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In M3 system, If an integration contains standard BOD, does it require MEC mapping/design to be done in mapper?
Definitely yes. M3 (OP or MT) communicates with ION by exchanging BODs (standard or custom); these messages go through MEC.
For a MT version of M3, you have to download the mapper from the cloud and install it locally with some credentials.
I believe you only need to download / use Mapper, If you are customizing. Standard BODs are in the deployment and can be enabled. These are documented in the Configuration Guide and in the Mapping Guides.