+environment_commands = "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_diags_20240731"
+grid = '180x360_aave'
+ref_final_yr = 2014
+ref_start_yr = 1985
+# TODO: this directory is missing OMI-MLS
+sets = "lat_lon","zonal_mean_xy","zonal_mean_2d","polar","cosp_histogram","meridional_mean_2d","enso_diags","qbo","diurnal_cycle","annual_cycle_zonal_mean","streamflow", "zonal_mean_2d_stratosphere",
+short_name = 'v2.LR.historical_0201'
+ts_num_years = 2
+walltime = "00:30:00"
+years = "1850:1854:2", "1850:1854:4",
+
+  [[ atm_monthly_180x360_aave ]]
+  climo_diurnal_frequency = "diurnal_8xdaily"
+  climo_diurnal_subsection = "atm_monthly_diurnal_8xdaily_180x360_aave"
+  partition = "compute"
+  qos = "regular"
+  sets = "lat_lon","zonal_mean_xy","zonal_mean_2d","polar","cosp_histogram","meridional_mean_2d","enso_diags","qbo","diurnal_cycle","annual_cycle_zonal_mean","streamflow", "zonal_mean_2d_stratosphere",
+  walltime = "5:00:00"
+
+  [[ atm_monthly_180x360_aave_mvm ]]
+  # Test model-vs-model using the same files as the reference
+  climo_diurnal_frequency = "diurnal_8xdaily"
+  climo_diurnal_subsection = "atm_monthly_diurnal_8xdaily_180x360_aave"
+  climo_subsection = "atm_monthly_180x360_aave"
+  diff_title = "Difference"
+  partition = "compute"
+  qos = "regular"
+  ref_final_yr = 1851
+  ref_name = "v2.LR.historical_0201"
+  ref_start_yr = 1850
+  ref_years = "1850-1851",
+  reference_data_path = "/lcrc/group/e3sm/ac.forsyth2/zppy_test_debug_output/unique_id/v2.LR.historical_0201/post/atm/180x360_aave/clim"
+  run_type = "model_vs_model"
+  short_ref_name = "v2.LR.historical_0201"
+  swap_test_ref = False
+  tag = "model_vs_model"
+  ts_num_years_ref = 2
+  ts_subsection = "atm_monthly_180x360_aave"
+  walltime = "5:00:00"
+  years = "1852-1853",
+
+  [[ lnd_monthly_mvm_lnd ]]
+  # Test model-vs-model using the same files as the reference
+  climo_subsection = "land_monthly_climo"
+  diff_title = "Difference"
+  #grid = 'native'
+  partition = "compute"
+  qos = "regular"
+  ref_final_yr = 1851
+  ref_name = "v2.LR.historical_0201"
+  ref_start_yr = 1850
+  ref_years = "1850-1851",
+  reference_data_path = "/lcrc/group/e3sm/ac.forsyth2/zppy_test_debug_output/unique_id/v2.LR.historical_0201/post/lnd/180x360_aave/clim"
+  run_type = "model_vs_model"
+  sets = "lat_lon_land",
+  short_ref_name = "same simulation"
+  swap_test_ref = False
+  tag = "model_vs_model"
+  ts_num_years_ref = 2
diff --git a/tests/integration/generated/test_min_case_add_dependencies_chrysalis.cfg b/tests/integration/generated/test_min_case_add_dependencies_chrysalis.cfg
index 6c0559c4..05c6db7f 100644
--- a/tests/integration/generated/test_min_case_add_dependencies_chrysalis.cfg
+++ b/tests/integration/generated/test_min_case_add_dependencies_chrysalis.cfg
@@ -81,7 +81,7 @@ years = "1985:1995:5"
 
