diff --git a/build/tasks/build-task.coffee b/build/tasks/build-task.coffee
index c606220ad..5ffdf6ce2 100644
--- a/build/tasks/build-task.coffee
+++ b/build/tasks/build-task.coffee
@@ -21,7 +21,9 @@ module.exports = (grunt) ->
 
     mkdir appDir
 
-    cp 'atom.sh', path.join(appDir, 'atom.sh')
+    if process.platform isnt 'win32'
+      cp 'atom.sh', path.join(appDir, 'atom.sh')
+
     cp 'package.json', path.join(appDir, 'package.json')
 
     packageDirectories = []
@@ -149,10 +151,8 @@ module.exports = (grunt) ->
           grunt.file.copy(sourcePath, path.resolve(appDir, '..', subDirectory, filename))
 
     if process.platform is 'win32'
-      # Set up chocolatey ignore and gui files
-      fs.writeFileSync path.join(appDir, 'apm', 'node_modules', 'atom-package-manager', 'bin', 'node.exe.ignore'), ''
-      fs.writeFileSync path.join(appDir, 'node_modules', 'symbols-view', 'vendor', 'ctags-win32.exe.ignore'), ''
-      fs.writeFileSync path.join(shellAppDir, 'atom.exe.gui'), ''
+      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'
diff --git a/resources/win/atom.cmd b/resources/win/atom.cmd
new file mode 100644
index 000000000..029763c52
--- /dev/null
+++ b/resources/win/atom.cmd
@@ -0,0 +1,22 @@
+@echo off
+
+SET EXPECT_OUTPUT=
+
+FOR %%a IN (%*) DO (
+  IF /I "%%a"=="-f"           SET EXPECT_OUTPUT=YES
+  IF /I "%%a"=="--foreground" SET EXPECT_OUTPUT=YES
+  IF /I "%%a"=="-h"           SET EXPECT_OUTPUT=YES
+  IF /I "%%a"=="--help"       SET EXPECT_OUTPUT=YES
+  IF /I "%%a"=="-t"           SET EXPECT_OUTPUT=YES
+  IF /I "%%a"=="--test"       SET EXPECT_OUTPUT=YES
+  IF /I "%%a"=="-v"           SET EXPECT_OUTPUT=YES
+  IF /I "%%a"=="--version"    SET EXPECT_OUTPUT=YES
+  IF /I "%%a"=="-w"           SET EXPECT_OUTPUT=YES
+  IF /I "%%a"=="--wait"       SET EXPECT_OUTPUT=YES
+)
+
+IF "%EXPECT_OUTPUT%"=="YES" (
+  "%~dp0\..\..\atom.exe" %*
+) ELSE (
+  "%~dp0\..\app\apm\node_modules\atom-package-manager\bin\node.exe" "%~dp0\atom.js" %*
+)
diff --git a/resources/win/atom.js b/resources/win/atom.js
new file mode 100644
index 000000000..df059aa5b
--- /dev/null
+++ b/resources/win/atom.js
@@ -0,0 +1,9 @@
+var path  = require('path');
+var spawn = require('child_process').spawn;
+
+var atomCommandPath = path.resolve(__dirname, '..', '..', 'atom.exe');
+var arguments = process.argv.slice(2);
+arguments.unshift('--executed-from', process.cwd());
+var options = {detached: true, stdio: 'ignore'};
+spawn(atomCommandPath, arguments, options);
+process.exit(0);
diff --git a/src/browser/squirrel-update.coffee b/src/browser/squirrel-update.coffee
index e976b15bb..93e0c464d 100644
--- a/src/browser/squirrel-update.coffee
+++ b/src/browser/squirrel-update.coffee
@@ -3,7 +3,8 @@ ChildProcess = require 'child_process'
 fs = require 'fs-plus'
 path = require 'path'
 
-rootAtomFolder = path.resolve(process.execPath, '..', '..')
+appFolder = path.resolve(process.execPath, '..')
+rootAtomFolder = path.resolve(appFolder, '..')
 binFolder = path.join(rootAtomFolder, 'bin')
 updateDotExe = path.join(rootAtomFolder, 'Update.exe')
 exeName = path.basename(process.execPath)
@@ -111,18 +112,12 @@ uninstallContextMenu = (callback) ->
 addCommandsToPath = (callback) ->
   installCommands = (callback) ->
     atomCommandPath = path.join(binFolder, 'atom.cmd')
-    relativeExePath = path.relative(binFolder, process.execPath)
-    atomCommand = """
-      @echo off
-      "%~dp0\\#{relativeExePath}" %*
-    """
+    relativeAtomPath = path.relative(binFolder, path.join(appFolder, 'resources', 'cli', 'atom.cmd'))
+    atomCommand = "@echo off\r\n\"%~dp0\\#{relativeAtomPath}\" %*"
 
     apmCommandPath = path.join(binFolder, 'apm.cmd')
     relativeApmPath = path.relative(binFolder, path.join(process.resourcesPath, 'app', 'apm', 'node_modules', 'atom-package-manager', 'bin', 'apm.cmd'))
-    apmCommand = """
-      @echo off
-      "%~dp0\\#{relativeApmPath}" %*
-    """
+    apmCommand = "@echo off\r\n\"%~dp0\\#{relativeApmPath}\" %*"
 
     fs.writeFile atomCommandPath, atomCommand, ->
       fs.writeFile apmCommandPath, apmCommand, ->