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Chrome Web Apps don't get a separate dock icon in Gnome 3. A way around this is to use Epiphany for web apps, but the downside is that all links will open in a new Epiphany window.

How can I have Epiphany Web App links to open in Chrome?

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I'm entirely ignorant* about how Epiphany's "Web Apps" work, but this post (of this thread) illuminates how Chrome does it:

what chromium does atm is just to find the browser desktop file, and use it as template for its webapps, by doing:

  • "Exec=" => updated to run the browser with the --app= flag
  • "Name=" => updated to match the webapp title
  • "GenericName", "Comment", "#" => dropped
  • "MimeType=" => dropped
  • "Icon=" => updated to use the site's favicon
  • everything else => copied vanilla.

Thus if you found these files and made GNOME Shell recognize them, you should also find their icons/starters in GNOME Shell's Application Menu (if that's what you're after, i.e. I didn't misunderstand your question).

* Oh, look, they use Desktop files, too.

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This doesn't actually help me. Despite the --app flag, and the .desktop file, Chrome groups all its application windows (on Gnome Shell, but not Unity -- which breaks alt-tab and window switching so is not a solution either :)) –  Syzygy Oct 26 '12 at 13:35
    
Oh. Maybe this helps? –  sr_ Oct 26 '12 at 21:22
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This method will allow you to add separate dock icon in Gnome 3 for chrome web apps https://support.google.com/chrome/answer/95710?hl=en

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