During the out of box setup process there should a step where it asks you if you have data to transfer from your old phone. You would then hold the phones back to back and let NFC do its magic. I think this migration only transfers your phone book and account credentials.

Therefore, I opted for a more manual process when migrating from Nexus 4 to Moto X. Again, it involves NFC/Android Beam. Working from memory so something may be off.
1. Load ES File Explorer on both phones and open it
2. On the old phone select the file or directory you want to send and tap ... then send
3. On the new phone navigate to the directory you want to save the file/directory
4. Touch the backs of two phones together
5. On the new phone tap the option to accept the file

I don't know if you need to connect both phones to the same WiFi network. You may not have to as ES File Explorer seems to use WiFi Direct for the transfer.

If you transfer the entire /sdcard directory (which is emulated on Nexus because no physical SD card) all of your application settings should make it to the new phone.