 [e3sm_diags]
 active = True
-environment_commands = "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_diags_20240731"
+environment_commands = "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_diags_cdat_branch_20240731"
 grid = '180x360_aave'
 multiprocessing = True
 num_workers = 8
diff --git a/tests/integration/generated/test_min_case_e3sm_diags_cdat_migrated_sets_chrysalis.cfg b/tests/integration/generated/test_min_case_e3sm_diags_cdat_migrated_sets_chrysalis.cfg
new file mode 100644
index 00000000..0cc9f437
--- /dev/null
+++ b/tests/integration/generated/test_min_case_e3sm_diags_cdat_migrated_sets_chrysalis.cfg
@@ -0,0 +1,125 @@
+[default]
+case = "v3.LR.historical_0051"
+constraint = ""
+dry_run = "False"
+environment_commands = ""
+input = /lcrc/group/e3sm2/ac.wlin/E3SMv3/v3.LR.historical_0051
+input_subdir = archive/atm/hist
+mapping_file = "map_ne30pg2_to_cmip6_180x360_aave.20200201.nc"
+output = "/lcrc/group/e3sm/ac.forsyth2/zppy_min_case_e3sm_diags_cdat_migrated_output/unique_id/v3.LR.historical_0051"
+partition = "debug"
+qos = "regular"
+www = "/lcrc/group/e3sm/public_html/diagnostic_output/ac.forsyth2/zppy_min_case_e3sm_diags_cdat_migrated_www/unique_id"
+years = "1985:1989:2",
+
+[climo]
+active = True
+walltime = "00:30:00"
+
+  [[ atm_monthly_180x360_aave ]]
+  frequency = "monthly"
+  input_files = "eam.h0"
+  input_subdir = "archive/atm/hist"
+  vars = ""
+
+  [[ atm_monthly_diurnal_8xdaily_180x360_aave ]]
+  frequency = "diurnal_8xdaily"
+  input_files = "eam.h3"
+  input_subdir = "archive/atm/hist"
+  vars = "PRECT"
+
+  [[ land_monthly_climo ]]
+  frequency = "monthly"
+  input_files = "elm.h0"
+  input_subdir = "archive/lnd/hist"
+  mapping_file = "map_r05_to_cmip6_180x360_aave.20231110.nc"
+  vars = ""
+
+[ts]
+active = True
+e3sm_to_cmip_environment_commands = ""
+walltime = "00:30:00"
+
+  [[ atm_monthly_180x360_aave ]]
+  frequency = "monthly"
+  input_files = "eam.h0"
+  input_subdir = "archive/atm/hist"
+  ts_fmt = "cmip"
+
+  [[ rof_monthly ]]
+  extra_vars = 'areatotal2'
+  frequency = "monthly"
+  input_files = "mosart.h0"
+  input_subdir = "archive/rof/hist"
+  mapping_file = ""
+  vars = "RIVER_DISCHARGE_OVER_LAND_LIQ"
+
+  [[ land_monthly ]]
+  extra_vars = "landfrac"
+  frequency = "monthly"
+  input_files = "elm.h0"
+  input_subdir = "archive/lnd/hist"
+  mapping_file = "map_r05_to_cmip6_180x360_aave.20231110.nc"
+  ts_fmt = "cmip"
+  vars = "FSH,RH2M,LAISHA,LAISUN,QINTR,QOVER,QRUNOFF,QSOIL,QVEGE,QVEGT,SOILICE,SOILLIQ,SOILWATER_10CM,TSA,TSOI,H2OSNO,TOTLITC,CWDC,SOIL1C,SOIL2C,SOIL3C,SOIL4C,WOOD_HARVESTC,TOTVEGC,NBP,GPP,AR,HR"
+
+[tc_analysis]
+active = True
+scratch = "/lcrc/globalscratch/ac.forsyth2/zppy_weekly_comprehensive_v3_scratch/unique_id/v3.LR.historical_0051"
+walltime = "00:30:00"
+
+[e3sm_diags]
+active = True
+environment_commands = "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_diags_cdat_branch_20240731"
+grid = '180x360_aave'
+multiprocessing = True
+num_workers = 8
+partition = "compute"
+qos = "regular"
+ref_final_yr = 1986
+ref_start_yr = 1985
+ref_years = "1985-1986",
+# Also lat_lon_land for mvm
+sets="lat_lon","lat_lon_river","cosp_histogram","zonal_mean_xy","zonal_mean_2d","zonal_mean_2d_stratosphere","aerosol_aeronet","polar","meridional_mean_2d","area_mean_time_series","aerosol_budget","annual_cycle_zonal_mean","diurnal_cycle",
+short_name = "v3.LR.historical_0051"
+ts_num_years = 2
+walltime = "5:00:00"
+years = "1987:1989:2"
+
+  [[ atm_monthly_180x360_aave ]]
+  climo_diurnal_frequency = "diurnal_8xdaily"
+  climo_diurnal_subsection = "atm_monthly_diurnal_8xdaily_180x360_aave"
+  climo_subsection = "atm_monthly_180x360_aave"
+  dc_obs_climo = '/lcrc/group/e3sm/public_html/e3sm_diags_test_data/unit_test_complete_run/obs/climatology'
+
+  [[ atm_monthly_180x360_aave_mvm ]]
+  # Test model-vs-model using the same files as the reference
+  climo_diurnal_frequency = "diurnal_8xdaily"
+  climo_diurnal_subsection = "atm_monthly_diurnal_8xdaily_180x360_aave"
+  climo_subsection = "atm_monthly_180x360_aave"
+  diff_title = "Difference"
+  partition = "compute"
+  qos = "regular"
+  ref_name = "v3.LR.historical_0051"
+  reference_data_path = "/lcrc/group/e3sm/ac.forsyth2/zppy_min_case_e3sm_diags_cdat_migrated_output/unique_id/v3.LR.historical_0051/post/atm/180x360_aave/clim"
+  run_type = "model_vs_model"
+  short_ref_name = "same simulation"
+  swap_test_ref = False
+  tag = "model_vs_model"
+  ts_num_years_ref = 2
+  ts_subsection = "atm_monthly_180x360_aave"
+
+  [[ lnd_monthly_mvm_lnd ]]
+ # Test model-vs-model using the same files as the reference
+  climo_subsection = "land_monthly_climo"
+  diff_title = "Difference"
+  partition = "compute"
+  qos = "regular"
+  ref_name = "v3.LR.historical_0051"
+  reference_data_path = "/lcrc/group/e3sm/ac.forsyth2/zppy_min_case_e3sm_diags_cdat_migrated_output/unique_id/v3.LR.historical_0051/post/lnd/180x360_aave/clim"
+  run_type = "model_vs_model"
+  sets = "lat_lon_land",
+  short_ref_name = "same simulation"
+  swap_test_ref = False
+  tag = "model_vs_model"
+  ts_num_years_ref = 2
diff --git a/tests/integration/generated/test_min_case_e3sm_diags_depend_on_climo_chrysalis.cfg b/tests/integration/generated/test_min_case_e3sm_diags_depend_on_climo_chrysalis.cfg
index 416771ae..782f5b91 100644
--- a/tests/integration/generated/test_min_case_e3sm_diags_depend_on_climo_chrysalis.cfg
+++ b/tests/integration/generated/test_min_case_e3sm_diags_depend_on_climo_chrysalis.cfg
@@ -24,7 +24,7 @@ walltime = "00:30:00"
 
