Use ATOM_HOME as config dir path

src/browser/atom-application.coffee

@@ -416,7 +416,7 @@ class AtomApplication
       PackageManager = require '../package-manager'
       fs = require 'fs-plus'
       @packages = new PackageManager
-        configDirPath: fs.absolute('~/.atom')
+        configDirPath: process.env.ATOM_HOME
         devMode: devMode
         resourcePath: @resourcePath