Amber-Cordova

Once you start developing your own app / lib, you should remove all unnecessary parts left from the sample app.

In index.html <body> tag, everything should be removed, except the <script> tag that initializes Amber and starts your app; then you can add elements specific to your own app to the page.
If you aren't going to use Web package from amber-contrib-web module, but want to retain the jQuery wrapper, you should run bower uninstall amber-contrib-web --save from your CLI.
If you aren't going to use the Web package from the amber-contrib-web module, nor the jQuery wrapper from amber-contrib-jquery, you should run bower uninstall amber-contrib-web amber-contrib-jquery --save from your CLI.
You cannot remove just the jQuery wrapper and retain the Web package, as it depends on the jQuery wrapper.
If you aren't going to use Silk package from silk module, but want to retain DOMite DOM wrapper, you should run bower uninstall silk --save from your CLI.
If you aren't going to use the Silk package from the silk module, nor the DOM wrapper from amber-contrib-domite, you should run bower uninstall silk amber-contrib-domite --save from your CLI.
You cannot remove just the DOMite DOM wrapper and retain the Silk package, as it depends on domite.
Your Gruntfile.js may contain references to Web and/or Silk in libraries field(s). Fix those fields to not contain non-existing libraries (optionally add other needed ones, like domite or Wrappers-JQuery).
As the last step, make sure the dependency tree is in a correct state by recreating it: first delete your bower_components folder, then run bower install from your CLI.