Create a separate packages directory for running pub.

sdk/bin/pub.bat

 @echo off
 REM Copyright (c) 2012, the Dart project authors.  Please see the AUTHORS file
 REM for details. All rights reserved. Use of this source code is governed by a
 REM BSD-style license that can be found in the LICENSE file.
 
 setlocal
 rem Handle the case where dart-sdk/bin has been symlinked to.
 set DIR_NAME_WITH_SLASH=%~dp0
 set DIR_NAME=%DIR_NAME_WITH_SLASH:~0,-1%%
 call :follow_links "%DIR_NAME%", RETURNED_BIN_DIR
 rem Get rid of surrounding quotes.
 for %%i in ("%RETURNED_BIN_DIR%") do set BIN_DIR=%%~fi
 
 rem Get absolute full name for SDK_DIR.
 for %%i in ("%BIN_DIR%\..\") do set SDK_DIR=%%~fi
 
 rem Remove trailing backslash if there is one
 IF %SDK_DIR:~-1%==\ set SDK_DIR=%SDK_DIR:~0,-1%
 
 set PUB=%SDK_DIR%\lib\_internal\pub\bin\pub.dart
 set DART=%BIN_DIR%\dart
 set SNAPSHOT=%BIN_DIR%\snapshots\pub.dart.snapshot
 set BUILD_DIR=%SDK_DIR%\..\build\ReleaseIA32
-set PACKAGES_DIR=%BUILD_DIR%\packages
+set PACKAGES_DIR=%BUILD_DIR%\pub_packages
 set DART_IN_BUILT_SDK=%BUILD_DIR%\dart-sdk\bin\dart
 set VM_OPTIONS=
 
 rem Give the VM extra memory for dart2js.
 rem # TODO(rnystrom): Remove when #8355 is fixed.
 rem See comments regarding options below in dart2js shell script.
 set VM_OPTIONS=%VM_OPTIONS% --old_gen_heap_size=1024
 
 if exist "%SNAPSHOT%" (
   "%DART%" %VM_OPTIONS% "%SNAPSHOT%" %*
@@ skipping 11 matching lines @@
 set current=
 for /f "usebackq tokens=2 delims=[]" %%i in (`dir /a:l "%~dp1" 2^>nul ^
                                              ^| find ">     %~n1 ["`) do (
   set current=%%i
 )
 if not "%current%"=="" call :follow_links "%current%", result
 endlocal & set %~2=%result%
 goto :eof
 
 :end