Fix bolt:setup by running doctrine scripts in new context #3649
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Doctrine caches the found migrations (which is logical), but that breaks when you generate a new migration and then try to run it in the same Application context. This was not shown on the console due to the usage of the NullOutput. By migrating to the existing Script helper we resolve the issue as each invocation now receives it's own Application context without cached migrations.
Fixes #3648