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The selected scope is not being maintained between searches. The scope from the previous search should be the default for all subsequent searches. This allows you do back to back searches more quickly. To see this in action: Select a file or project folder, open the Search dialog and select 'Enclosing Project', do a file search. The search dialog will be dismissed, now bring up the search dialog again. Enclosing projects won't be enabled. To enable it again you must click on a file in the project explorer and reset your scope in the search dialog.
Works for me using 3.5 M6.