diff --git a/resources/win/atom.cmd b/resources/win/atom.cmd
index d3188b3ea..c9bfdd5ba 100644
--- a/resources/win/atom.cmd
+++ b/resources/win/atom.cmd
@@ -1,6 +1,7 @@
 @echo off
 
 SET EXPECT_OUTPUT=
+SET WAIT=
 
 FOR %%a IN (%*) DO (
   IF /I "%%a"=="-f"           SET EXPECT_OUTPUT=YES
@@ -11,13 +12,41 @@ FOR %%a IN (%*) DO (
   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 /I "%%a"=="-w"           (
+    SET EXPECT_OUTPUT=YES
+    SET WAIT=YES
+  )
+  IF /I "%%a"=="--wait"       (
+    SET EXPECT_OUTPUT=YES
+    SET WAIT=YES
+  )
 )
 
+rem Getting the process ID in cmd of the current cmd process: http://superuser.com/questions/881789/identify-and-kill-batch-script-started-before
+set T=%TEMP%\atomCmdProcessId-%time::=%.tmp
+wmic process where (Name="WMIC.exe" AND CommandLine LIKE "%%%TIME%%%") get ParentProcessId /value | find "ParentProcessId" >%T%
+set /P A=<%T%
+set PID=%A:~16%
+del %T%
+
 IF "%EXPECT_OUTPUT%"=="YES" (
   SET ELECTRON_ENABLE_LOGGING=YES
-  "%~dp0\..\..\atom.exe" %*
+  IF "%WAIT%"=="YES" (
+    "%~dp0\..\..\atom.exe" --pid=%PID% %*
+    rem If the wait flag is set, don't exit this process until Atom tells it to.
+    goto waitLoop
+  )
+  ELSE (
+    "%~dp0\..\..\atom.exe" %*
+  )
 ) ELSE (
   "%~dp0\..\app\apm\bin\node.exe" "%~dp0\atom.js" %*
 )
+
+goto end
+
+:waitLoop
+  sleep 1
+  goto waitLoop
+
+:end
diff --git a/resources/win/atom.sh b/resources/win/atom.sh
index 9e2c6da65..0eaf193c0 100644
--- a/resources/win/atom.sh
+++ b/resources/win/atom.sh
@@ -4,12 +4,26 @@ while getopts ":fhtvw-:" opt; do
   case "$opt" in
     -)
       case "${OPTARG}" in
-        foreground|help|test|version|wait)
+        wait)
+          WAIT=1
+          ;;
+        help|version)
+          REDIRECT_STDERR=1
           EXPECT_OUTPUT=1
-        ;;
+          ;;
+        foreground|test)
+          EXPECT_OUTPUT=1
+          ;;
       esac
       ;;
-    f|h|t|v|w)
+    w)
+      WAIT=1
+      ;;
+    h|v)
+      REDIRECT_STDERR=1
+      EXPECT_OUTPUT=1
+      ;;
+    f|t)
       EXPECT_OUTPUT=1
       ;;
   esac
@@ -17,9 +31,19 @@ done
 
 directory=$(dirname "$0")
 
+WINPS=`ps | grep -i $$`
+PID=`echo $WINPS | cut -d' ' -f 4`
+
 if [ $EXPECT_OUTPUT ]; then
   export ELECTRON_ENABLE_LOGGING=1
-  "$directory/../../atom.exe" "$@"
+  "$directory/../../atom.exe" --executed-from="$(pwd)" --pid=$PID "$@"
 else
   "$directory/../app/apm/bin/node.exe" "$directory/atom.js" "$@"
 fi
+
+# If the wait flag is set, don't exit this process until Atom tells it to.
+if [ $WAIT ]; then
+  while true; do
+    sleep 1
+  done
+fi
diff --git a/src/browser/squirrel-update.coffee b/src/browser/squirrel-update.coffee
index 0e4743a21..3660158fc 100644
--- a/src/browser/squirrel-update.coffee
+++ b/src/browser/squirrel-update.coffee
@@ -139,7 +139,7 @@ addCommandsToPath = (callback) ->
 
     atomShCommandPath = path.join(binFolder, 'atom')
     relativeAtomShPath = path.relative(binFolder, path.join(appFolder, 'resources', 'cli', 'atom.sh'))
-    atomShCommand = "#!/bin/sh\r\n\"$(dirname \"$0\")/#{relativeAtomShPath.replace(/\\/g, '/')}\" \"$@\""
+    atomShCommand = "#!/bin/sh\r\n\"$(dirname \"$0\")/#{relativeAtomShPath.replace(/\\/g, '/')}\" \"$@\"\r\necho"
 
     apmCommandPath = path.join(binFolder, 'apm.cmd')
     relativeApmPath = path.relative(binFolder, path.join(process.resourcesPath, 'app', 'apm', 'bin', 'apm.cmd'))