Do the files in the snapshot directory count toward your storage quota?
AFAIK it doesn’t count.
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I think someone once explained that any files outwith your control such as logs, backups, mysql backups etc are not counted towards your quota.
Absolutely not. First of all, the .snapshot isn’t a full copy of your home directory. The way it works on the NetApp is that only changes from your last backup are kept.
Plus what the other poster said about it being beyond your control, so it’s not held against you.