 [e3sm_diags]
 active = True
-environment_commands = "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_diags_20240731"
+environment_commands = "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_diags_cdat_branch_20240731"
 grid = '180x360_aave'
 multiprocessing = True
 num_workers = 8
diff --git a/tests/integration/generated/test_min_case_e3sm_diags_depend_on_climo_mvm_2_chrysalis.cfg b/tests/integration/generated/test_min_case_e3sm_diags_depend_on_climo_mvm_2_chrysalis.cfg
index 036e17a7..ee85a81f 100644
--- a/tests/integration/generated/test_min_case_e3sm_diags_depend_on_climo_mvm_2_chrysalis.cfg
+++ b/tests/integration/generated/test_min_case_e3sm_diags_depend_on_climo_mvm_2_chrysalis.cfg
@@ -24,7 +24,7 @@ walltime = "00:30:00"
 
 [e3sm_diags]
 active = True
-environment_commands = "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_diags_20240731"
+environment_commands = "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_diags_cdat_branch_20240731"
 grid = '180x360_aave'
 multiprocessing = True
 num_workers = 8
diff --git a/tests/integration/generated/test_min_case_e3sm_diags_depend_on_ts_chrysalis.cfg b/tests/integration/generated/test_min_case_e3sm_diags_depend_on_ts_chrysalis.cfg
index 5a686029..99433c41 100644
--- a/tests/integration/generated/test_min_case_e3sm_diags_depend_on_ts_chrysalis.cfg
+++ b/tests/integration/generated/test_min_case_e3sm_diags_depend_on_ts_chrysalis.cfg
@@ -25,7 +25,7 @@ walltime = "00:30:00"
 
 [e3sm_diags]
 active = True
-environment_commands = "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_diags_20240731"
+environment_commands = "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_diags_cdat_branch_20240731"
 grid = '180x360_aave'
 multiprocessing = True
 num_workers = 8
diff --git a/tests/integration/generated/test_min_case_e3sm_diags_depend_on_ts_mvm_2_chrysalis.cfg b/tests/integration/generated/test_min_case_e3sm_diags_depend_on_ts_mvm_2_chrysalis.cfg
index 72219931..8c8892ae 100644
--- a/tests/integration/generated/test_min_case_e3sm_diags_depend_on_ts_mvm_2_chrysalis.cfg
+++ b/tests/integration/generated/test_min_case_e3sm_diags_depend_on_ts_mvm_2_chrysalis.cfg
@@ -25,7 +25,7 @@ walltime = "00:30:00"
 
 [e3sm_diags]
 active = True
-environment_commands = "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_diags_20240731"
+environment_commands = "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_diags_cdat_branch_20240731"
 grid = '180x360_aave'
 multiprocessing = True
 num_workers = 8
diff --git a/tests/integration/generated/test_min_case_e3sm_diags_diurnal_cycle_chrysalis.cfg b/tests/integration/generated/test_min_case_e3sm_diags_diurnal_cycle_chrysalis.cfg
index 481b7fc1..66070972 100644
--- a/tests/integration/generated/test_min_case_e3sm_diags_diurnal_cycle_chrysalis.cfg
+++ b/tests/integration/generated/test_min_case_e3sm_diags_diurnal_cycle_chrysalis.cfg
@@ -24,7 +24,7 @@ walltime = "00:30:00"
 
 [e3sm_diags]
 active = True
-environment_commands = "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_diags_20240731"
+environment_commands = "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_diags_cdat_branch_20240731"
 grid = '180x360_aave'
 multiprocessing = True
 num_workers = 8
diff --git a/tests/integration/generated/test_min_case_e3sm_diags_diurnal_cycle_mvm_2_chrysalis.cfg b/tests/integration/generated/test_min_case_e3sm_diags_diurnal_cycle_mvm_2_chrysalis.cfg
index b0109858..596cccb1 100644
--- a/tests/integration/generated/test_min_case_e3sm_diags_diurnal_cycle_mvm_2_chrysalis.cfg
+++ b/tests/integration/generated/test_min_case_e3sm_diags_diurnal_cycle_mvm_2_chrysalis.cfg
@@ -24,7 +24,7 @@ walltime = "00:30:00"
 
