diff --git a/rose-stem/flow.cylc b/rose-stem/flow.cylc
index c206f9a..f968aa7 100644
--- a/rose-stem/flow.cylc
+++ b/rose-stem/flow.cylc
@@ -30,7 +30,7 @@
 {% set SITE_VARS = {} %}
 
 {#- Import variable definitions #}
-%include 'include/variables.rc'
+%include 'include/variables.cylc'
 
 [scheduler]
     UTC mode = True
@@ -42,14 +42,14 @@
         stall handlers = "suite_report_git.py -S $CYLC_WORKFLOW_RUN_DIR"
 
 {#- Import any Cylc task parameters #}
-%include 'include/parameters.rc'
+%include 'include/parameters.cylc'
 
 {#- Import the dependency graphs for the available jobs and groups #}
-%include 'include/graph.rc'
+%include 'include/graph.cylc'
 
 [scheduling]
 {#- Import any queues #}
-%include 'include/queues.rc'
+%include 'include/queues.cylc'
 
     [[graph]]
         R1 = """
@@ -103,5 +103,5 @@ export FCM_VERSION={{FCM_VERSION}}
 {% endfor %}
 
 {#- Import family and job definitions #}
-%include 'include/runtime.rc'
-%include 'runtime-common.rc'
+%include 'include/runtime.cylc'
+%include 'runtime-common.cylc'
diff --git a/rose-stem/include/graph.rc b/rose-stem/include/graph.cylc
similarity index 82%
rename from rose-stem/include/graph.rc
rename to rose-stem/include/graph.cylc
index a8c18e9..977be57 100644
--- a/rose-stem/include/graph.rc
+++ b/rose-stem/include/graph.cylc
@@ -5,7 +5,7 @@
 ###############################################################################
 
 {% if SITE == 'meto' %}
-%include 'include/meto/graph.rc'
+%include 'include/meto/graph.cylc'
 {% elif SITE == 'vm' %}
-%include 'include/vm/graph.rc'
+%include 'include/vm/graph.cylc'
 {% endif %}
diff --git a/rose-stem/include/meto/graph.rc b/rose-stem/include/meto/graph.cylc
similarity index 100%
rename from rose-stem/include/meto/graph.rc
rename to rose-stem/include/meto/graph.cylc
diff --git a/rose-stem/include/meto/queues.rc b/rose-stem/include/meto/queues.cylc
similarity index 100%
rename from rose-stem/include/meto/queues.rc
rename to rose-stem/include/meto/queues.cylc
diff --git a/rose-stem/include/meto/runtime.rc b/rose-stem/include/meto/runtime.cylc
similarity index 90%
rename from rose-stem/include/meto/runtime.rc
rename to rose-stem/include/meto/runtime.cylc
index 14e2bc0..662cc97 100644
--- a/rose-stem/include/meto/runtime.rc
+++ b/rose-stem/include/meto/runtime.cylc
@@ -16,7 +16,7 @@
 
 
 # Redefine site-independent SCRIPTS group
-# (normally found in runtime-common.rc, Done to enforce loading of
+# (normally found in runtime-common.cylc, Done to enforce loading of
 # scitools  when running on MONSooN ; Python 3 is req'd by UMDP3 checker)
     [[SCRIPTS]]
         inherit = None, METO_AZSPICE
diff --git a/rose-stem/include/parameters.rc b/rose-stem/include/parameters.cylc
similarity index 65%
rename from rose-stem/include/parameters.rc
rename to rose-stem/include/parameters.cylc
index a5a0a31..acaf661 100644
--- a/rose-stem/include/parameters.rc
+++ b/rose-stem/include/parameters.cylc
@@ -1,5 +1,5 @@
 # Import site-specific parameter sets
 
 # {% if SITE == 'niwa' %}
-# %include 'include/niwa/parameters.rc'
+# %include 'include/niwa/parameters.cylc'
 # {% endif %}
\ No newline at end of file
diff --git a/rose-stem/include/queues.rc b/rose-stem/include/queues.cylc
similarity index 56%
rename from rose-stem/include/queues.rc
rename to rose-stem/include/queues.cylc
index 21c00ba..39cba7a 100644
--- a/rose-stem/include/queues.rc
+++ b/rose-stem/include/queues.cylc
@@ -1,7 +1,7 @@
 # Import site-specific queues
 
 {% if SITE == 'meto' %}
-%include 'include/meto/queues.rc'
+%include 'include/meto/queues.cylc'
 {% elif SITE == 'vm' %}
-%include 'include/vm/queues.rc'
+%include 'include/vm/queues.cylc'
 {% endif %}
diff --git a/rose-stem/include/runtime.rc b/rose-stem/include/runtime.cylc
similarity index 90%
rename from rose-stem/include/runtime.rc
rename to rose-stem/include/runtime.cylc
index 8a00688..2cca5fb 100644
--- a/rose-stem/include/runtime.rc
+++ b/rose-stem/include/runtime.cylc
@@ -8,11 +8,12 @@
 
