You can configure the website path in the ispconfig server settings.
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however the resulting apache vhost file still contains /var/www as the base path for DocumentRoot. Switching it back, and using a symlink makes it all work again.
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This is nescessary and cant be changed if you want to use php or cgi with suexec on your server.
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Secondly, a symlink is made into /var/www/[domain]. This symlink points to the directory containing [cgi-bin, log, ssl, tmp, web]. That is also the home directory for shell users. Seems like the symlink should point to the "web" directory instead?
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No.