How do I export all issues out of JIRA in to a csv file for uploading to our reporting system?
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You don't.
The exports are limited to prevent you from overloading the system. If you were on server, you'd have a number of options, but Cloud is aimed at doing things in one place, live reporting and real-time updates, not doing (instantly obsolete) extracts.
What reports are you trying to get to?
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