Shifter does not use or support htaccess files in production.
Htaccess is a feature specific only to Apache web servers. Since Shifter serves traffic from a static hosting environment software such as NGINX or Apache are not necessary or used.
If you need to modify to your htaccess file for a particular feature or purpose such as redirects there are options available.
Htaccess for Redirects
If you customize your .htaccess for the purpose of vanity URLs or SEO you can still do this using the supported Redirections WordPress Plugin.