How do you minify and/or compress JavaScript that is in a php file?

Your PHP script generates the Javascript code, so it can minify the code before outputting it: generate the code in a variable, then pass that variable to the minifier, and only then output to the browser.

You are starting your optimization off the wrong end. Obviously if you have hard-coded JavaScript, HTML and whatever else inside your PHP files, you seriously need to refactor the code. But even if you don't, you shouldn't minify the code in place because it would be even harder to maintain.

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