Best directory structure for modified addons in /node_modules in an ember.js app?

I have a number of addons that I have modified, all managed with git. When upgrading, I need to be careful to not delete these modules when emptying the node_modules directory in preparation for npm install.

Is there a solution to this, such as nesting customized modules in another directory, either under node_modules or elsewhere? What configuration, if any, would be needed?