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if i do ScriptAlias = /script.cgi:/usr/lib/script.cgi , then every link i have on website has http://www.bla.com/script.cgi/subdir instead of http://www.bla.com/subdir

i tried doing ScriptAlias = /:/usr/lib/script.cgi, but hiawatha refuses to start then.

Is it a match rule i need to use maybe?

The first '/' in your ScriptAlias parameter is not a script and therefor invalid for ScriptAlias. Have you tried a UrlToolkit rule yet?

UrlToolkit {
  ToolkitID = my_rule
  RequestURI exists Return
  Match .* /script.cgi
}

This UrlToolkit rule is just a guess. I have no idea what CMS/framework you are using or how your website works.