diff --git a/buildconfig/Jenkins/doctests.bat b/buildconfig/Jenkins/doctests.bat
index d22f84d622632a8ef0a8f0ba3a6001891fabc816..bca4fb55d30569f21529776ebb7cfd71d14e4fc7 100755
--- a/buildconfig/Jenkins/doctests.bat
+++ b/buildconfig/Jenkins/doctests.bat
@@ -19,15 +19,15 @@ echo %sha1%
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
 :: Get or update the third party dependencies (basically just to get python)
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
-cd %WORKSPACE%\Code
+cd %WORKSPACE%
 call fetch_Third_Party --libs-only win64
 cd %WORKSPACE%
 
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
 :: Find and install package
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
-set PYTHON_EXE=%WORKSPACE%\Code\Third_Party\lib\win64\Python27\python.exe
-set INSTALLER_SCRIPT=%WORKSPACE%/Code/Mantid/Testing/SystemTests/scripts/mantidinstaller.py
+set PYTHON_EXE=%WORKSPACE%\Third_Party\lib\win64\Python27\python.exe
+set INSTALLER_SCRIPT=%WORKSPACE%/Testing/SystemTests/scripts/mantidinstaller.py
 start "Install package" /B /WAIT %PYTHON_EXE% %INSTALLER_SCRIPT% install %WORKSPACE%
 if ERRORLEVEL 1 exit /B %ERRORLEVEL%
 
@@ -35,7 +35,7 @@ if ERRORLEVEL 1 exit /B %ERRORLEVEL%
 :: Update the PATH so that we can find everything for cmake
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
 set PATH_AT_START=%PATH%
-set PATH=%WORKSPACE%\Code\Third_Party\lib\win64;%WORKSPACE%\Code\Third_Party\lib\win64\Python27;%PATH%
+set PATH=%WORKSPACE%\Third_Party\lib\win64;%WORKSPACE%\Third_Party\lib\win64\Python27;%PATH%
 
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
 :: Set up the location for local object store outside of the build and source
@@ -64,7 +64,7 @@ cd %BUILD_DIR%
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
 :: CMake configuration. We only need the doc-tests targets
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
-"%CMAKE_BIN_DIR%\cmake" -G "Visual Studio 11 Win64" -DMANTID_DATA_STORE=!MANTID_DATA_STORE! ..\Code\Mantid
+"%CMAKE_BIN_DIR%\cmake" -G "Visual Studio 11 Win64" -DMANTID_DATA_STORE=!MANTID_DATA_STORE! ..
 
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
 :: Build step
@@ -85,7 +85,7 @@ echo usagereports.enabled = 0 >> C:\MantidInstall\bin\Mantid.user.properties
 :: User properties file cannot contain backslash characters
 set WORKSPACE_UNIX_STYLE=%WORKSPACE:\=/%
 set DATA_ROOT=!WORKSPACE_UNIX_STYLE!/build/ExternalData/Testing/Data
-echo datasearch.directories = !DATA_ROOT!/UnitTest;!DATA_ROOT!/DocTest;!WORKSPACE_UNIX_STYLE!/Code/Mantid/instrument >> C:\MantidInstall\bin\Mantid.user.properties
+echo datasearch.directories = !DATA_ROOT!/UnitTest;!DATA_ROOT!/DocTest;!WORKSPACE_UNIX_STYLE!/instrument >> C:\MantidInstall\bin\Mantid.user.properties
 
 :: Run tests
 C:\MantidInstall\bin\MantidPlot.exe -xq %BUILD_DIR%\docs\runsphinx_doctest.py