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Now that an SQL file can be saved in a project, the connection is missing. The connection could be saved, in project.properties
What do you mean "save the connection?" You mean the connection they were using with this SQL file the last time it was open? That wasn't there before, even with console files - you restart and no connection is selected. I think this ties into the work Mike and I are doing on setting a connection for the project and remembering overrides chosen by specific users. I'll assign this one to Mike for now and we'll keep this in mind for the overall design.
Reassigned to new owner.