how to control how wiredep generates bower file path and how to control which files is added/removed

my app has directory as follows

app -> appName -> index.html (js,css)

and for some reason, this appName wrapper folder is messing up wiredire

{ dest: '.tmp/concat/scripts/vendor.js',
      src: 
       [ '../bower_components/es5-shim/es5-shim.js',
         '../bower_components/angular/angular.js',
         '../bower_components/json3/lib/json3.js',
         '../bower_components/angular-resource/angular-resource.js',
         '../bower_components/angular-cookies/angular-cookies.js',
         '../bower_components/angular-sanitize/angular-sanitize.js',
         '../bower_components/angular-animate/angular-animate.js',
         '../bower_components/angular-touch/angular-touch.js',
         '../bower_components/angular-route/angular-route.js' ] },

this is what would've been produced if directory is as follows

app -> index.html(js,css)

{ dest: '.tmp/concat/scripts/vendor.js',
      src: 
       [ 'bower_components/es5-shim/es5-shim.js',
         'bower_components/angular/angular.js',
         'bower_components/json3/lib/json3.js',
         'bower_components/angular-resource/angular-resource.js',
         'bower_components/angular-cookies/angular-cookies.js',
         'bower_components/angular-sanitize/angular-sanitize.js',
         'bower_components/angular-animate/angular-animate.js',
         'bower_components/angular-touch/angular-touch.js',
         'bower_components/angular-route/angular-route.js' ] },

and wiredep does change the index.html's script content and how can I control that flow? sometimes its stripping out angular-sanitize from its script[src]

You Should use the replace option of wiredep:

wiredep(
    {
        fileTypes: {
            html: {
                replace: {
                    js: '<script src="/app/appName/{{filePath}}"></script>'
                }
            }
        }
    })

Will generate:

<script src="/app/appName/bower_components/angular/angular.js"></script>