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proper steps for rooting, deodex, etc

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Default proper steps for rooting, deodex, etc

So I am trying to build a stock ROM, and it has been a while since I've done this, but was curious of what are the proper steps to take a working ODEX rom, add root, busybox, init.d, and deodexing. Meaning do I deodex first, then add root, then busybox, then init.d, or is that not the right order. Secondly, I remember with deodexing some files require a different api level, how will I know which is the proper api level for them? Thanks!

P.S. I am doing this for the HTC One (M7)
Device: Google Nexus 7 2013 2nd Gen FHD
ROM: CleanRom
Kernel: faux123

Device: HTC One M8
Provider: AT&T
Kernel: ElementalX
faisal nafis
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Thumbs up Android Everything Tool by Ricky

Dude download Android everything tool by Ricky it has all what you need. Deodex, Zipalign, Sign etc. And a proper guide is also available.
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