Migrate files from an old HDD to a new one

I'm going to switch my HDD inside my MacBook Pro and I don't know how I should get my old files to the new hard drive. I see two possibilites: I use my Time Capsule to restore the backup or I just copy the old HDD to the new one. My question is whether I can use the OS X's migration assistant to clone a bootable drive, which is connected via USB 3.0. This would be the easiest solution for me, since some folders are excluded from the backup and USB 3.0 is faster than the Ethernet of my Time Capsule. So is this possible or not?

I would use something such as carboncopycloner to clone the old hdd to the new one

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