diff --git a/tools/conventions/analyze_gfortran_warnings.py b/tools/conventions/analyze_gfortran_warnings.py
index e04a60bfa5..924d534a5b 100755
--- a/tools/conventions/analyze_gfortran_warnings.py
+++ b/tools/conventions/analyze_gfortran_warnings.py
@@ -54,13 +54,15 @@ def check_warnings(fn):
             loc = line.rsplit(":")[0].strip()
             loc_short = path.basename(loc)
             if not path.exists(loc):
-                return # source file missing - skipping
+                return # source file gone - skipping
             continue
 
         # fypp line directives that leaked through as part of warning messages
         if(line.startswith(' # 1 "')):
             loc = line[6:-1]
             loc_short = path.basename(loc)
+            if not path.exists(loc):
+                return # source file gone - skipping
             continue
 
         if(loc.endswith("include/fftw3.f")): continue # an external file
diff --git a/tools/conventions/analyze_src.py b/tools/conventions/analyze_src.py
index 5bb92dbf7b..5fe7f9bd22 100755
--- a/tools/conventions/analyze_src.py
+++ b/tools/conventions/analyze_src.py
@@ -95,7 +95,7 @@ def main():
 
     # check linebreaks and encoding
     for root, _, files in os.walk(cp2k_dir):
-        if any(x in root for x in (".git", "obj", "lib", "exe", "regtesting")):
+        if any(x in root for x in (".git", "obj", "lib", "exe", "regtesting", "exts")):
             continue
         for fn in files:
             absfn = path.join(root, fn)
diff --git a/tools/docker/scripts/ci_entrypoint.sh b/tools/docker/scripts/ci_entrypoint.sh
index 42d75328e4..70851486db 100755
--- a/tools/docker/scripts/ci_entrypoint.sh
+++ b/tools/docker/scripts/ci_entrypoint.sh
@@ -30,9 +30,9 @@ function upload_file {
 if [ -n "${GIT_REF}" ]; then
     echo -e "\n========== Fetching Git Commit ==========" | tee -a $REPORT
     cd /workspace/cp2k
-    git fetch origin "${GIT_BRANCH}"         |& tee -a $REPORT
-    git checkout "${GIT_REF}"                |& tee -a $REPORT
-    git submodule update --init --recursive  |& tee -a $REPORT
+    git fetch origin "${GIT_BRANCH}"                       |& tee -a $REPORT
+    git -c advice.detachedHead=false checkout "${GIT_REF}" |& tee -a $REPORT
+    git submodule update --init --recursive                |& tee -a $REPORT
     git --no-pager log -1 --pretty='%nCommitSHA: %H%nCommitTime: %ci%nCommitAuthor: %an%nCommitSubject: %s%n' |& tee -a $REPORT
 
 elif [ -d  /mnt/cp2k ]; then