diff --git a/shallow-server/Dockerfile b/shallow-server/Dockerfile
index 593878a5..f0b87d73 100644
--- a/shallow-server/Dockerfile
+++ b/shallow-server/Dockerfile
@@ -21,7 +21,9 @@ COPY opcache-recommended.ini /usr/local/etc/php/conf.d/
 
 WORKDIR /var/www/html
 
-RUN rm -rf /var/www/html
+# Looks like there's an issue on self-hosted runners with fuse-overlayfs that prevents us deleting the directory directly
+# so rename it first and then remove it
+RUN mv /var/www/html/ /var/www/html2/ && rm -rf /var/www/html2/
 RUN mkdir -p /var/www/html
 
 RUN git clone --depth 1 https://github.com/nextcloud/server.git .
diff --git a/shallow-server/initnc.sh b/shallow-server/initnc.sh
index 5a3ab39a..823d67d8 100755
--- a/shallow-server/initnc.sh
+++ b/shallow-server/initnc.sh
@@ -5,6 +5,11 @@ export BRANCH=${BRANCH:=master}
 # Where we do all the work
 cd /var/www/html/
 
+# Run 'apt-get update' to unlock files. This seems neccessary on self hosted runners with fuse-overlayfs,
+# otherwise git checkout will error out with 'file exists' error. Needs to be run here, doesn't work when 
+# done inside the Dockerfile
+apt-get update
+
 # Update code
 su www-data -c "
 git fetch --force --depth 1 origin $BRANCH:refs/remotes/origin/$BRANCH