I wrote a package manager: https://github.com/eltanin-os/venus
Complemented by a ports-like {source-based package manager/build system}: https://github.com/eltanin-os/ports

It fetches, does a integrity check, and unpack the files into the $root directory. It's actually a little more complex than one would expect a "simple package manager" to be, it has its own archiver and manifest/config file format.
The "database" is a directory $root/var/pkg with the data files
$root/var/pkg/remote: packages that can be fetched
$root/var/pkg/*: arbitrary sources (such as a cd, another hd, etc.)
$root/var/pkg/local: installed packages
A "database entry" looks like this:
It's painful to deal with cases where you want to statically link a package, but some of its dependencies can only be linked dynamically, so you need to differ construction/static deps from runtime/dynamic ones.

It has a configuration file under /etc/venus.conf or $HOME/.config/venus.conf
See an example below using /usr/local as $root:
There are two repository entries to avoid needing to trust a mirror, as the integrity values (crypto hash) and entries would be downloaded from the official repository.

It has no automatic dependency resolution to this moment, although i am considering to add a simple recursive one (similar to the one used by the ports).

About the discussion on separating the packages under /whatever/package_name, like nix/guix/janus/gobo does: It seems a good way to organize things at first, but then you fall to the problem that the entire OS expect a different organization; most of the advantages of separating the packages are lost when you try to solve this (maybe union being an exception, but then you have its own problems)