Install cli folder to resources directory

build/tasks/build-task.coffee

@@ -151,8 +151,8 @@ module.exports = (grunt) ->
           grunt.file.copy(sourcePath, path.resolve(appDir, '..', subDirectory, filename))
 
     if process.platform is 'win32'
-      cp path.join('resources', 'win', 'atom.cmd'), path.join(shellAppDir, 'cli', 'atom.cmd')
-      cp path.join('resources', 'win', 'atom.js'), path.join(shellAppDir, 'cli', 'atom.js')
+      cp path.join('resources', 'win', 'atom.cmd'), path.join(shellAppDir, 'resources', 'cli', 'atom.cmd')
+      cp path.join('resources', 'win', 'atom.js'), path.join(shellAppDir, 'resources', 'cli', 'atom.js')
 
     dependencies = ['compile', 'generate-license:save', 'generate-module-cache', 'compile-packages-slug']
     dependencies.push('copy-info-plist') if process.platform is 'darwin'

resources/win/atom.cmd

@@ -18,5 +18,5 @@ FOR %%a IN (%*) DO (
 IF "%EXPECT_OUTPUT%"=="YES" (
   "%~dp0\..\atom.exe" %*
 ) ELSE (
-  "%~dp0\..\resources\app\apm\node_modules\atom-package-manager\bin\node.exe" "%~dp0\atom.js" %*
+  "%~dp0\..\app\apm\node_modules\atom-package-manager\bin\node.exe" "%~dp0\atom.js" %*
 )