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Can I just update directly from App Store?


ergot
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Generally, yes. But worth to note, upgrading any o.s, on any hardware has its risks. Especially .0 releases as they usually have bugs. Backups are your friend.

 

Many people insist to do clean installs but this is user preference rather than the "safer" method.

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I tried Upgrading Yosemite to El Capitan GM. Mounted Efi Partition, copied fakesmc and other kexts to clover/kext/10.11 folder.

Double clicked El Cap install.App in Applications folder, it rebooted automatically. When rebooting it created a "install El Capitan" setting in Clover GUI, i selectedt it, it run the install and was able to boot into the freshly upgraded El Capitan GM without any bigger Problems.

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Yes, an easy install directly from the AppStore using Clover boot loader.  As previously stated make a backup of your present install (because accidents do happen).  Update Clover to the latest version (I know 2370 works). Get El Capitan Install from the App Store.  In the Clover folder on your HD navigate to the Kexts folder and copy kexts in 10.10 folder to 10.11 folder. Add Rootless=0 as a boot flag in the "config.plist" in the Clover folder. Double click El Capitan in Applications. Install will begin. After a couple of minutes the computer will reboot. At the Clover boot screen select "OS X Install from (HD Name)". Computer will boot into the install process.  At this point you can take a break while the computer runs it will reboot a couple of times during the install process. Assuming you have Clover set to boot into your HD automatically, you have nothing to do until the install is complete - takes about 45 minutes from double click on El Capitan Install until the computer finishes the install and boots into El Capitan.

 

You can accomplish a clean install using basically the same procedure by installing to a second HD on your computer.  Updated Clover, copy kexts to 10.11 folder, modify config.plist and copy El Capitan Install to the new HD.  Double click on that El Capitan (new HD). At the Clover screen select "OS X Install on (new HD name)". At the next reboot, at the Clover screen select "boot OS X from (new HD name"). Once the installation is complete install Clover to the new HD (10.11 folder kexts and modified config.plist) and you are done.

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