I replaced the Superdrive of my iMac with an SSD. Next, I trimmed down the partition of my existing HDD (2TB) as much as possible using Disk utility. This resulted in a 140GB partition. Then I used Disk Utility to clone the reduced partition over to the 250GB SSD. If I check with DU, it tells me the amount of data is around 140GB and Finder shows me the same.
However all directory structure scanners like GrandPerspective, DiskInventory, etc. show me a usage of 46GB.
GrandPerspective gives me the information that 93GB "miscellaneous used space" is occupied (the huge gray part in the image).
My Yosemite installation is all fresh, so the 46GB is the correct amount. What about the missing 100GB? How can I get these back?
Note that there are no hidden Time Machine backups. I have already checked that.