Cleaning the mess on package.json
$ npm install -g sweeper
The best way to clean your package.json is to utilize de executable sweeper(1)
to show a list of used and unused dependencies.
$ npm install -g sweeper
$ cd /YOUR_PROJECT_DIRECTORY/
$ sweeper
After that, you can clean your package.json knowing what is used and what is not. Be sure to double check Sweeper's output, as dynamic generators for requires are not detected yet.
Hit sweeper --help
for usage help and other options