diff --git a/data_stream_xml_generation/generate_xml_datm.py b/data_stream_xml_generation/generate_xml_datm.py
index 698295a..9fec3eb 100644
--- a/data_stream_xml_generation/generate_xml_datm.py
+++ b/data_stream_xml_generation/generate_xml_datm.py
@@ -92,7 +92,7 @@
     SubElement(stream_info, "year_last").text = str(year_last)
     SubElement(stream_info, "year_align").text = str(year_align)
     SubElement(stream_info, "vectors").text = "null"
-    SubElement(stream_info, "meshfile").text = "./input/JRA55do-ESMFmesh.nc"
+    SubElement(stream_info, "meshfile").text = "./INPUT/JRA55do-ESMFmesh.nc"
     SubElement(stream_info, "lev_dimname").text = "null"
 
     datafiles = SubElement(stream_info, "datafiles")
@@ -131,7 +131,7 @@
         if year_first == year_last:
             file_element = SubElement(datafiles, "file")
             file_element.text = (
-                f"./input/RYF.{var_name_parts[0]}.{year+90}_{year + 90 + 1}.nc"
+                f"./INPUT/RYF.{var_name_parts[0]}.{year+90}_{year + 90 + 1}.nc"
             )
         else:
             file_element = SubElement(datafiles, "file")
@@ -143,14 +143,14 @@
                 "CORE_IAF_JRA55do.V_10",
             ]:
                 if year != 2019:
-                    file_element.text = f"./input/atmos/3hr/{var_name_parts[0]}/gr/v20190429/{var_name_parts[0]}_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_{year}01010130-{year}12312230.nc"
+                    file_element.text = f"./INPUT/atmos/3hr/{var_name_parts[0]}/gr/v20190429/{var_name_parts[0]}_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_{year}01010130-{year}12312230.nc"
                 else:
-                    file_element.text = f"./input/atmos/3hr/{var_name_parts[0]}/gr/v20190429/{var_name_parts[0]}_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_{year}01010130-{year}01052230.nc"
+                    file_element.text = f"./INPUT/atmos/3hr/{var_name_parts[0]}/gr/v20190429/{var_name_parts[0]}_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_{year}01010130-{year}01052230.nc"
             else:
                 if year != 2019:
-                    file_element.text = f"./input/atmos/3hrPt/{var_name_parts[0]}/gr/v20190429/{var_name_parts[0]}_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_{year}01010000-{year}12312100.nc"
+                    file_element.text = f"./INPUT/atmos/3hrPt/{var_name_parts[0]}/gr/v20190429/{var_name_parts[0]}_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_{year}01010000-{year}12312100.nc"
                 else:
-                    file_element.text = f"./input/atmos/3hrPt/{var_name_parts[0]}/gr/v20190429/{var_name_parts[0]}_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_{year}01010000-{year}01052100.nc"
+                    file_element.text = f"./INPUT/atmos/3hrPt/{var_name_parts[0]}/gr/v20190429/{var_name_parts[0]}_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_{year}01010000-{year}01052100.nc"
 
 
 # Convert the XML to a nicely formatted string
diff --git a/data_stream_xml_generation/generate_xml_drof.py b/data_stream_xml_generation/generate_xml_drof.py
index bba287e..ca29672 100644
--- a/data_stream_xml_generation/generate_xml_drof.py
+++ b/data_stream_xml_generation/generate_xml_drof.py
@@ -72,7 +72,7 @@
     SubElement(stream_info, "year_last").text = str(year_last)
     SubElement(stream_info, "year_align").text = str(year_align)
     SubElement(stream_info, "vectors").text = "null"
-    SubElement(stream_info, "meshfile").text = "./input/JRA55do-ESMFmesh.nc"
+    SubElement(stream_info, "meshfile").text = "./INPUT/JRA55do-ESMFmesh.nc"
     SubElement(stream_info, "lev_dimname").text = "null"
 
