node_modules directory is usually added to .gitignore.
I don't think it is usually commited by accident as it results in a huge file list in diffs and git status command.
That's what he's saying. While the author's statement may not necessarily be incorrect, the trend these days is to manage your JS (both server and client side code) with package managers like NPM and Bower.
> the JavaScript development philosophy that encourages bundling of dependencies in the same repo as the primary codebase
I wonder how much this is still an issue with the rise of npm, bower and other package managers.