Using unionfs or similar as root file system in Linux?

After building Linux From Scratch several times I realized that package management is really a hard thing to do. After thinking for some time, I came across an idea. My idea is to install all packages into separate directories, then combine them into one file system and mount as root (required). Also, I want to attach and detach packages without a reboot (optional, preferred).

How can I do this from scratch (or with a package)? (No problem if I need to program (C or C++ preferred))