404 Not Found | only Homepage working

The only homepage is working. Other pages are not working with the following message.

Not Found
The requested URL /croy/publications was not found on this server.

Out of interest, do you have all your .htaccess setup? Just wondering if one of your rewrite rules might be interfering.

Newbie question:
I would like to change over from my html webpage www.myserver/mysite/ to GRAV. In order to learn the basics I have copied the base grav page under www.myserver/mysite/grav/

In .htaccess I tried all three of
RewriteBase /
RewriteBase /mysite/
RewriteBase /mysite/grav/

without success; Error 500.

My Server Helpdesk advised me to remove the .htaccess file, and now I can at least see the home page. However, the link to "Typography" produces the expected Error 404.

Thanks for any hint.