     [[SOURCE_EXTRACTION]]
         post-script = """
+mkdir $CYLC_WORKFLOW_RUN_DIR/bin/
 cp $SOURCE_DIRECTORY/ukca/dependencies.yaml $CYLC_WORKFLOW_RUN_DIR
-cp $SOURCE_DIRECTORY/SimSys_Scripts/github_scripts/suite_report_git.py $CYLC_WORKFLOW_RUN_DIR/bin
-cp $SOURCE_DIRECTORY/SimSys_Scripts/github_scripts/suite_data.py $CYLC_WORKFLOW_RUN_DIR/bin
-cp $SOURCE_DIRECTORY/SimSys_Scripts/github_scripts/git_bdiff.py $CYLC_WORKFLOW_RUN_DIR/bin
-cp $SOURCE_DIRECTORY/SimSys_Scripts/github_scripts/get_git_sources.py $CYLC_WORKFLOW_RUN_DIR/bin
+cp $SOURCE_DIRECTORY/SimSys_Scripts/github_scripts/suite_report_git.py $CYLC_WORKFLOW_RUN_DIR/bin/
+cp $SOURCE_DIRECTORY/SimSys_Scripts/github_scripts/suite_data.py $CYLC_WORKFLOW_RUN_DIR/bin/
+cp $SOURCE_DIRECTORY/SimSys_Scripts/github_scripts/git_bdiff.py $CYLC_WORKFLOW_RUN_DIR/bin/
+cp $SOURCE_DIRECTORY/SimSys_Scripts/github_scripts/get_git_sources.py $CYLC_WORKFLOW_RUN_DIR/bin/
 """
         [[[environment]]]
             ROSE_TASK_APP = extract_source
@@ -58,7 +59,7 @@ rsync -avz --exclude=".*" $SOURCE_DIRECTORY/* $hostname:$RELATIVE_SOURCE_DIRECTO
 ## Site-specific runtime definitions
 ###############################################################################
 {% if SITE == 'meto' %}
-%include 'include/meto/runtime.rc'
+%include 'include/meto/runtime.cylc'
 {% elif SITE == 'vm' %}
-%include 'include/vm/runtime.rc'
+%include 'include/vm/runtime.cylc'
 {% endif %}
diff --git a/rose-stem/include/variables.rc b/rose-stem/include/variables.cylc
similarity index 100%
rename from rose-stem/include/variables.rc
rename to rose-stem/include/variables.cylc
diff --git a/rose-stem/include/vm/graph.rc b/rose-stem/include/vm/graph.cylc
similarity index 100%
rename from rose-stem/include/vm/graph.rc
rename to rose-stem/include/vm/graph.cylc
diff --git a/rose-stem/include/vm/queues.rc b/rose-stem/include/vm/queues.cylc
similarity index 100%
rename from rose-stem/include/vm/queues.rc
rename to rose-stem/include/vm/queues.cylc
diff --git a/rose-stem/include/vm/runtime.rc b/rose-stem/include/vm/runtime.cylc
similarity index 87%
rename from rose-stem/include/vm/runtime.rc
rename to rose-stem/include/vm/runtime.cylc
index caec87f..cc849c4 100644
--- a/rose-stem/include/vm/runtime.rc
+++ b/rose-stem/include/vm/runtime.cylc
@@ -1,5 +1,5 @@
 # Redefine site-independent SCRIPTS group
-# (normally found in runtime-common.rc)
+# (normally found in runtime-common.cylc)
 # Need to use python3 for this script
     [[SCRIPTS]]
         inherit = None, LINUX
diff --git a/rose-stem/lib/python/read_sources.py b/rose-stem/lib/python/read_sources.py
index a651ea7..5028716 100644
--- a/rose-stem/lib/python/read_sources.py
+++ b/rose-stem/lib/python/read_sources.py
@@ -1,3 +1,9 @@
+##############################################################################
+# (c) Crown copyright 2025 Met Office. All rights reserved.
+# The file LICENCE, distributed with this code, contains details of the terms
+# under which the code may be used.
+##############################################################################
+
 import yaml
 import tempfile
 import os
@@ -13,7 +19,7 @@ def get_dependencies_file(wc_loc):
     tempdir = tempfile.mkdtemp()
 
     try:
-        host, path = wc_loc.split(":")
+        host, path = wc_loc.split(":", 1)
         path = os.path.join(path, "dependencies.yaml")
         copy_command = f"scp -o StrictHostKeyChecking=no {host}:"
     except ValueError:
diff --git a/rose-stem/lib/python/utils.py b/rose-stem/lib/python/utils.py
index 8aa4b11..2f8c3d6 100644
--- a/rose-stem/lib/python/utils.py
+++ b/rose-stem/lib/python/utils.py
@@ -1,3 +1,9 @@
+##############################################################################
+# (c) Crown copyright 2025 Met Office. All rights reserved.
+# The file LICENCE, distributed with this code, contains details of the terms
+# under which the code may be used.
+##############################################################################
+
 from subprocess import Popen, PIPE
 
 
@@ -8,4 +14,7 @@ def get_site():
     out, _ = proc.communicate()
     if proc.returncode or "SITE" not in out:
         raise Exception('Could not determine the rose-stem "SITE"')
-    return out.replace("SITE=", "").strip()
+    # At some sites there may be many variables that are returned by rose config rose-stem
+    # Try to just grab the thing after SITE= and then ignore anything afterwards
+    site = out.split("SITE=")[1].split(' ')[0].strip()
+    return site
diff --git a/rose-stem/runtime-common.rc b/rose-stem/runtime-common.cylc
similarity index 100%
rename from rose-stem/runtime-common.rc
rename to rose-stem/runtime-common.cylc