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I am in the template editor for my WP site, and I want to upload a new file, but I can't find that option anywhere. I want to make a new php file for a custom portion of the site. Where can I find this functionality?

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You can install a File Manager within Wordpress, Search the Plugins.

Or the easyist way to be honest is simply login via FTP to your web host locate the template folder within wp-content/themes/yourtheme/ and create a file with the name you want to have it. i.e wp-content/themes/yourtheme/mycustom.php just insert in the empty file. and then your see it editable within the theme editor.

Hope this helps you out.

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I recommend always using FTP to edit Theme/Plugin files. The admin editor is raw, has no fail-safes, and can and will white-screen your site if you screw up the code. – Chip Bennett Dec 11 '12 at 0:14
+1 to chip's comment but I consider this important enough to say it out loud too. There is no end to the "I was editing my theme and now I can't get back to fix it please help" threads over at the wordpress.org forums. – s_ha_dum Dec 11 '12 at 1:43

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