The bug also applies to chromium current stable Version 49.0.2623.108 Ubuntu 14.04 (64-bit) and to shortcuts generated from Menu -> More tools -> Add to desktop (New bookmark flag enabled) or Add application shortcuts (New bookmark flag disabled). A bash script to generate the icons is attached.

Dear all, 

The following two links may provide more helpful information in solving the issue:

1. Why do some Chrome Apps don't display a Unity launcher icon? [1]
2. Extension doesn't have its own icon on ubuntu sidebar (using chromium) [2]

Thankfully,

~Robert

[1] https://askubuntu.com/questions/757594/why-do-some-chrome-apps-dont-display-a-unity-launcher-icon
[2] https://github.com/WhisperSystems/Signal-Desktop/issues/245#issue-81583917

bmoss@ - Could you please check this issue on latest chrome stable M50-50.0.2661.102 as per comment #4. 

Thanks!

As stated in the original report, Chrome: Version 49.0.2623.108 (64-bit) was OK. I will check chrome stable M50-50.0.2661.102. A chromium update for ubuntu trusty has not been released so the bug has not been fixed there.

Tested Chrome 50.0.2661.102. It does not have the bug. App desktop and icon files are created when the shortcut is created. They are deleted when the App is removed. Chrome 49 ... did not have the bug either. My report was and still is about Chromium 49 ...

Thank you for providing more feedback. Adding requester "brajkumar@chromium.org" for another review and adding "Needs-Review" label for tracking.

For more details visit https://www.chromium.org/issue-tracking/autotriage - Your friendly Sheriffbot

As of the current stable Chromium Version 50.0.2661.102 Ubuntu 14.04 (64-bit), the bug has been fixed. Desktop shortcuts generated by right-clicking an App icon at chrome://apps or by using the More Tools menu are written to the following directories.

Desktop files: $HOME/Desktop
Icons files: $HOME/.local/share/icons/hicolor/128x128/apps

An Application shortcut generated by right-clicking an App icon is written to the following directories.

Desktop files: $HOME/.local/share/applications
Icons files: $HOME/.local/share/icons/hicolor/128x128/apps 

For Linux it is unnecessary to have duplicate shortcuts. The More Tools menu only produces Desktop shortcuts. 

I can confirm that it does work now. 

Thank you so much for fixing this very annoying bug! :)

~Robert

As per comment #10 and #11 closing this issue. Please raise a new issue if you come across the similar bug on latest chrome version.

Thanks for confirming it!

Some added detail for comment 10.

As of the current stable Chromium Version 50.0.2661.102 Ubuntu 14.04 (64-bit), the bug has been fixed. A Desktop shortcut generated by right-clicking an App/Website icon at chrome://apps is written to the following directories.

Desktop files: $HOME/Desktop
Icons files: $HOME/.local/share/icons/hicolor/128x128/apps

An Application shortcut generated by right-clicking an App/Website icon at chrome://apps is written to the following directories.

Desktop files: $HOME/.local/share/applications
Icons files: $HOME/.local/share/icons/hicolor/128x128/apps
A Desktop shortcut for a Website generated by using the More Tools menu is written to the following directories.

Desktop files: $HOME/Desktop
Icons files: 
$HOME/.local/share/icons/hicolor/16x16/apps
$HOME/.local/share/icons/hicolor/32x32/apps
$HOME/.local/share/icons/hicolor/48x48/apps
$HOME/.local/share/icons/hicolor/128x128/apps
$HOME/.local/share/icons/hicolor/256x256/apps
 
When an App/Website is removed by by right-clicking its icon at chrome://apps, the Desktop file is removed but the icon file(s) are not removed. This behavior can be viewed as a bug or a feature.

The behavior of the current stable Chrome Version 50.0.2661.102 Ubuntu 14.04 (64-bit) with the new bookmark app system flag (chrome://flags) enabled is identical.