Links don't output in subdirectories

[reintroducing]

Hello, I'd love to use this plugin but I'm having an issue which I don't think is accounted for properly. I have my Gruntfile.js at the root and all my actual files (HTML/JS/CSS) inside of a deploy folder at the root. When I set my task as such I get nothing output:

link_html: {
            dev: {
                jsFiles: [
                    'js/libs/jquery/jquery-2.0.3.min.js',
                    'js/main.js'
                ],
                cssFiles: ['css/main.css'],
                targetHtml: ['index.html']
            }
        }

Event if I change the path to targetHtml to be 'deploy/index.html' it does not put the files correctly. If i add deploy/ in front of all the paths, however, it works, except then my paths include deploy/ in them which, when testing the index.html file inside of deploy, makes that path incorrect.

Is there a way to currently solve for this?