Currently, there's no way to reorder project shortcuts that I can see. Is this possible?
Yes this is possible. But that will be a complete manual upgrade. You cannot use the automatic installers.
See the documentation here: http://confluence.atlassian.com/display/JIRA044/Upgrading+JIRA+Manually
You can upgrade in one step. Check out http://confluence.atlassian.com/display/JIRA044/Upgrading+JIRA+Manually
Make sure you read http://confluence.atlassian.com/display/JIRA044/Upgrading+JIRA
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