I know where the general launchers are, the ones in /usr/share/applications and the likes. What I'm wondering is where unity stores the launchers that are actually pinned to the side bar. Anyone know?
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You can access this information using dconf-editor. Expand com → canonical → unity → launcher node and see the favorites key:

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Am I to assume then that window matching information is embedded in the .desktop files themselves? – JaySee Jul 23 '13 at 03:46
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What do you mean speaking "window matching information"? `.desktop` files generally contain command and icon, and the key is shown also keeps arrangement. – Danatela Jul 23 '13 at 03:52
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What I mean by window matching is matching a specific window being drawn to a specific icon. I've had some applications that when I pin them and use the launcher to start them, they create a new icon on the launcher instead of using the existing icon. *cough* netbeans *cough* – JaySee Jul 23 '13 at 03:53
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This means that `.desktop` files on your desktop (or where did you pick them from) have another path to the icon then those in `/usr/share/applications`. – Danatela Jul 23 '13 at 03:59
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Ok looking at the .desktop files it seems to be stored under the "StartupWMClass" property. You can find this property by running "xprop WM_CLASS" in a terminal then click the window you're wondering about – JaySee Jul 23 '13 at 04:01
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Could one check which applications are running and then change this settings so that the ones running are always at the top of the launcher? – Joschua Jun 29 '14 at 18:21
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1@Joschua there is `unity://running-apps` entry in the setting. Put it at the very beginning of the list. – Danatela Jul 01 '14 at 02:53
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@Danatela Thanks, but putting it at the very beginning didn't work out. And apparently `unity://running-apps` is already in the list.. – Joschua Jul 01 '14 at 16:37
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@Joschua there should be only one entry of running apps. If the tip doesn't help, ask a new question. – Danatela Jul 02 '14 at 01:58