I've set some custom icons (via editing .desktop files) for some apps using png files stored in my home directory. In the Slingshot menu they are showing the generic grey square with gear icon. Yet when launching the app the proper icon appears on Plank. Any thoughts?

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Try "AppEditor" from Appstore - it saves you the chore of editing the *.desktop files manually, but includes that option if you still want to. When editing files manually there is always greater chance for an error. This app minimizes it. Ofcourse it can also set icons of menu entries. Very useful.

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