Worst Case
Bunch of files thrown into BOOT:/ or RD0:/ with minimal documentation (current scenario as of 1.0.1).
Best Case
Every component neatly packaged and easy to enable, disable or switch out in a particular system build.
Likely Compromise
System programs will go in the drive’s /DOS directory and development tools will go in a /SDK directory, maybe with other top-levels for other optional stuff. This will be managed by simply extending mkfs to build “release packaged” disk images, the regular package manager will be included in /DOS but not overly relied on by the system itself.
This works in well with the PATH system allowing users to look up programs from the current drive or from their BOOT: or equivalent drive. E.g. a possible PATH setting would be “/DOS;BOOT:/DOS” allowing lookup of system programs from the current drive’s installation first when available or otherwise from the BOOT: drive. A fully packaged approach may need a more complicated PATH instead.
This also allows for easy packaging in the future as any new large components can easily be broken off into subdirectories first and then packaged separately whenever it makes sense.
So that will probably be the compromise used for later 1.x releases rather than the full packaging approach or the “just chuck the files in” approach.