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Our SharePoint 2013 on-premisis installation is going to be upgraded to SharePoint 2016 in a few months. My understanding is that with the native upgrade option only the databases will be migrated. We have a variety of customizations using Content Editor Web Parts and workflows that would be nice to include in the migration if possible. Is there a third party tool out there that would include these types of features?

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Yes, databases will be migrated and upgraded, but inside will be upgraded everything, if you have workflows, pages, etc. Everything will be migrated.

I recommend to do a test migration, when you test migration process and after this verify that migrated and upgraded content is ok and everything works fine.

You dont need any 3rd part tool.

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