I'm having to do a manual upgrade because we have an older version of JIRA on our server. The server is Windows Server 2003 R2 SP2, JIRA version 4.2#587. There are no services running that are labeled with JIRA in the name. The only "help" I'm able to find is to "shutdown JIRA" but no instructions on how to do that.
No Atlassian service, no Tomcat on the server.
It won't let me reply because of my karma rating, but I did finally figure it out - shutdown_bundled_jre.bat. This should really be mentioned in the help files!!
The official answer in JIRA Startup and Shutdown Scripts for windows is to call either:
Stops JIRA by running "catalina.bat stop"
Both can be found in the bin folder of the Install Directory.
By default, this is in the following folder:
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