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It depend what exactly you move-for example,for me easiest is when i complete data from one dedicated server to another fresh dedicated server-I just do either rsync over ssh or i first archive files in tar.gz files and then transfer.That depend on howmuch files you have in directories - if there is tons of files,then it's better to archive directory first,as with rsync would take ages to move when there is a lot of files.
But potencial problem with archiving,then you need to pay attention on avalaible hard drive space on server,since if there is not enough space to make archive then you are forced to rysnc.And the reason what is good on transfering from server to new server - is very easy way to transfer mysql databases - all you had to do is to copy /var/lib/mysql directory and archive it,and then extract it on new server and you get automaticly transfered all users and databases then compared to when manualy exporting and importing databases with tools like mysqldump or phpmyadmin.But using that is requied in case when you dont transfer sites to completely new server.
Also i would recommend for exporting databases to use instead phpmyadmin or mysqldump script adminer,which have feature which can import a database from server.
And finaly,if you transfering sites from server where ssh is not avalaible,just make sure you are able to make archive there as transfering from ftp to computer computer to ftp is worse then doing rsync.
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