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I have an Alcatel Idol 3 (6045Y variant) with TWRP and yesterday i received the Marshmallow update notification. As other users noticed, this update also removes fastboot commands and reverts the recovery back to stock. Now, i have downloaded the update.zip file and transferred it on my PC in order to edit updater-script (possibly other files?) so i can keep fastboot and/or TWRP. If this is my updater-script content, am i safe with removing this line and keep TWRP?

package_extract_dir("recovery", "/system");

Please note recovery folder contains file recovery-from-boot.p and bin folder which contains this script.

Also, some devs at XDA reported we can't have both fastboot commands and a working Marshmallow system, why is it so? Can't i simply remove the line where it flashes the new aboot partition (which, i'm not sure, contains fastboot commands)?

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It usually requires a new boot.img which contains your kernel..
If you flash the update, it should flash all images, Network, Boot, System, Recovery and even sometimes the Cache..
I would imagine that you need to Patch the boot.img to work with TWRP, or other custom recovery...
Sometimes it's a simple as changing SElinux permissions off enforcing ...

You can try to edit the recovery script because it does work on some devices, but you will most likely hit some sort of " checking update.zip is valid "... ( this usually makes a md5 and then calculates the update.zip md5 against the original )

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