Yes I think that section could be clearer. Basically installation should work as normal with npm i or npm i <existing-dependency> The process of adding a dependency right now requires two steps:

1. Run gpm -n .. -t .. -i <new-dependency>
2. npm i ../<new-dependency>

I agree that uninstalling is also not covered. I'm debating between adding these as npm scripts or making more PRs to gpm.

As far as the directory structure, I think it is actually easier to scale. Node_modules and webpack are currently obfuscating a snake pit for you. This way everything is de-duped and deployable from a permanent and easily reproducible path.

A classic example would be JQuery. Why import a node build of it to your node_modules, and then jump through build hoops to get it accessible in your other code, at run time? Just keep jquery at /js/jquery in every build, and every module and app will know how to find it.