A fairly clean way is to make a pkglist of the installed.packages() that are not Priority "base" or "recommended", store it somewhere, then install.packages(pkglist) after upgrading.

I’m happy to help!

I mostly structure new projects as targets - code that get reused gets spun into a pkg.

The targets structure looks like Miles’s {tflow} design: github.com/njtierney/de...

At the other end of complexity, here are 2 larger projects:

github.com/njtierney/tt...

And

github.com/idem-lab/map...