Some Links Lose the Base URL
When adding a user, instead of going to http://localhost:8080/secure/admin/user/AddUser!default.jspa, users are redirected to http:///secure/admin/user/AddUser!default.jspa . The base URL is removed.
The context path in
server.xml has been set to be simply "/".
Change to context path to be either "/jira" (or any other path you prefer} or simply remove it all together:
<Context path="" docBase="$ /atlassianjira" reloadable="false">