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Hi, thank you for your forum post.
If using the Command Line there is (as you already discovered) the includesourcetables (alias o) via the /comparison switch. Further reading here.
For the GUI, there is the 'Take schema from the source' option. Via the GUI, Edit Project -> Select Options tab ->Comparison Behavior section.
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My problem is that I do not want to have two different dco files. One for the execution from scratch and one between branches.
Regards