It looks like SQL Data Compare automatically skips system tables. Is there any way to selectively convince it to include them? For the most part, I think leaving them out is the right decision. But if I could synchronize dbo.sysdiagrams between SQL Server 2005 databases, then I'd have a way to propagate database diagrams, and that would surely be nice.
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We don't support migrating any system tables including dbo.sysdiagrams. We have no plans to support this in the future unless it is something that we get many requests for.
Hope this clears it up at least.
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