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- editing apache, php or mysql config files cannot be done in ISPConfig, still need terminal
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Normally you dont have to do that after initial setup of the server as you can do all required settings for the sites, databases etc. in ispconfig.
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- ssh, ftp or webdav can not be created with the same directory, username, password in one time
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You can access the same directory with ssh and ftp users. Users were not created together as ispconfig offers a more fine grained control over users as it is required by larger hosting companies. If you run a small home server, then this might be too much for you indeed.
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- some stuff with "The perfect server..." don't fit my need for Wordpress or don't work the good way (file upload in Wordpress get a server error, etc...)
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I run several wordpress sites on perfect setup debian servers, they work all out of the box.