Now it alternates between showing the /var/www/index file or redirecting to the new website, and I'm not sure why.
RewriteCond %{HTTP_HOST} ^full.website.base.URL$ [NC]
RewriteRule ^/$
https://full.website.base.URL/url-path/ [L,R]
alias /url-path "/local/www/path"
<Directory "/local/www/path">
Require all granted
RewriteEngine on
RewriteBase /url-path
Redirect permanent
https://new.website.base.url/ RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php?q=$1 [L,QSA]
RewriteCond %{HTTPS} off
RewriteRule (.*) https://%{HTTP_HOST}%{REQUEST_URI}
RewriteCond %{HTTP_HOST} !full.website.base.URL
RewriteRule ^.*$
https://full.website.base.URL%{REQUEST_URI} [R]
<Files "cron.php">
RewriteCond %{REQUEST_URI} /url-path/cron.php$ [NC]
RewriteRule "^/url-path/cron.php$"
http://full.website.base.URL%{REQUEST_URI} [L]
</Files>
</Directory>