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Tested it with a tiny container, and apt-get upgrade successfully finished for me without any complaint about disk quota. @akarasulu do you remember what was the template for your container? Or maybe any steps to reproduce this behavior?
Result:
first time I generated 150GB which is over than 100GB
second time I generated 20GB file it start giving error Disk quota exceeded but there were 80 GB free space according to quota rules.
This cannot be true even for the tiny container size:
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