There's not a lot of information here. For instance, what do you want to happen with all your other URLs (do you have any other URLs)? For the sake of this answer I assume you just have a single URL, / that needs to rewrite to /website/index.php (as stated in your question).
Anyway, you don't do this entirely in .htaccess. The first thing you must do is:
Change the URL in your application. Change your links to point to https://example.com/ (not https://example.com/website/index.php)
You can then use mod_rewrite in .htaccess to internally rewrite the URL from https://example.com/ to https://example.com/website/index.php (the underlying filesystem path):
RewriteEngine On
# Rewrite "/" to "/website/index.php"
RewriteRule ^$ /website/index.php [L]
Optionally, if you are changing an existing URL structure and you need to preserve SEO then you can also implement an external redirect from /website/index.php to /. However, you must only do this if you have implemented step #1 above. This goes before the above rewrite:
# Redirect "/website/index.php" to "/"
RewriteCond %{ENV:REDIRECT_STATUS} ^$
RewriteRule ^website/index\.php$ / [R=302,L]
The RewriteCond (condition) is necessarily to prevent a redirect loop. To prevent the rewritten URL (above) being redirected.
(Change to a 301 only after you have tested that this works OK - to avoid caching issues whilst testing.)
In Summary:
RewriteEngine On
# Redirect "/website/index.php" to "/"
RewriteCond %{ENV:REDIRECT_STATUS} ^$
RewriteRule ^website/index\.php$ / [R=302,L]
# Rewrite "/" to "/website/index.php"
RewriteRule ^$ /website/index.php [L]
index.phpfile into/var/www/directly? If you do that, what you want automatically happens. Alternately, you could edit your webserver config to set theDocumentRootto/var/www/website/rather than/var/www/. Both of those are simple changes that prevent a lot of ugliness in .htaccess