     datafiles = SubElement(stream_info, "datafiles")
@@ -91,19 +91,19 @@
     for year in range(year_first, year_last + 1):
         if year_first == year_last:
             file_element = SubElement(datafiles, "file")
-            file_element.text = f"./input/RYF.{var_prefix}.{year+90}_{year + 90 + 1}.nc"
+            file_element.text = f"./INPUT/RYF.{var_prefix}.{year+90}_{year + 90 + 1}.nc"
         else:
             file_element = SubElement(datafiles, "file")
             if var_prefix == "friver":
                 if year != 2019:
-                    file_element.text = f"./input/land/day/{var_prefix}/gr/v20190429/friver_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_{year}0101-{year}1231.nc"
+                    file_element.text = f"./INPUT/land/day/{var_prefix}/gr/v20190429/friver_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_{year}0101-{year}1231.nc"
                 else:
-                    file_element.text = f"./input/land/day/{var_prefix}/gr/v20190429/friver_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_{year}0101-{year}0105.nc"
+                    file_element.text = f"./INPUT/land/day/{var_prefix}/gr/v20190429/friver_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_{year}0101-{year}0105.nc"
             else:
                 if year != 2019:
-                    file_element.text = f"./input/landIce/day/{var_prefix}/gr/v20190429/licalvf_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_{year}0101-{year}1231.nc"
+                    file_element.text = f"./INPUT/landIce/day/{var_prefix}/gr/v20190429/licalvf_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_{year}0101-{year}1231.nc"
                 else:
-                    file_element.text = f"./input/landIce/day/{var_prefix}/gr/v20190429/licalvf_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_{year}0101-{year}0105.nc"
+                    file_element.text = f"./INPUT/landIce/day/{var_prefix}/gr/v20190429/licalvf_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_{year}0101-{year}0105.nc"
 
 # Convert the XML to a nicely formatted string
 xml_str = minidom.parseString(tostring(root)).toprettyxml(indent="  ")
diff --git a/payu_config/archive_scripts/archive_cice_restarts.sh b/payu_config/archive_scripts/archive_cice_restarts.sh
index c55aa7c..9e254f9 100755
--- a/payu_config/archive_scripts/archive_cice_restarts.sh
+++ b/payu_config/archive_scripts/archive_cice_restarts.sh
@@ -3,9 +3,9 @@
 # SPDX-License-Identifier: Apache-2.0
 # clean up cice_restarts.sh
 
-if [ -f archive/output*/input/iced.1900-01-01-10800.nc ] 
+if [ -f archive/output*/INPUT/iced.1900-01-01-10800.nc ]
 then
-rm archive/output*/input/iced.1900-01-01-10800.nc
+rm archive/output*/INPUT/iced.1900-01-01-10800.nc
 return 0
 fi
 
@@ -17,4 +17,4 @@ ic_restart=$(ls -dv $latest_o/access-om3.cice.r.* | head -1)
 if [ -f $latest_o/access-om3.cice.r.* ]
 then
 rm $latest_o/access-om3.cice.r.*
-fi
\ No newline at end of file
+fi
diff --git a/payu_config/setup_scripts/setup_cice_restarts.sh b/payu_config/setup_scripts/setup_cice_restarts.sh
index e800e07..941e8c7 100755
--- a/payu_config/setup_scripts/setup_cice_restarts.sh
+++ b/payu_config/setup_scripts/setup_cice_restarts.sh
@@ -3,9 +3,9 @@
 if ! [ -f work/access-om3.cice.r.* ]
 then 
 # no restart files yet, use initial conditions
-IC=$(readlink work/input/iced.1900-01-01-10800.nc)
-rm work/input/iced.1900-01-01-10800.nc
-cp $IC work/input/iced.1900-01-01-10800.nc
+IC=$(readlink work/INPUT/iced.1900-01-01-10800.nc)
+rm work/INPUT/iced.1900-01-01-10800.nc
+cp $IC work/INPUT/iced.1900-01-01-10800.nc
 else
 # change restart symlink to hardlink
 RESTART=$(echo work/access-om3.cice.r.*)