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When installing a custom ROM shouldn't we wipe system partition along with data, dalvik, and cache? What are the differences with and without wipe?

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You should. That is a "clean flash" and is normally recommended in installation instructions. This ensures that the ROM is written on a clean slate

At times, like in the case of "nightly" ROMs or some mods to ROM, /system is not wiped but written over the existing system called "dirty flash" (not even /data or cache is wiped)

As a thumb rule, switching over from stock to custom ROM or from one custom ROM to another, clean flash is recommended. ROM chefs clearly mention this in instructions. Also, if you are upgrading to a higher version of ROM by clean flashing it (Thanks to Izzy who pointed this in comments)

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    Strictly speaking, a "dirty flash" is a flash were you don't wipe anything (i.e. not even /data). But your advice is correct: when switching between different ROMs, one should always do a "clean flash" (i.e. wipe /cache and /data, and best also /system) – also when doing a "major upgrade" to a newer Android version. In the latter case it might not always be necessary (there are even some OTAs performing a "dirty upgrade" – I've seen this e.g. on the Galaxy 7 Edge updating from MM to N), but it never hurts (except you've got to install/configure everything again).
    – Izzy
    Jan 6 '18 at 14:31
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    @Izzy: thanks for adding useful inputs. I deliberately left out the dirty flash distinction to focus on the /system but added it now, as also higher OS bit. My upgrade to Oreo via OTA a couple of days back was also "dirty"
    – beeshyams
    Jan 6 '18 at 14:43
  • So if I upgrade from 6.0 stock to 7.1.2 lineage OS nightly I should do that with a clean wipe or a dirty wipe?I did that with both of them and I don't see any difference. Jan 6 '18 at 16:03
  • I am not familiar with Lineage but you would need to see the instructions. However, it is best to do a clean flash not to have problems. And problems may pop up later too, not visible immediately on dirty flashing
    – beeshyams
    Jan 6 '18 at 16:07

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