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Hello Ed,
You can use SQL Compare's filters to show only the stored procedures, then use the 'select all' icon on the toolbar. When you generate a report, only the selected stored procedures will be selected as well. The only issue is that you don't get the stored procedures that are equal included in the report; just the ones that are different.
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2) Also, when the compare is done I'm given the option of checking which SPs to report (HTML). I have hundreds to compare and report and don't want to check every single one of them.