diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/Diffraction_Workflow_Test.py b/Code/Mantid/Testing/SystemTests/tests/analysis/Diffraction_Workflow_Test.py
index c5d8891379615bff7f094be9b9d731de5e969b44..1749239bac9a5f52975068c3542178decabc2692 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/Diffraction_Workflow_Test.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/Diffraction_Workflow_Test.py
@@ -42,9 +42,6 @@ class Diffraction_Workflow_Test(stresstesting.MantidStressTest):
         filename = ws+"_event.nxs"
         LoadEventNexus(Filename=filename,OutputWorkspace=ws,FilterByTofMin='3000',FilterByTofMax='16000')
         
-        # Load optimized DetCal file
-        #LoadIsawDetCal(InputWorkspace=ws,Filename="/SNS/TOPAZ/shared/Spectra/TOPAZ_8Sept11.DetCal")
-        
         # Spherical Absorption and Lorentz Corrections
         AnvredCorrection(InputWorkspace=ws,OutputWorkspace=ws,LinearScatteringCoef="0.451",LinearAbsorptionCoef="0.993",Radius="0.14")
         
@@ -165,8 +162,7 @@ class Diffraction_Workflow_Test(stresstesting.MantidStressTest):
 
         # load output hkl file and the golden one
         LoadHKL(Filename="TOPAZ_3132.hkl", OutputWorkspace="TOPAZ_3132")
-        LoadHKL(Filename=os.path.join(os.path.dirname(__file__), 'ReferenceResults','TOPAZ_3132_reference.hkl'), 
-                OutputWorkspace="TOPAZ_3132_golden")
+        LoadHKL(Filename='TOPAZ_3132_reference.hkl', OutputWorkspace="TOPAZ_3132_golden")
 
     def validateMethod(self):
         return "ValidateWorkspaceToWorkspace"
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/DirectInelasticDiagnostic.py b/Code/Mantid/Testing/SystemTests/tests/analysis/DirectInelasticDiagnostic.py
index 9262949c94743fc4b519aaf279f1761667f14022..f491e3bedfba3cc4cc9c1b239c4a81e6ce4addee 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/DirectInelasticDiagnostic.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/DirectInelasticDiagnostic.py
@@ -63,5 +63,4 @@ class DirectInelasticDiagnostic(MantidStressTest):
         return 'validateASCII'
         
     def validate(self):
-        return self.saved_diag_file, \
-            os.path.join(os.path.dirname(__file__), 'ReferenceResults','DirectInelasticDiagnostic.txt')
+        return (self.saved_diag_file,'DirectInelasticDiagnostic.txt')
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/DirectInelasticDiagnostic2.py b/Code/Mantid/Testing/SystemTests/tests/analysis/DirectInelasticDiagnostic2.py
index 238d5c266cdc9c02a394ee65279867fb139d14ae..38ff1f6958f43bf22acd4ea413bb74b83aafa438 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/DirectInelasticDiagnostic2.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/DirectInelasticDiagnostic2.py
@@ -86,6 +86,4 @@ class DirectInelasticDiagnostic2(MantidStressTest):
         return 'validateASCII'
         
     def validate(self):
-        return self.saved_diag_file, \
-            os.path.join(os.path.dirname(__file__), 
-                         'ReferenceResults', 'DirectInelasticDiagnostic.txt')
+        return (self.saved_diag_file, 'DirectInelasticDiagnostic.txt')
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/LOQSANSUtilityTest.py b/Code/Mantid/Testing/SystemTests/tests/analysis/LOQSANSUtilityTest.py
index e98d307ebe6634d3d37b34498c2b46ca086ef21f..ecaa625a5e5c792a85e99696535fd65829059ddb 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/LOQSANSUtilityTest.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/LOQSANSUtilityTest.py
@@ -15,14 +15,14 @@ class SANSUtilityTest(stresstesting.MantidStressTest):
     def runTest(self):
         # created after issue reported in #8156
         ws = Load('LOQ54432')
-        self.assertTrue('Data/LOQ/LOQ54432.raw' in unixLikePathFromWorkspace(ws))
+        self.assertTrue('Data/SystemTest/LOQ/LOQ54432.raw' in unixLikePathFromWorkspace(ws))
         ws = Load('LOQ99618.RAW')
-        self.assertTrue('Data/LOQ/LOQ99618.RAW' in unixLikePathFromWorkspace(ws))
+        self.assertTrue('Data/SystemTest/LOQ/LOQ99618.RAW' in unixLikePathFromWorkspace(ws))
         add.add_runs(('LOQ54432','LOQ54432'),'LOQ','.raw')
         ws = Load('LOQ54432-add')
         file_path =  unixLikePathFromWorkspace(ws)
         logger.information("File Path from -add: "+str(file_path))
         file_path = file_path.replace('-ADD','-add') # MAC seems to report that the file is LOQ54432-ADD.nxs
-        self.assertTrue('logs/LOQ54432-add' in file_path)
+        self.assertTrue('LOQ54432-add' in file_path)
         os.remove(file_path)
         
