I have a grunt project backed by a yeoman-generator that I\'ve built based on the generator-webapp, if it\'s of any help, you can find it on GitHub
The grunt project mak
If I'm understanding your question correctly I think you need the 'root' option:
{ useminPrepare: { html: 'html/index.html', options: { root: 'app' dest: 'dist' } } }
Though index.html is in the html/ folder the files lookup will be from app/ not html/