What I can read from the source output:
You read in the config file (this case clean.js). In that config file I add my extraPlugins.
After that you overwrite the extraPlugins line, so the extraplugins I add in my config file would be overwritten by that.
This is in my clean.js (and attached is the Screenshot of the admin page):
CKEDITOR.editorConfig = function(config) {
// Define changes to default configuration here.
// For the complete reference:
// http://docs.ckeditor.com/#!/api/CKEDITOR.config
config.toolbar = [
{ name: 'document', items: ['Save','Source', '-', 'A11ychecker', 'NewPage', 'Preview', 'Print', '-', 'Templates'] },
{ name: 'clipboard', items: ['Cut', 'Copy', 'Paste', 'PasteText', 'PasteFromWord', '-', 'Undo', 'Redo'] },
{ name: 'editing', items: ['Find', 'Replace', '-', 'SelectAll', '-', 'Scayt'] },
{ name: 'forms', items: ['Form', 'Checkbox', 'Radio', 'TextField', 'Textarea', 'Select', 'Button', 'ImageButton', 'HiddenField'] },
'/',
{ name: 'basicstyles', items: ['Bold', 'Italic', 'Underline', 'Strike', 'Subscript', 'Superscript', '-', 'CopyFormatting', 'RemoveFormat'] },
{ name: 'paragraph', items: ['NumberedList', 'BulletedList', '-', 'Outdent', 'Indent', '-', 'Blockquote', 'CreateDiv', '-', 'JustifyLeft', 'JustifyCenter', 'JustifyRight', 'JustifyBlock', '-', 'BidiLtr', 'BidiRtl', 'Language'] },
{ name: 'links', items: ['Link', 'Unlink', 'Anchor'] },
{ name: 'insert', items: ['Image', 'Flash', 'Table', 'HorizontalRule', 'Smiley', 'SpecialChar', 'PageBreak', 'Iframe', 'Youtube'] },
'/',
{ name: 'styles', items: ['Styles', 'Format', 'Font', 'FontSize'] },
{ name: 'colors', items: ['TextColor', 'BGColor'] },
{ name: 'tools', items: ['Maximize', 'ShowBlocks'] },
{ name: 'about', items: ['About'] }
];
config.extraPlugins = 'A11ychecker';
config.filebrowserBrowseUrl = '/Admin/Editor/ckeditor/browser.aspx?type=link';
config.filebrowserImageBrowseUrl = '/Admin/Editor/ckeditor/browser.aspx?type=image';
};