Grunt.js manipulate parent directory

I’m trying to make a build structure where files aren’t just “floating about”.

The reason for this is that I’m using Drupal and don’t want to have the gruntfile, package.json and “node_modules”-folder placed loosely in the “themes”-folder.

My desired file structure:

- sites
    - all
        - themes
            - grunt_environment
                - Gruntfile.coffee
                - node_modules
                - src
                - package.json
            - theme_name
                - theme_name.info

I’m using grunt-contrib-clean and want to clean up my “theme_name”-folder each time I re-build my project. Unfortunately I get the following message:

Warning: Cannot delete files outside the current working directory. Use --force to continue.

So I guess my options are:
1 – Live with the fact that files are “floating about” in the themes folder.
2 – Find another way of structuring my files
3 – Clean the folder manually

or (what I hope for):

4 – Set an option to allow certain folders to be deleted by the grunt-contrib-clean module.

So – I’d really like to go with the 4th option, but the 2nd could do if anyone has a clever way of structuring my files.

Anyone who’s experienced and overcome a similar structuring problem when working with Drupal (or WordPress for that matter?)

Thanks in advance.