<IfModule mod_rewrite.c>    
  RewriteEngine on

  RewriteRule ^.well-known/ - [L,NC]

  RewriteCond %{HTTP_HOST} ^www\.(.*)$ [NC]
  RewriteRule ^(.*)$ https://%1/$1 [R=301,L]

  RewriteCond %{HTTPS} !=on
  RewriteRule ^(.*)$ https://%{HTTP_HOST}/$1 [R=301,L]

  RewriteRule    ^$ app/webroot/    [L]
  RewriteRule    (.*) app/webroot/$1 [L]
</IfModule>

https://stackoverflow.com/questions/38790421/letsencrypt-with-htaccess/41391957#41391957

This .htaccess actually forces all traffic to https, and allows cakephp app to work properly, as well as letsencrypt to go thru

Htaccess rewrite file for Letsencrypt and CakePHP app

cakephp, htaccess

Apache