 [e3sm_diags]
 active = True
-environment_commands = "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_diags_20240731"
+environment_commands = "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_diags_cdat_branch_20240731"
 grid = '180x360_aave'
 multiprocessing = True
 num_workers = 8
diff --git a/tests/integration/generated/test_min_case_e3sm_diags_lat_lon_land_mvm_2_chrysalis.cfg b/tests/integration/generated/test_min_case_e3sm_diags_lat_lon_land_mvm_2_chrysalis.cfg
index bb585138..d6cc26b4 100644
--- a/tests/integration/generated/test_min_case_e3sm_diags_lat_lon_land_mvm_2_chrysalis.cfg
+++ b/tests/integration/generated/test_min_case_e3sm_diags_lat_lon_land_mvm_2_chrysalis.cfg
@@ -24,7 +24,7 @@ walltime = "00:30:00"
 
 [e3sm_diags]
 active = True
-environment_commands = "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_diags_20240731"
+environment_commands = "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_diags_cdat_branch_20240731"
 grid = '180x360_aave'
 multiprocessing = True
 num_workers = 8
diff --git a/tests/integration/generated/test_min_case_e3sm_diags_streamflow_chrysalis.cfg b/tests/integration/generated/test_min_case_e3sm_diags_streamflow_chrysalis.cfg
index 797adc44..860efacb 100644
--- a/tests/integration/generated/test_min_case_e3sm_diags_streamflow_chrysalis.cfg
+++ b/tests/integration/generated/test_min_case_e3sm_diags_streamflow_chrysalis.cfg
@@ -27,7 +27,7 @@ walltime = "00:30:00"
 
 [e3sm_diags]
 active = True
-environment_commands = "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_diags_20240731"
+environment_commands = "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_diags_cdat_branch_20240731"
 grid = '180x360_aave'
 multiprocessing = True
 num_workers = 8
diff --git a/tests/integration/generated/test_min_case_e3sm_diags_streamflow_mvm_2_chrysalis.cfg b/tests/integration/generated/test_min_case_e3sm_diags_streamflow_mvm_2_chrysalis.cfg
index f7d43fc6..7b0dd8aa 100644
--- a/tests/integration/generated/test_min_case_e3sm_diags_streamflow_mvm_2_chrysalis.cfg
+++ b/tests/integration/generated/test_min_case_e3sm_diags_streamflow_mvm_2_chrysalis.cfg
@@ -27,7 +27,7 @@ walltime = "00:30:00"
 
 [e3sm_diags]
 active = True
-environment_commands = "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_diags_20240731"
+environment_commands = "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_diags_cdat_branch_20240731"
 grid = '180x360_aave'
 multiprocessing = True
 num_workers = 8
diff --git a/tests/integration/generated/test_min_case_e3sm_diags_tc_analysis_chrysalis.cfg b/tests/integration/generated/test_min_case_e3sm_diags_tc_analysis_chrysalis.cfg
index ee24e496..8b02b1d9 100644
--- a/tests/integration/generated/test_min_case_e3sm_diags_tc_analysis_chrysalis.cfg
+++ b/tests/integration/generated/test_min_case_e3sm_diags_tc_analysis_chrysalis.cfg
@@ -19,7 +19,7 @@ walltime = "00:30:00"
 
 [e3sm_diags]
 active = True
-environment_commands = "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_diags_20240731"
+environment_commands = "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_diags_cdat_branch_20240731"
 grid = '180x360_aave'
 multiprocessing = True
 num_workers = 8
diff --git a/tests/integration/generated/test_min_case_e3sm_diags_tc_analysis_mvm_2_chrysalis.cfg b/tests/integration/generated/test_min_case_e3sm_diags_tc_analysis_mvm_2_chrysalis.cfg
index 3e42bc99..8b782b23 100644
--- a/tests/integration/generated/test_min_case_e3sm_diags_tc_analysis_mvm_2_chrysalis.cfg
+++ b/tests/integration/generated/test_min_case_e3sm_diags_tc_analysis_mvm_2_chrysalis.cfg
@@ -19,7 +19,7 @@ walltime = "00:30:00"
 
 [e3sm_diags]
 active = True
-environment_commands = "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_diags_20240731"
+environment_commands = "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_diags_cdat_branch_20240731"
 grid = '180x360_aave'
 multiprocessing = True
 num_workers = 8
diff --git a/tests/integration/generated/test_min_case_e3sm_diags_tropical_subseasonal_mvm_2_chrysalis.cfg b/tests/integration/generated/test_min_case_e3sm_diags_tropical_subseasonal_mvm_2_chrysalis.cfg
index 7a997083..d17b484c 100644
--- a/tests/integration/generated/test_min_case_e3sm_diags_tropical_subseasonal_mvm_2_chrysalis.cfg
+++ b/tests/integration/generated/test_min_case_e3sm_diags_tropical_subseasonal_mvm_2_chrysalis.cfg
@@ -25,7 +25,7 @@ walltime = "00:30:00"
 
