The non-source code stuff can be ignored via .gitignore (more on that in a moment), assuming you do not want it in the repo at all.

Your 'B' use case sounds like one we have right now: A framework, if you will ('A') and apps delivered via that framework ('B', 'C', etc.). Eventually, we will deliver A as a package and the apps as plug-ins to that package (more or less) but right now they all live together (npm run start in A brings in the apps in B, C, etc.).

Our top-level folder has a .gitignore that looks like this:

  *
  !thisProjectFile.js
  !that.css
  !images/\*
  !otherArtefacts/\*

where the items preceded by ! are all in the A repo, things we want git to consider when in A but not in B, C, etc.

In A's top-level folder, do a git clone of the repos for B, C, etc., and their folders will be created in that folder, but

  1. All git operations in A will ignore B, C, etc., because of the .gitignore, and

  2. Operations in B, C, etc., will ignore A, because it is "outside"

Works well enough for now.