coffeelint.defaultRules settings not respected after npm install

[brucedjones]

I have set coffeelint.defaultRules in my user settings. This works as expected until I run npm install, now the settings I have in coffeelint.defaultRules are no long respected. After npm install I have the following files in my directory structure:

$ find . -name "coffeelint.json"
./node_modules/coffeelint/coffeelint.json
./node_modules/coffeelint-newline-after-function/coffeelint.json

I believe one of these files is taking precedent over my user settings. This is undesired, and according to the documentation, should not happen since I don't have a coffeelint.json in the root of my project.