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Okay, my problem is that when I need to compare two schemas, I always need to reset the tables that I need to compare.

This is because my source database keeps changing as we need to spin up a new one per development branch and the application treats this as whole new comparison.

Given that we have over 300+ tables in each database this becomes a very tedious and error prone process to do each time.

Is there a way that I can specify to the application a list of the 50 or so reference tables only that I want compare each time?

Kindly note that table exclusions can be configured on the Options page (data comparison wizard): Include tables or views by mask Exclude tables or views by mask.

And on the Mapping page (data comparison wizard). Save the .dcomp file and change the database name in a text editor.
You can use Command Line.
Please, check our Documentation https://docs.devart.com/studio-for-mysql/