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Hi Lewis,
I think this may be related to a known bug in SQL Compare. Since SQL Compare shares some components with Dependency Tracker, this should be fixed at the same time as SQL Compare.
Note that there is support for CTE in Dependency Tracker, it's only when a UDF, and I suppose this also applies to stored procedures, returns a CTE.
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The thing that they all seem to have in common is the use of common table expressions. This was introduced with SQL Server 2005. I use these help speed up paging operations for large sets of data.
Will there be future support for this?
http://msdn2.microsoft.com/en-us/library/ms190766.aspx