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$config['text_editor'] = 'ckeditor';
// ck editor specific settings... if you use a PHP array, it will use json_encode
$config['ck_editor_settings'] = "{
	toolbar:[
			['Source'],
			['Bold','Italic','Strike','Subscript','Superscript','Underline'],
			['Format','Resize','Colors'],
			['FUELImage','HorizontalRule'],
			['NumberedList','BulletedList'],
			['FUELLink','FUELUnlink'],
			['Undo','Redo','RemoveFormat'],
			['PasteFromWord','PasteText'],
			['Preview'],
			['Maximize']
		],
	contentsCss: '".WEB_PATH."assets/css/main.css',
	htmlEncodeOutput: false,
	entities: false,
	bodyClass: 'ckeditor',
	protectedSource: [/\{fuel_\w+\(.+\)\}/g, /<\?[\s\S]*?\?>/g],
	toolbarCanCollapse: false,
	extraPlugins: 'fuellink,fuelimage',
	removePlugins: 'link,image',
	allowedContent: true
	}";
CKEDITOR.editorConfig = function( config ) {
	// Define changes to default configuration here.
	// For complete reference see:
	// http://docs.ckeditor.com/#!/api/CKEDITOR.config
	// The toolbar groups arrangement, optimized for two toolbar rows.
	config.toolbarGroups = [
		{ name: 'clipboard',   groups: [ 'clipboard', 'undo' ] },
		{ name: 'editing',     groups: [ 'find', 'selection', 'spellchecker' ] },
		{ name: 'links' },
		{ name: 'insert' },
		{ name: 'forms' },
		{ name: 'tools' },
		{ name: 'document',	   groups: [ 'mode', 'document', 'doctools' ] },
		{ name: 'others' },
		'/',
		{ name: 'basicstyles', groups: [ 'basicstyles', 'cleanup' ] },
		{ name: 'paragraph',   groups: [ 'list', 'indent', 'blocks', 'align', 'bidi' ] },
		{ name: 'styles' },
		{ name: 'colors' },
		{ name: 'about' }
	];
	// Remove some buttons provided by the standard plugins, which are
	// not needed in the Standard(s) toolbar.
	config.removeButtons = '';
	// Set the most common block elements.
	config.format_tags = 'p;h1;h2;h3;pre';
	// Simplify the dialog windows.
	config.removeDialogTabs = 'image:advanced;link:advanced';
};
                
Comments
Use 'contentsCss' => WEB_PATH.'assets/css/ckeditor.css' to change the way the editor's content looks.
Any other thoughts?