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Thanks for the feedback. Unfortunately this isn't going to make it into the initial release of v 5. We will, however, look at it for a future release.
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Do you have any idea on when we might see support for them?
This is a major issue for us as well. Our application uses user instances quite heavily. We've been forced to implement some rather ugly code to support them in 4.0.
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Currently the only way I can use your tools with SQL Express .mdf files is to connect them to the local .\SQLEXPRESS instance. I write lots of projects that use user instance connection strings with .mdf files (Win Forms, etc.). This allows you to just copy the .mdf file and during execution the .Net runtime will seek and attach the specified .mdf file in th connection string while the application is being executed. Being able to browse to a .mdf file versus having to attach it to the .\SQLEXPRESS instance would be killer. If I want to compare a baseline .mdf with another version of it I have to attach them both to the default .\SQLEXPRESS instance and then run the SQL compare tool.