Unix at its heart is a multiuser operating system. Migration is equivalent to merging the users from computer A with the users of computer B assuming computer B is the one running migration. It does NOT merge the contents of user Bob on computer A with the contents of user Bob on computer B. If you try this you'll end up with TWO Bob accounts on computer B.
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Computer B should end up with the applications of computer A in my example. When you run migration you get the option of transfering applications. Migration does not run both directions when invoked by computer B for example. Computer A is not changed.
Here is the apple article