Every other Atlassian product comes with instructions on how to run as a windows service?
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Since Stash comes with embedded tomcat just like the Standalone Confluence et al., you should be able to follow the same documentation to run it as a service. They are specific to tomcat and not specific to the individual apps.
Make sure you use the approrpiate names. For example, Stash instead of Confluence ;)
See http://tomcat.apache.org/tomcat-6.0-doc/windows-service-howto.html for more!
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