Hi, .htaccess files are blacklisted by default (search for ‘blacklisted_files’ parameter in doc).
But this can be overriden in your config/config.php file by adding 'blacklisted_files' => array(),
This empty array will allow .htaccess files to be synced!
As stated in the doc, WARNING: USE THIS ONLY IF YOU KNOW WHAT YOU ARE DOING
I think you can add your own other blacklist rules in that array as it will override the global setting.