Fixing redundant package.json in visuald-combined generated projects when using sub-packages

Let's say I have a package.json which define two sub-packages:

mypackage:foo and mypackage:bar

As the two packages have the same package.json, it will be included twice in visuald-combined generated projects.

This pull request checks that when adding package files in topological order that package.json is only added at the first time we see a base package.