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I've just flashed my Nexus5 with Android 5.1 factory image using this how to:

http://www.droid-life.com/2013/11/05/how-to-flash-nexus-5-factory-images/

I've made a complete backup off all my data since I was sure I'll loose it. Also the how to states:

"*Flashing factory images wipes your phone completely clean, leaving it at a factory, out-of-the-box state."

This also happened after flashing my Note 4 with Android 5 withe the rom downloaded from sammobile.com. (flashed via Odin)

So - why is all my data (photos, apps, calendar/contacts) still present after flashing the new rom?

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The apps and user data (everything that gets erased by factory reset) are contained within the /data partition (in fact, "factory reset" simply formats the /data partition). This partition is independent of other partitions. Android system is located on the /system partition. That means that, as long you don't wipe your /data partition, your apps and data will stay in the phone even when you change your Android version.

It is, however, recommended to wipe your /data partition when moving from one Android version to another, due to incompatibility issues.

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In that guide it says:

*If you don’t want to wipe data, remove the “-w” in the second to last command.

Therefore if you removed the "-w" then your user data will not have be touched/wiped when flashing the factory image.

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