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Thanks for your inquiry!
Given you case, it is recommended that you try using SQL Change Automation instead. You can see more details in the following documentation: https://documentation.red-gate.com/sca3/tutorials/worked-examples/embed-change-script-into-application
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There are options that I can use in my c# project (eg. use SMO, or split the statements at GO), but I'd prefer not to have that dependency. I thought of generating separate files, but I would like to be able to control the order of processing the files.
Has anyone else faced this problem?