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Yes, I think that's what he was asking too.
To the best of my knowledge, there is no way to do this from the command line.
When I've had trouble starting JIRA in the past and suspect a plugin, I simply pull the jar out of \installed-plugins and dump it in a temporary folder. Then I can try starting JIRA again.
If JIRA is already running, then Gabrielle's answer will work, as you can go to
Add-ons–> Manage Add-ons–> Enter safe mode
And disable all add-ons there.
One improvement Atlassian could make would be to move "Enter safe mode" to the top of that page, as perhaps users don't see it where it is now, at the bottom.
Hope this helps