When I go to manage add-ons, click the settings link, I believe i should see a way to enable development mode per the directions here: https://developer.atlassian.com/static/connect/docs/latest/guides/development-setup.html#enable-development-mode
However, for my server instance of JIRA, the settings dialog shows this, with no way to turn on development mode. How can I turn on development mode?
image2016-7-8 12:14:34.png
This developer mode is for Cloud, not Server.
Does that mean the only way to run a cloud based plugin would be to run it though Atlassian Connect Express in a JIRA standalone development environment (atlas-run-standalone)?
No, you can run it on a Cloud development service as well - as explained in the doc you linked to. But that's not a server edition of JIRA, it's a Cloud install.
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