 [e3sm_diags]
 active = True
-environment_commands = "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_diags_20240731"
+environment_commands = "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_diags_cdat_branch_20240731"
 grid = '180x360_aave'
 multiprocessing = True
 num_workers = 8
diff --git a/tests/integration/generated/test_weekly_bundles_chrysalis.cfg b/tests/integration/generated/test_weekly_bundles_chrysalis.cfg
index c4c1b5db..df561ac7 100644
--- a/tests/integration/generated/test_weekly_bundles_chrysalis.cfg
+++ b/tests/integration/generated/test_weekly_bundles_chrysalis.cfg
@@ -103,7 +103,7 @@ years = "1985:1989:2",
 
 [e3sm_diags]
 active = True
-environment_commands = "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_diags_20240731"
+environment_commands = "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_diags_cdat_branch_20240731"
 grid = '180x360_aave'
 ref_final_yr = 1989
 ref_start_yr = 1985
diff --git a/tests/integration/generated/test_weekly_comprehensive_v2_chrysalis.cfg b/tests/integration/generated/test_weekly_comprehensive_v2_chrysalis.cfg
index 7b6987e1..d753eae4 100644
--- a/tests/integration/generated/test_weekly_comprehensive_v2_chrysalis.cfg
+++ b/tests/integration/generated/test_weekly_comprehensive_v2_chrysalis.cfg
@@ -84,7 +84,7 @@ walltime = "00:30:00"
 
 [e3sm_diags]
 active = True
-environment_commands = "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_diags_20240731"
+environment_commands = "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_diags_cdat_branch_20240731"
 grid = '180x360_aave'
 multiprocessing = True
 num_workers = 8
diff --git a/tests/integration/generated/test_weekly_comprehensive_v3_chrysalis.cfg b/tests/integration/generated/test_weekly_comprehensive_v3_chrysalis.cfg
index 6d37de66..2cbbe392 100644
--- a/tests/integration/generated/test_weekly_comprehensive_v3_chrysalis.cfg
+++ b/tests/integration/generated/test_weekly_comprehensive_v3_chrysalis.cfg
@@ -86,7 +86,7 @@ walltime = "00:30:00"
 
