I would like to backup and restore manually all partitions. I know this is not the first time this issue has been raised. There are already many links and questions on this issue, and I have reviewed most of them probably.
The suggested answers are divided to the following:
Root the device, install appropriate recovery tool (nexus root toolkit, TWRP or clockworkmod recovery), and boot into recovery, then do the backup from the tool.
Other solution suggest to use "dd command" but only for boot partitions, not all partitions. I'm not sure why. for example the follwing page warns not to use dd on system partition: http://www.addictivetips.com/mobile/how-to-backup-your-android-phones-boot-recovery-and-system-partition-images/
I wonder how the suggested tools are capable of backup all partitions. If "dd command" is not used, what is the way to manually backup all partitions (which is probably the way these tools do backup in source code) ?