The com.ibm.msg.client.wmq.v6.* packages are used when a version 7 or higher JMS client is running in migration mode. The scenarios for running migration mode are documented in the infocenter:
The mode switching is internal to the WMQ JMS client, and doesn't affect the public APIs which your application will be calling. So unless you really want to programmatically force migration mode as described in the infocenter, no application changes are required.
To answer your final question - these packages don't exist before v7, so if you see v6 in a package name, it's definitely not a v6 client!
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