1. Uses class.phpmailer.php which is a duplicate of the joomla supplied libraryIt is set to var $CharSet = "iso-8859-1";
the joomla version is set to var $CharSet = "utf-8";
This could cause issues especialy for users debugging
Suggest to change file contents to something like
<?php
require_once( dirname(__FILE__) . '/../../libraries/phpmailer/phpmailer.php' );
Do the same thing for class.smtp.php
2. Zero byte filessite/include/index.html
site/images/index.html
site/lib/index.html
This can cause issues as some ftp clients and servers cant create/move zero byte files and is an issue with some backup solutions such as joomlapak
3 removed4. mambot directory link admin\themes\themes.phpline 274 $xmlfile = $mosConfig_absolute_path . '/mambots/editors/extcal/jscripts/tiny_mce/themes/' .$row->theme . '/' . $row->theme .'.xml';
Not sure what this is for?

5. Installs in legacy mode if required now6. Install themesError "Upload failed as /media directory does not exist."
I think this is because you are using $mosConfig_absolute_path = JPATH_BASE;
when it should be $mosConfig_absolute_path = JPATH_SITE;