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Sarah, you’ve forgot to mention that by setting “apple-mobile-web-app-capable” in meta tag web app/site must be fully “AJAX-ed” – that means, any page call must be done inside JS. If it’s outside page call or simple operation like clicking/tapping on default link, iOS (since it’s the only platfom that recognizes this value, not sure about the others) will exit the app and launch requested page in Safari with defaut view (chrome, etc.).
Also, browser sniffing with JS is kind-of a bad practice and prone to errors, but unfortunately widely used.
Otherwise, great discussion and comments, especially regarding context of mobile web apps/sites.