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I have a VPS server and 3 domains to set up. I will be the only user on the server. How to organize my home directory ?

/Home/user1/site1
/Home/user2/site2
/Home/user3/site3

or

/Home/user1/site1
/Home/user1/site2
/Home/user1/site3
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I would go with option one, since you always want to separate the sites as much as possible. You probably also want to be able to host some other guys website later on or maybe you sell one of your own and the new owner should have access to one but not the others.

Maybe even go as far as:

/home/site

example:

/home/askubuntu.com/public/index.php

Just my opinion - not entirely sure you can have dots in the homefolder name, else use underscore.

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