What's the solution for that case though (one which requires no nesting)? I don't think a solution with no nesting exists given the current module resolution algorithm of Node.js, which allows for only a single version of a particular package to exist at a given level.
nesting can't be prevented in that case (at least with the current node require() design). It gets really bad if you have 10 packages that depend on c@1.0.0 and 10 packages that depend on c@2.0.0 -- one of them will install in the root directory and the other 10 will be duplicated. ied stores a single copy of each package@version and uses symlinks which is an improvement. Apparently yarn tried something similar but it breaks some packages (that check where they're located for example).
I could be prevented. Another project does this by using a hash of the project to all all dependencies at one level then symlinks the dependencies from hash to name so it references the correct version.
