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If no tags are found in the background job, the user gets interrupted by a popup asking for further steps (deep search or manual configuration). That's intrusive, I think the job should just fail gracefully and let the user be in charge of taking additional mesures.
I think that prompting is a bit intrusive given that there is already a dialog open. I don't think we should just go ahead with the deep search as it may take a very long time if the project is big. My vote would be to show a message in the existing dialog that would give the user the same information that the prompt does. The options to Refresh or Configure manually are already in the existing dialog so the message would just need to point to them.
As pointed out in bug 80478, comment 17 and also agreed upon by Michael (see 80478, comment 18) I suggest to close this one as WONTFIX or WORKSFORME :-)
I agree with comment 1.
+1 if users who enabled auto-refresh get some feedback that there might be more tags. Out of curiosity: Michael, what is the scenario that you think of in bug 80478, comment 18?
You will get the deep prompt any time you are fetching tags for a folder that doesn't contain files but does contain other folders. For instance, if I do a Compare With in the CVS Repositories view on the src folder of an Eclipse project, I will get the prompt if auto-refresh is enabled.
released fix.