I’m making an AIR application (so the download time doesn’t have a huge impact). Does combining and minifing all the JavaScript files affect the performance? How would obfuscating affect the performance?
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Minifying improves performance for your page overall by decreasing the load time (even if only slightly).
Neither minifying nor obfuscating alter the execution time by any perceivable amount for the vast majority of JavaScript code out there.
I do recommend minifying for those reasons and more. Minifying multiple scripts together (like jQuery and its plugins) can yield even greater savings.
As pointed out, on constrained devices and/or with very large codebases minifying could yield a noticeable result.