Move scripts and styles to functions.php and enqueue them there properly #18
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Since TwentyTwelve will serve as a best practice example for Theme Developers, I would be thrilled if we could move all scripts and styles to functions.php, to adhere to this guideline in the Theme Review process.
From what I understand, leaving the comment-reply script in header.php is technically still acceptable, but let's set a good example! :)
Maybe, to top it off, we could add a comment to that html5.js script in header.php, explaining that scripts wrapped in conditionals there, are okay.