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This is the default Mac behavior, as far as I'm aware. When you cop&paste website content, it is copied as rich text. However, when you copy the address of a website, it is copied as plain text. For instance, if you paste website content into Pages, it is pasted with clickable links (because it is rich text, RTF), if you do the same with a website address, it is not clickable either (because it is plain text). So this is not a "bug" in Ulysses, but just the way Safari or OS X in general behave.