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I then tried simply to display an index.html file in the cgi-bin directory and got "object not found", but if I changed the name to cgibin and typed in "URL/cgibin" then the file was displayed (!!??)
When I tried to execute "URL/cgi-bin/hello.cgi" I got "server error: premature end of script headers", but when I tried it with cgibin/hello.cgi I got "access forbidden". I also get this message if I comment out all the ScriptAlias directives.
"/home/sites" seems like a rather obscure location to keep it in. this would be reserved for the "sites" user and would have inherited permissions for that user and usually a "sites" group only. Using the "/var/www/cgi-bin" would make the most sense from a permissions standpoint.
You are probably right about the directory structure. The idea was to give each website its own virtual server space with separate permissions. I wouldn't want to give users access to a global directory like /var/www/cgi-bin and not sure how to get round that. They could interfere with scripts belonging to other users/sites.
What would I have to do to give each virtual server the correct set of permissions in the conf file?
I am not sure what need you have to meet in terms of permissions. Outsiders only have read permission to system directories anyway. And file location is all in your scripting. That's all the help I can be I'm afraid.