Every MDM repository is managed as an MDM Cloud in Boomi AtomSphere so any name/state changes made to the Atom Cloud will be automatically reflected in MDM.
In order to rename your MDM repository, just open your Boomi AtomSphere account, click on the Manage menu and select Atom Management. Then from the Environments panel on the left, click on the atom cloud you wish to rename. Then in the center of the screen, scroll down and click on the Account Properties link. Once the pop-up window displays, you will be able to change the Atom Name property and click the Save button.
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