The File Manager URL in the server.conf file should match the one specified in Java client under the Admin tab > Server settings > Locations > File Manager

In Agile 9.3.2 and above
Update server.conf file under [Agile home]\agileDomain\config\server.conf:
1. Stop Filemgr (Tomcat server).
2. Backup [Agile home]\agileDomain\config\server.conf
3. Make the necessary changes to the server.conf.
4. Start Filemgr (Tomcat server)The URLs specified in the server.conf configuration file are:
app.server.url =http://[application server or load balancer FQDN]:[port]/Agile/services/FSHelper (Or App Server and App server port if not using proxy forwarding)
file.server.url =http://[File Manager FQDN]:8080/Filemgr/services/FileServer (Or Web Server and Port 80 is using Tomcat Proxy Forwarding)
dms.server.url =http://[application server or load balancer FQDN]:[port]/Agile/services/DmsService (Or App Server and App server port if not using proxy forwarding)
The URLs specified in this file are used only by the Filemgr server. They should no be pointing to the DMZ or the web proxy used by external users as this would route traffic through the DMZ/proxy unnecessarily.

In Agile 9.3.x.x to Agile 9.3.1.2
Update the Filemgr deployment archive (webfs.war):

1. Backup [Agile home]\agileDomain\applications\webfs.war
2. Extract the server.conf from webfs.war:cd [Agile home]\agiledomain\applications[Enter]
[Agile home]\jdk\bin\jar -xvf webfs.war WEB-INF/classes/com/agile/webfs/configuration/server.conf[Enter]

This will created a sub-folder ‘WEB-INF’ under the applications folder, which contains the extracted file.
 
3. Make the necessary changes to the extracted server.conf.
4. Update the webfs.war archive with the new version of server.conf.[Agile home]\jdk\bin\jar -uvf webfs.war WEB-INF/classes/com/agile/webfs/configuration/server.conf[Enter]

5.  Stop Filemgr (Tomcat server)
6. Delete the folder [Agile home]\Tomcat\webapps\Filemgr
7. Start Filemgr (Tomcat server)
8. Delete the folder created while extracted server .conf: [Agile home]\agileDomain\applications\WEB-INF
9. Start Filemgr (Tomcat server) 

Update server.conf file within the agile-sso.jar file:
1. Stop Filemgr (Tomcat server).
2. Backup [AgileHome]\apache-tomcat\lib\agile-sso.jar
3. Extract server.conf:
    cd [Agile home]\apache-tomcat\lib[Enter]
    [Agile home]\jdk\bin\jar -xvf agile-sso.jar com/agile/webfs/configuration/server.conf[Enter]
    This will created a sub-folder ‘com’ under the lib folder, which contains the extracted file.
4. Make the necessary changes to the extracted server.conf.
5. Update the agile-sso.jar archive with the new version of server.conf.
    [Agile home]\jdk\bin\jar -uvf agile-sso.jar com/agile/webfs/configuration/server.conf[Enter]
6. Start Filemgr (Tomcat server)
7. Delete the folder [Agile home]\Tomcat\server\lib\com