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I did, web1, web2, web3 etc... correct? ISPConfig also generated directories with the site domain names and when I placed the files in the root directories they were copied into the domain directories also by ISPConfig I assume.
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ISPConfig is not copying any files in the websites. You will have to upload your files to the web directory of the website. Example:
/srv/www/www.thefractalfarm.net/web/
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Each time I tried the setup with ISPConfig an ls of /srv/www/ would look like this
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Thats perfect, exactly as it should be.