 [e3sm_diags]
 active = True
-environment_commands = "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_diags_20240731"
+environment_commands = "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_diags_cdat_branch_20240731"
 grid = '180x360_aave'
 multiprocessing = True
 num_workers = 8
diff --git a/tests/integration/template_debug.cfg b/tests/integration/template_debug.cfg
new file mode 100644
index 00000000..2635585c
--- /dev/null
+++ b/tests/integration/template_debug.cfg
@@ -0,0 +1,149 @@
+[default]
+case = v2.LR.historical_0201
+constraint = "#expand constraint#"
+dry_run = "#expand dry_run#"
+environment_commands = "#expand environment_commands#"
+input = "#expand user_input#/E3SMv2/v2.LR.historical_0201"
+input_subdir = archive/atm/hist
+mapping_file = "map_ne30pg2_to_cmip6_180x360_aave.20200201.nc"
+# To run this test, edit `output` and `www` in this file, along with `actual_images_dir` in test_debug.py
+output = "#expand user_output#zppy_test_debug_output/#expand unique_id#/v2.LR.historical_0201"
+partition = "#expand partition_short#"
+qos = "#expand qos_short#"
+www = "#expand user_www#zppy_test_debug_www/#expand unique_id#"
+
+[climo]
+active = True
+walltime = "00:30:00"
+years = "1850:1854:2", "1850:1854:4",
+
+  [[ atm_monthly_180x360_aave ]]
+  frequency = "monthly"
+  input_files = "eam.h0"
+  input_subdir = "archive/atm/hist"
+  vars = ""
+
+  [[ atm_monthly_diurnal_8xdaily_180x360_aave ]]
+  frequency = "diurnal_8xdaily"
+  input_files = "eam.h4"
+  input_subdir = "archive/atm/hist"
+  vars = "PRECT"
+
+  [[ land_monthly_climo ]]
+  frequency = "monthly"
+  input_files = "elm.h0"
+  input_subdir = "archive/lnd/hist"
+  vars = ""
+
+[ts]
+active = True
+e3sm_to_cmip_environment_commands = "#expand e3sm_to_cmip_environment_commands#"
+walltime = "00:30:00"
+years = "1850:1854:2",
+
+  [[ atm_monthly_180x360_aave ]]
+  frequency = "monthly"
+  input_files = "eam.h0"
+  input_subdir = "archive/atm/hist"
+  ts_fmt = "cmip"
+
+  [[ atm_daily_180x360_aave ]]
+  frequency = "daily"
+  input_files = "eam.h1"
+  input_subdir = "archive/atm/hist"
+  vars = "PRECT"
+
+  [[ atm_monthly_glb ]]
+  # Note global average won't work for 3D variables.
+  frequency = "monthly"
+  input_files = "eam.h0"
+  input_subdir = "archive/atm/hist"
+  mapping_file = "glb"
+  years = "1850:1860:5",
+
+  [[ land_monthly ]]
+  e3sm_to_cmip_environment_commands = "#expand e3sm_to_cmip_environment_commands#"
+  extra_vars = "landfrac"
+  frequency = "monthly"
+  input_files = "elm.h0"
+  input_subdir = "archive/lnd/hist"
+  vars = "LAISHA,LAISUN"
+  ts_fmt = "cmip"
+
+  [[ lnd_monthly_glb ]]
+  frequency = "monthly"
+  input_files = "elm.h0"
+  input_subdir = "archive/lnd/hist"
+  mapping_file = "glb"
+  vars = "LAISHA,LAISUN"
+  years = "1850:1860:5",
+
+  [[ rof_monthly ]]
+  extra_vars = 'areatotal2'
+  frequency = "monthly"
+  input_files = "mosart.h0"
+  input_subdir = "archive/rof/hist"
+  mapping_file = ""
+  vars = "RIVER_DISCHARGE_OVER_LAND_LIQ"
+
+[e3sm_diags]
+active = True
+environment_commands = "#expand diags_environment_commands#"
+grid = '180x360_aave'
+ref_final_yr = 2014
+ref_start_yr = 1985
+# TODO: this directory is missing OMI-MLS
+sets = "lat_lon","zonal_mean_xy","zonal_mean_2d","polar","cosp_histogram","meridional_mean_2d","enso_diags","qbo","diurnal_cycle","annual_cycle_zonal_mean","streamflow", "zonal_mean_2d_stratosphere",
+short_name = 'v2.LR.historical_0201'
+ts_num_years = 2
+walltime = "00:30:00"
+years = "1850:1854:2", "1850:1854:4",
+
+  [[ atm_monthly_180x360_aave ]]
+  climo_diurnal_frequency = "diurnal_8xdaily"
+  climo_diurnal_subsection = "atm_monthly_diurnal_8xdaily_180x360_aave"
+  partition = "#expand partition_long#"
+  qos = "#expand qos_long#"
+  sets = "lat_lon","zonal_mean_xy","zonal_mean_2d","polar","cosp_histogram","meridional_mean_2d","enso_diags","qbo","diurnal_cycle","annual_cycle_zonal_mean","streamflow", "zonal_mean_2d_stratosphere",
+  walltime = "#expand diags_walltime#"
+
+  [[ atm_monthly_180x360_aave_mvm ]]
+  # Test model-vs-model using the same files as the reference
+  climo_diurnal_frequency = "diurnal_8xdaily"
+  climo_diurnal_subsection = "atm_monthly_diurnal_8xdaily_180x360_aave"
+  climo_subsection = "atm_monthly_180x360_aave"
+  diff_title = "Difference"
+  partition = "#expand partition_long#"
+  qos = "#expand qos_long#"
+  ref_final_yr = 1851
+  ref_name = "v2.LR.historical_0201"
+  ref_start_yr = 1850
+  ref_years = "1850-1851",
+  reference_data_path = "#expand user_output#zppy_test_debug_output/#expand unique_id#/v2.LR.historical_0201/post/atm/180x360_aave/clim"
+  run_type = "model_vs_model"
+  short_ref_name = "v2.LR.historical_0201"
+  swap_test_ref = False
+  tag = "model_vs_model"
+  ts_num_years_ref = 2
+  ts_subsection = "atm_monthly_180x360_aave"
+  walltime = "#expand diags_walltime#"
+  years = "1852-1853",
+
+  [[ lnd_monthly_mvm_lnd ]]
+  # Test model-vs-model using the same files as the reference
+  climo_subsection = "land_monthly_climo"
+  diff_title = "Difference"
+  #grid = 'native'
+  partition = "#expand partition_long#"
+  qos = "#expand qos_long#"
+  ref_final_yr = 1851
+  ref_name = "v2.LR.historical_0201"
+  ref_start_yr = 1850
+  ref_years = "1850-1851",
+  reference_data_path = "#expand user_output#zppy_test_debug_output/#expand unique_id#/v2.LR.historical_0201/post/lnd/180x360_aave/clim"
+  run_type = "model_vs_model"
+  sets = "lat_lon_land",
+  short_ref_name = "same simulation"
+  swap_test_ref = False
+  tag = "model_vs_model"
+  ts_num_years_ref = 2
diff --git a/tests/integration/template_min_case_e3sm_diags_cdat_migrated_sets.cfg b/tests/integration/template_min_case_e3sm_diags_cdat_migrated_sets.cfg
new file mode 100644
index 00000000..ec77ec4b
--- /dev/null
+++ b/tests/integration/template_min_case_e3sm_diags_cdat_migrated_sets.cfg
@@ -0,0 +1,125 @@
+[default]
+case = "#expand case_name#"
+constraint = "#expand constraint#"
+dry_run = "#expand dry_run#"
+environment_commands = "#expand environment_commands#"
+input = /lcrc/group/e3sm2/ac.wlin/E3SMv3/#expand case_name#
+input_subdir = archive/atm/hist
