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You'll love version 6 which will hopefully be out next week. Projects are file based, so that you choose when to save them and what to name them. Basically we've stopped the UI from trying to be so clever.
I don't think there would be an issue if you renamed the project file. One other thing to bear in mind is that in version 5 not all the settings from the project file are used in the command line - for example where clauses and custom comparison keys aren't picked up from the project file. You have to set all of these separately in the arcane xml argument file.
In version 6 however we've fixed thatso that a project via the command line should work the same way it does in the UI.
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C:\Documents and Settings\Administrator.SJC\Local Settings\Application Data\Red Gate\SQL Data Compare 5\INET3218 MSMSQL05.HS1Data v DAN DAN.HS1Data 05-06-2007.09-43-12.3283.sdc
To something that is more managable and understandable? I have a number of data compares that I automate but it is hard to know what is going on with each one, other than the date/time stamp used on the file name.
For the example above, I would prefer to name it something more like "DAN To INET HS1Data Parcels Archive.sdc" and still be able to use it both in the command line and the RedGate Data Compare software interface.
Thanks!