Advantages/disadvantages of bundling source code from separate, related papers?
I face a similar situation. I'll tell you what I'm planning to do, although I don't claim this is the best approach. I think it's a reasonable compromise between making things easy for the reader, and making things easy for me.

First, I wrote several libraries that I keep on GitHub. One or more of these is needed to reproduce the research I'll discuss in each paper. I'll create a release for each library, with a citable DOI using Zenodo. A set of instructions is available.

Likewise, I'll have a configuration file, plus some scripts, and maybe some data, that are unique to each experiment. This is where I'll put the README file describing how to build/run everything. I'll create a GitHub repo for those as well, and create a release using Zenodo.

So each paper I write will cite all the library/other releases needed to reproduce the software.

EDIT: One advantage of this is that while the DOI will point to the exact version of everything I used for my published results, it will also be clear where people can go for the latest version of everything.