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I am currently running a 2013 macbook pro with a dual boot of mac osx/Ubuntu For some reason, after I got refind working properly, the only option I have for booting into Mac Osx is through recovery HD.

To top it all off, once I actually go through recovery and boot into my Mac Osx, it seems that the operating system changes the boot order to starting on Mac Osx instead of refind, which causes a whole heap of trouble (I am aware this is a separate issue of Mac Osx initiating a "coup" on my boot order, but it just makes the problem that much harder to troubleshoot). I know how to work around this but it is super time consuming.

I have already ensured that fileVault is off, as that is the only real suggestion that comes up on a google search.

Does anybody have any idea what is going on with this?

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First, booting OS X through Recovery HD is normal, at least for recent installations of OS X. This method is a consequence of how Apple has chosen to design its system. Specifically, in the past, the OS X boot loader resided on the OS X root (/) partition; however, the firmware (and therefore rEFInd) cannot read this partition if it's encrypted or uses an LVM setup. As Apple switched to LVM by default a version or two ago, it had to put the boot loader elsewhere. Rather than put it on the EFI System Partition (ESP), like everybody else, Apple decided to put it on the Recovery HD partition. Because rEFInd reports the name of the volume from which the boot loader is loaded, you see this accurately represented in the menu.

As to the boot coup, your use of that term suggests you may have already read it, but if you haven't, please read my page on the subject. Persistent boot coups caused by OS X are extremely rare, in my experience. I have a couple of suggestions:

  • Automate the bless solution -- My page describes using bless to recover from a boot coup. You could create a short script that mounts your ESP, issues the bless command with appropriate options, and optionally unmounts your ESP, then call this script as a startup or login script. I'm not an expert on this aspect of OS X, but see references like this or this for information.
  • Re-install rEFInd on an HFS+ volume -- If you re-install rEFInd on a (non-LVM) HFS+ volume by using the --ownhfs option to refind-install, that might be enough to get OS X to stop with its boot coups. (This solution assumes that rEFInd is currently installed to the ESP. If it's already installed to an HFS+ volume, you might try switching it to an ESP-based installation.) This solution is likely to require shrinking your existing OS X installation by a small amount to make room for a dedicated rEFInd volume; however, if you happen to have a separate HFS+ partition that you use for user files or some other purpose, adding rEFInd to it might be possible.

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