Regarding the .htaccess file
I was looking through my .htaccess file and all that is written in it is:
# Custom 404 Not Found Error Page ErrorDocument 404 https://profreehost.com/404/index.php
I'm almost certain that this is not normal... Any thoughts?
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This is completely normal, as this is the default rule for 404 pages configured in ProFreeHost, you can easily set your own from the panel or by modifying the URL in the file.
I'm not sure exactly what you mean, where you expecting it to have more contents? What were you expecting?
Where is the DirectoryIndex? Shouldn't that be in the .htaccess file?
Not necessarily, it's using the default configuration, you can set it if you want to change it.