Flashed recovery ?
Its important to flash recovery before you do anything else like this with your mako.
But at the same time, once you have flashed the recovery, flashing anything on your phone is very easy.
Rooting
Android is linux at heart, so permissions work just like they do in linux. That means you don’t have the ultimate permissions in the normal context. This keeps you from being able to change most of the things on the phone.
To change this and do whatever you want (provided you know what you’re doing), the phone can be rooted. For that you need to get another zip, most commonly, SuperSU.
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Just grab the file and copy it to your device’s sdcard.
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Boot into recovery
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Choose “Install zip from sdcard” -> “Choose zip from sdcard” -> “SuperSu.zip” -> “Yes” and let it flash
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Once it finishes, select back to get to the main menu, then reboot.
You must have gotten “SuperSU” as an app in your phone. Use it to regulate the permissions given to other apps. Now you can use any app requiring rooted phone. And ya, “with power comes responsibilities”, so be cautious.
Custom ROMs and kernels
There are several custom ROMs available out there, but my favourite is Carbon ROM. The best place to get all the ROMs is http://goo.im and ya of course xda.
Once you decide which ROM to get, you need to get its file and the gapps file corresponding to the android version your ROM is based on. Once you have both, just go ahead and flash the rom followed by the respective gapps. Then just reboot and enjoy. You must have guessed by now that flashing a kernel is just the same, download -> recovery -> flash -> reboot.
Pretty simple, wasn’t it ?