Problem/Motivation
Migration::set() was provided as a work-around for the inability to properly modify migration plugin configuration at run time (#2681869: Provide clean way to merge configuration into migration plugins) - once that is committed, set() should be deprecated. The only core usages remaining after that commit are in tests, which should be changed to use the plugin manager to merge configuration.
Note that set() is documented with {@inheritdoc}, yet is not in MigrationInterface and thus is not properly documented. This fix should properly document it in the Migration class.
Proposed resolution
Move test in MigrationTest to MigrationPluginConfigurationTest.php
Rework MigrateUploadTest and FileMigrateSetupTrait to not use Migration::set().
Add doc bloc for Migration::set().