A clean install means you install from nothing. If you want to keep your your OS and installed apps, you can do so by cloning.
The problem with cloning a boot drive is that you have to pre-size it to be smaller than the available SSD after it is set as a boot drive. When I cloned my install of Win 7 on a HDD to a SSD I had to resize the partition (for a 128 GB SSD) to just under 119 GB fopr the cloning to work. By cloming I kept all of the settings on my OS, and installed apps on C: drive.
As most storage remains on the HDDs, I did not have to migrate any storage.