Yugipedia has been experiencing an issue for the last couple months where user CSS and JS were not being loaded. The following was set in our LocalSettings.php:
$wgAllowUserCSS = true; $wgAllowUserJS = true;
As it turns out the variables are case-sensitive. Meaning that the default values of false were being applied.
Variables such as these should be case-insensitive in order to prevent confusion like this. Aliases should be added of the following form to DefaultSettings.php, or another appropriate location:
$wgAllowUserCSS = $wgAllowUserCss; $wgAllowUserJS = $wgAllowUserJs; $wgUseSiteCSS = $wgUseSiteCss; $wgUseSiteJS = $wgUseSiteJs;