+mapping_file = "map_ne30pg2_to_cmip6_180x360_aave.20200201.nc"
+output = "#expand user_output#zppy_min_case_e3sm_diags_cdat_migrated_output/#expand unique_id#/#expand case_name#"
+partition = "#expand partition_short#"
+qos = "#expand qos_short#"
+www = "#expand user_www#zppy_min_case_e3sm_diags_cdat_migrated_www/#expand unique_id#"
+years = "1985:1989:2",
+
+[climo]
+active = True
+walltime = "00:30:00"
+
+  [[ atm_monthly_180x360_aave ]]
+  frequency = "monthly"
+  input_files = "eam.h0"
+  input_subdir = "archive/atm/hist"
+  vars = ""
+
+  [[ atm_monthly_diurnal_8xdaily_180x360_aave ]]
+  frequency = "diurnal_8xdaily"
+  input_files = "eam.h3"
+  input_subdir = "archive/atm/hist"
+  vars = "PRECT"
+
+  [[ land_monthly_climo ]]
+  frequency = "monthly"
+  input_files = "elm.h0"
+  input_subdir = "archive/lnd/hist"
+  mapping_file = "map_r05_to_cmip6_180x360_aave.20231110.nc"
+  vars = ""
+
+[ts]
+active = True
+e3sm_to_cmip_environment_commands = "#expand e3sm_to_cmip_environment_commands#"
+walltime = "00:30:00"
+
+  [[ atm_monthly_180x360_aave ]]
+  frequency = "monthly"
+  input_files = "eam.h0"
+  input_subdir = "archive/atm/hist"
+  ts_fmt = "cmip"
+
+  [[ rof_monthly ]]
+  extra_vars = 'areatotal2'
+  frequency = "monthly"
+  input_files = "mosart.h0"
+  input_subdir = "archive/rof/hist"
+  mapping_file = ""
+  vars = "RIVER_DISCHARGE_OVER_LAND_LIQ"
+
+  [[ land_monthly ]]
+  extra_vars = "landfrac"
+  frequency = "monthly"
+  input_files = "elm.h0"
+  input_subdir = "archive/lnd/hist"
+  mapping_file = "map_r05_to_cmip6_180x360_aave.20231110.nc"
+  ts_fmt = "cmip"
+  vars = "FSH,RH2M,LAISHA,LAISUN,QINTR,QOVER,QRUNOFF,QSOIL,QVEGE,QVEGT,SOILICE,SOILLIQ,SOILWATER_10CM,TSA,TSOI,H2OSNO,TOTLITC,CWDC,SOIL1C,SOIL2C,SOIL3C,SOIL4C,WOOD_HARVESTC,TOTVEGC,NBP,GPP,AR,HR"
+
+[tc_analysis]
+active = True
+scratch = "#expand scratch#zppy_weekly_comprehensive_v3_scratch/#expand unique_id#/#expand case_name#"
+walltime = "00:30:00"
+
+[e3sm_diags]
+active = True
+environment_commands = "#expand diags_environment_commands#"
+grid = '180x360_aave'
+multiprocessing = True
+num_workers = 8
+partition = "#expand partition_long#"
+qos = "#expand qos_long#"
+ref_final_yr = 1986
+ref_start_yr = 1985
+ref_years = "1985-1986",
+# Also lat_lon_land for mvm
+sets="lat_lon","lat_lon_river","cosp_histogram","zonal_mean_xy","zonal_mean_2d","zonal_mean_2d_stratosphere","aerosol_aeronet","polar","meridional_mean_2d","area_mean_time_series","aerosol_budget","annual_cycle_zonal_mean","diurnal_cycle",
+short_name = "#expand case_name#"
+ts_num_years = 2
+walltime = "#expand diags_walltime#"
+years = "1987:1989:2"
+
+  [[ atm_monthly_180x360_aave ]]
+  climo_diurnal_frequency = "diurnal_8xdaily"
+  climo_diurnal_subsection = "atm_monthly_diurnal_8xdaily_180x360_aave"
+  climo_subsection = "atm_monthly_180x360_aave"
+  dc_obs_climo = '/lcrc/group/e3sm/public_html/e3sm_diags_test_data/unit_test_complete_run/obs/climatology'
+
+  [[ atm_monthly_180x360_aave_mvm ]]
+  # Test model-vs-model using the same files as the reference
+  climo_diurnal_frequency = "diurnal_8xdaily"
+  climo_diurnal_subsection = "atm_monthly_diurnal_8xdaily_180x360_aave"
+  climo_subsection = "atm_monthly_180x360_aave"
+  diff_title = "Difference"
+  partition = "#expand partition_long#"
+  qos = "#expand qos_long#"
+  ref_name = "#expand case_name#"
+  reference_data_path = "#expand user_output#zppy_min_case_e3sm_diags_cdat_migrated_output/#expand unique_id#/#expand case_name#/post/atm/180x360_aave/clim"
+  run_type = "model_vs_model"
+  short_ref_name = "same simulation"
+  swap_test_ref = False
+  tag = "model_vs_model"
+  ts_num_years_ref = 2
+  ts_subsection = "atm_monthly_180x360_aave"
+
+  [[ lnd_monthly_mvm_lnd ]]
+ # Test model-vs-model using the same files as the reference
+  climo_subsection = "land_monthly_climo"
+  diff_title = "Difference"
+  partition = "#expand partition_long#"
+  qos = "#expand qos_long#"
+  ref_name = "#expand case_name#"
+  reference_data_path = "#expand user_output#zppy_min_case_e3sm_diags_cdat_migrated_output/#expand unique_id#/#expand case_name#/post/lnd/180x360_aave/clim"
+  run_type = "model_vs_model"
+  sets = "lat_lon_land",
+  short_ref_name = "same simulation"
+  swap_test_ref = False
+  tag = "model_vs_model"
+  ts_num_years_ref = 2
diff --git a/tests/integration/utils.py b/tests/integration/utils.py
index 2c6d6bdf..03009ba3 100644
--- a/tests/integration/utils.py
+++ b/tests/integration/utils.py
@@ -139,7 +139,7 @@ def get_chyrsalis_expansions(config):
         "constraint": "",
         # To run this test, replace conda environment with your e3sm_diags dev environment
         # To use default environment_commands, set to ""
-        "diags_environment_commands": "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_diags_20240731",
+        "diags_environment_commands": "source /home/ac.forsyth2/miniconda3/etc/profile.d/conda.sh; conda activate e3sm_diags_cdat_branch_20240731",
         "diags_walltime": "5:00:00",
         "e3sm_to_cmip_environment_commands": "",
         "environment_commands_test": "",
@@ -273,6 +273,7 @@ def generate_cfgs(unified_testing=False, dry_run=False):
         "min_case_add_dependencies",
         "min_case_tc_analysis_simultaneous_1",
         "min_case_tc_analysis_simultaneous_2",
+        "min_case_e3sm_diags_cdat_migrated_sets",
         "min_case_e3sm_diags_depend_on_climo_mvm_1",
         "min_case_e3sm_diags_depend_on_climo_mvm_2",
         "min_case_e3sm_diags_depend_on_climo",
diff --git a/zppy/e3sm_diags.py b/zppy/e3sm_diags.py
index d874d8e3..98ab2921 100644
--- a/zppy/e3sm_diags.py
+++ b/zppy/e3sm_diags.py
@@ -148,6 +148,7 @@ def e3sm_diags(config, scriptDir, existing_bundles, job_ids_file):  # noqa: C901
             depend_on_climo = set(
                 [
                     "lat_lon",
+                    "lat_lon_land",
                     "zonal_mean_xy",
                     "zonal_mean_2d",
                     "polar",
@@ -271,6 +272,8 @@ def e3sm_diags(config, scriptDir, existing_bundles, job_ids_file):  # noqa: C901
                 else:
                     print("...adding to bundle '%s'" % (c["bundle"]))
 
