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This fixes the issue with the icon not showing up on OS X Mavericks when building. It seems that copying it to /Application file by file causes the icon to not show up while moving it atomically there does.
Atom Build
This folder contains the grunt configuration and tasks to build Atom.
It was moved from the root of the repository so that any native modules used
would be compiled against node's v8 headers since anything stored in
node_modules at the root of the repo is compiled against atom's v8 headers.
New build dependencies should be added to the package.json file located in
this folder.