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It used to be that you could at least add code to a template file and have it work, nope.
The theme editor injects <p> tags around javascript making it useless. I guess no one tested wp6 before rolling it out.
How can I add my code BY FILE NOT EDITOR and have it appear on the page?
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Go into the theme file editor. Appearance > Theme > Files
Or if you are already live and have hosting, log into cPanel and insert the code in the relevant place.
Make sure you back up your site first though