+            for d in dependencies:
+                print(f"   d: {d}")
             print(f"   environment_commands={c['environment_commands']}")
             print_url(c, "e3sm_diags")
 
diff --git a/zppy/templates/e3sm_diags.bash b/zppy/templates/e3sm_diags.bash
index b32eed54..4e691035 100644
--- a/zppy/templates/e3sm_diags.bash
+++ b/zppy/templates/e3sm_diags.bash
@@ -101,19 +101,9 @@ create_links_ts()
       YYYY=`printf "%04d" ${year}`
       for file in ${ts_dir_source}/${v}_${YYYY}*.nc
       do
-        # Add this time series file to the list of files for cdscan to use
-        echo ${file} >> ${v}_files.txt
+        cp ${file} ${ts_dir_destination}/${v}_${YYYY}*.nc
       done
     done
-    # xml file will cover the whole period from year1 to year2
-    xml_name=${v}_${begin_year}01_${end_year}12.xml
-    export CDMS_NO_MPI=true
-    cdscan -x ${xml_name} -f ${v}_files.txt
-    if [ $? != 0 ]; then
-      cd {{ scriptDir }}
-      echo "ERROR (${error_num})" > {{ prefix }}.status
-      exit ${error_num}
-    fi
   done
   cd ..
 }
@@ -128,13 +118,7 @@ create_links_ts_rof()
   mkdir -p ${ts_rof_dir_destination}
   cd ${ts_rof_dir_destination}
   v="RIVER_DISCHARGE_OVER_LAND_LIQ"
-  xml_name=${v}_${begin_year}01_${end_year}12.xml
-  cdscan -x ${xml_name} ${ts_rof_dir_source}/${v}_*.nc
-  if [ $? != 0 ]; then
-    cd {{ scriptDir }}
-    echo "ERROR (${error_num})" > {{ prefix }}.status
-    exit ${error_num}
-  fi
+  cp ${ts_rof_dir_source}/${v}_*.nc ${v}_*.nc
   cd ..
 }