In conclusion, for other noobs using ISPConfig 2, this is my list for what needs to be backed up for a move to a new installation:
cp /etc/passwd /disk2/backup1/ispconfigfiles
cp /etc/shadow /disk2/backup1/ispconfigfiles
cp /etc/group /disk2/backup1/ispconfigfiles
cp /etc/apache2/vhosts/Vhosts_ispconfig.conf /disk2/backup1/ispconfigfiles
cp /etc/postfix/local-host-names /disk2/backup1/ispconfigfiles
cp /etc/postfix/virtusertable /disk2/backup1/ispconfigfiles
cp /var/lib/named/etc/bind/named.conf /disk2/backup1/ispconfigfiles
cp /etc/proftpd/modules.conf /disk2/backup1/ispconfigfiles
cp /etc/proftpd/proftpd.conf /disk2/backup1/ispconfigfiles
cp /etc/proftpd_ispconfig.conf /disk2/backup1/ispconfigfiles
duplicity --no-encryption /var/www file:///disk2/backup1/allsitesbackup
plus the MySQL databases
and all the pri.* zone files for domains that use the local dns.
I use duplicity because it compresses the www files so they have proper ownership/permissions/location when extracted and it only backs up changes after the first backup, so it's very fast.
I use cp for the other files because root owns them all
You can also use duplicity to ftp the backup, like:
FTP_PASSWORD=yourpassword duplicity /var/www
ftp://user@serveriporaddress/
with encryption for security--duplicity will ask for a passphrase unless you specify --no-encryption
You can modify the list for your backup location and save it as a text file called yourbackupfile, for example, on your server and made executable by chmod to 755, then you can execute it with ./yourbackupfile
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