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how to transfer a site by shell

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you can transfer files, but not running mysql. for safety you need to use mysqldump first to backup your runnning mysql database. (google it)

to transfer some directory do like:

rsync -avz /old/server/directory -e "ssh -p YOURSSHPORT" root@yournewserverip:/new/server/directory
ssh default port is 22
 
You can use rsync to copy your web source by the command which wdc was stated.

If you use mysql, you must rsync mysql database to new server.

But remember please install your software on your new before.
 
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