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If the branch.master.merge entry is not specified in configuration, you get the following error message: "no values for key branch.master.merge" found in configuration". From that message, it's not easy to know what to do to solve the issue. It's probably possible to improve usability by adding some explanations like "add the branch.master.merge entry in the repository config file" or something like that. With an example, it's even better. (just a suggestion, of course)
IMO, if there is just one remote branch in the repo EGit should be even smarter and assume that the user wanted to pull from this branch. That would improve usability even more.
Even better, we should show a wizard which helps with setting up the "upstream", see bug 343593. *** This bug has been marked as a duplicate of bug 343593 ***