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So I store my websites on a partition of my laptops hard drive. Programs and my bash scripts say that this partition does not exist, until I personally open the partition up by clicking the icon on the left side.

I am not sure why that is, and then how I could fix it so it either auto loads on startup or my bash script automatically loads it.

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Use blkid to get the UUID for the partition, then add a line to /etc/fstab to tell the system where you'd like it mounted. You will find advice on doing that in many places, such as here

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