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Automated

From your old phone make a decentralized Backup with ADB.

adb backup -apk -shared -all -f backup.ab

And restore it on your new phone

adb restore backup.ab

Manually

Or manually backup/restore your phone from the following directorys

/data/data       # the DATA of all app's

/data/app        # MANUALLY INSTALLED apk's

/system/app      # PRE-INSTALLED system-apk's

/system/users/0  # SYSTEM settings