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Hi
Thank you for your forum post.
I believe what you are seeking cannot be achieved. The deployment script generated follows the Transact-SQL syntax conventions. Therefore when making changes to a procedure, an ALTER PROCEDURE command is used and SQL Compare will generate the script so that the deployment is successful.
This msdn ARTICLE describes how to modify a stored procedure.
Many Thanks
Eddie
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For instance, most source control software allows you to compare and merge hand picked differences and I was hoping that SQL Compare would have some feature that was similar?
I realise that you can quite easily right click on the comparison pane and select "Show Object Synchronization Script" and take out the lines you don't want (or edit them), but for larger changes it would help to only need to modify particular differences.