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Once you updated to the latest Atlassian Migration Assistant in Server, you can use it to

(tick) Assess and prepare your apps

The Comala Document Management app is not migrated and must be installed separately in your cloud site

(tick) Prepare and Connect to your Cloud site

You can link your chosen Cloud site at this step.  Simply select your existing Cloud site from the dropdown options. They must be linked to you as a site administrator

(tick) Migrate your data

This includes users, groups and content data

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