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So I noticed something was wrong with my partitions in Disk Utility as the Mac HD only occupied half of the storage, I booted into UBuntu on a USB and from there I found out that the recovery partition was occupying half of the disk, I don't know why, I could not resize it in Disk Utility, or via the Ubuntu live, a search suggests that it is related to Boot Camp, but I never had that set up.

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I was able to fix it by erasing the recovery partition with diskutil eraseVolume JHFS+ Blank disk0s3 and resiizng the main partition in Disk Utility, but I am still not sure why it got that big in the first place.

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