Currently we have jira configured into a linux box and connected to a mysql server. We mainly use jira through the front end, but occasionally access the mysql DB directly. If we transition to JIRA Cloud will we still have access to query the DB via mysql command line tool?
You'd have to run them remotely, you don't get any access to the servers at all. Add-ons are your best bet, as they run within the applications. You can write your own as well, for Cloud - it might be neater for you than finding another server and extracting information to be reprocessed. Both your external stuff and "Connect" add-ons would be relying on the REST interface to read (and write!) the JIRA data.
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