Here is my problem: the Minecraft icon in the Unity launcher is inconsistent with the icon theme, even though the icon theme has a minecraft icon in it. The theme I am using is Numix-Circle and I am on Ubuntu 12.04.5 LTS Unity. The way I even got Minecraft in the launcher was by installing Graham Edgecombe's minecraft-installer package. Here is a screenshot:
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possible duplicate of Where are icons stored? – kos May 05 '15 at 00:55
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When you have found the icon, just replace it with a higher-resolution one. You'll need to restart Unity to see the changes – kos May 05 '15 at 00:56
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1The Minecraft icon has no circle because that's not the way the icon was made. The rest of the icons are part of the Numix set, which has specially made icons for most programs on Ubuntu. Not everything is going to conform with your theme, since the theme makers can't possibly make a special icon for every app out there. – TheWanderer May 05 '15 at 01:11
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I think, actually, this needs to be an answer. Tell me if I'm wrong.
The Minecraft icon has no circle and isn't flat because that's not the way the icon was made. The rest of the icons are part of the Numix set, which has specially made icons for most programs on Ubuntu. Not everything is going to conform with your theme, since the theme makers can't possibly make a special icon for every app out there.
If you really want it to conform with the rest of your icons, you're going to have to edit the icon manually, with GIMP or PhotoShop, to put a circle around it and flatten out the colors.

TheWanderer
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Yep, that's what happens when an app is not included in the theme you are using, the app will default to the icon made available from the deb package. – mchid May 05 '15 at 03:13
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It might for the jar otself, but not for the custom launcher you made. – TheWanderer May 06 '15 at 02:08
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