Change directory to /opt/shrine/tomcat/webapps. Delete all the files and directories.
cd /opt/shrine/tomcat/webapps rm -rf *
Now change directory to /opt/shrine/tomcat/work, and delete all files and directories within that location too.
cd /opt/shrine/tomcat/work rm -rf *
Finally change directory to /opt/shrine/tomcat/temp, and delete all files and directories within that location.
cd /opt/shrine/tomcat/temp rm -rf *
Now change back to /opt/shrine/tomcat/webapps directory. Download the shrine-api.war into webapps.
cd /opt/shrine/tomcat/webapps wget https://repo.open.catalyst.harvard.edu/nexus/content/groups/public/net/shrine/shrine-api-war/3.3.2/shrine-api-war-3.3.2.war -O shrine-api.war
Vulnerability Note: We have discovered that there is a vulnerability with commons-text-1.9.jar located in the directory /opt/shrine/tomcat/webapps/shrine-api/WEB-INF/lib/. The fix for this is to update this file with the latest version from here: https://commons.apache.org/proper/commons-text/download_text.cgi
It's possible that your institutions security scanner may not detect this as a vulnerability.