How to ignore specific files in Atom/JSHint

Question

I'm on Windows using Atom 1.0.0, linter-jshint 0.1.7 and am working on a web project. I'm using gulp, so I have some javascript files that are concatenated (this is why I can't simply add /* jshint ignore:start */ to the file, because it's overwritten after calling gulp later).

I added a .jshintignore file to my projects root folder, but it doesn't seem to work (although, according to the linter-jshint sources, there are some lines committed to load the .jshintignore file with --exclude-path.

The content of my .jshintignore file is:

public/js/bundle.js
public/js/vendor.js

edit: Contents of gulp is as simple as:

mix.scripts([
    'jquery.js',
    'vue.js'
], 'vendor.js');

Because my linter settings dont apply to jquery or vue, I get tons of errors slowing down the application. Adding /* jshint ignore:start */ helps, but I for one really don't want to edit the vendor files or the merged one.