Xcode is rebuilding everything after I cleaned
Expected after clearing DerivedData; each project rebuilds once.
That's expected after cleaning DerivedData. Xcode rebuilds it the next time you build each project, which takes a few minutes the first time, then it's back to normal. Nothing you wrote lives in DerivedData.
If you'd rather keep it for a project you're working on now, untick it next time; Cachet remembers your choice when it scans again.