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/LoadLotsOfFiles.py b/Code/Mantid/Testing/SystemTests/tests/analysis/LoadLotsOfFiles.py
index 0a12b119767ca59bca69b5dc65092095a67a501b..f3934442d9599cb818491129f2a00996ddb9ee6d 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/LoadLotsOfFiles.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/LoadLotsOfFiles.py
@@ -97,14 +97,18 @@ PRIORITY_FILES = ['HYS_13658_event.nxs',
 def useDir(direc):
     """Only allow directories that aren't test output or
     reference results."""
-    if "ReferenceResults" in direc:
+    if "reference" in direc:
         return False
-    if "logs" in direc:
+    if config["defaultsave.directory"] == direc:
         return False
     return ("Data" in direc)
 
 def useFile(direc, filename):
     """Returns (useFile, abspath)"""
+    # if it is an -stamp file then assume these are cmake created files
+    if filename.endswith("-stamp"):
+        return (False, filename)
+
     # list of explicitly banned files at the top of this script
     if filename in BANNED_FILES:
         return (False, filename)
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/ReduceOneSCD_Run.py b/Code/Mantid/Testing/SystemTests/tests/analysis/ReduceOneSCD_Run.py
index 20f26976d16700da2134c087f57b72053c0af040..8f777f68979982fcb3099a388682a155085278d4 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/ReduceOneSCD_Run.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/ReduceOneSCD_Run.py
@@ -39,11 +39,8 @@ class ReduceOneSCD_Run( stresstesting.MantidStressTest):
       instrument_name           = "TOPAZ"
       calibration_file_1        = "TOPAZ_2011_02_16.DetCal"
       calibration_file_2        = None
- #data_directory            = params_dictionary[ "data_directory" ]
  
-      import os
-      self.output_directory          =  os.path.abspath(os.path.curdir)
- #         = params_dictionary[ "output_directory" ]
+      self.output_directory          =  config["defaultsave.directory"]
       
       min_tof                   = "400"
       max_tof                   = "16666"
@@ -220,11 +217,11 @@ class ReduceOneSCD_Run( stresstesting.MantidStressTest):
       LoadIsawUB(InputWorkspace="XX1",Filename=self.run_conventional_matrix_file )      
       s1 = mtd["XX1"].sample()
       
-      LoadIsawPeaks(OutputWorkspace="PeaksP", Filename=os.path.join(os.path.dirname(__file__), 'ReferenceResults',"3132_Orthorhombic_P.integrate"))
-      LoadIsawUB(InputWorkspace=peaks_ws,Filename=os.path.join(os.path.dirname(__file__), 'ReferenceResults',"3132_Orthorhombic_P.mat"))
+      LoadIsawPeaks(OutputWorkspace="PeaksP", Filename="3132_Orthorhombic_P.integrate")
+      LoadIsawUB(InputWorkspace=peaks_ws,Filename="3132_Orthorhombic_P.mat")
       IndexPeaks( PeaksWorkspace=peaks_ws, Tolerance=tolerance )
       CreateSingleValuedWorkspace(OutputWorkspace="XX2",DataValue="3")
-      LoadIsawUB(InputWorkspace="XX2",Filename=os.path.join(os.path.dirname(__file__), 'ReferenceResults',"3132_Orthorhombic_P.mat"))  
+      LoadIsawUB(InputWorkspace="XX2",Filename="3132_Orthorhombic_P.mat")
       
       s2 = mtd["XX2"].sample()
       ol = s1.getOrientedLattice()
@@ -252,6 +249,3 @@ class ReduceOneSCD_Run( stresstesting.MantidStressTest):
    def validate(self):
       return [self.__reduced_ws_name,'PeaksP']
       
-   def requiredFiles(self):
-   
-      return [os.path.join(os.path.dirname(__file__), 'ReferenceResults',"3132_Orthorhombic_P.integrate"),os.path.join(os.path.dirname(__file__), 'ReferenceResults',"3132_Orthorhombic_P.mat")]
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/SANSLoadersTest.py b/Code/Mantid/Testing/SystemTests/tests/analysis/SANSLoadersTest.py
index 6bcbcb3ddeb0babaf105d7d86fe2a5569d969021..0de445f4f489091e0eb656fa3ea07b82be08e7a1 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/SANSLoadersTest.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/SANSLoadersTest.py
@@ -29,7 +29,7 @@ class LoadRunTest(unittest.TestCase):
 
 
     def basicChecks(self, loadRun, file_path, runnum, periods_in_file, ws_name):
-        self.assertTrue('Data/SANS2D/'+file_path in loadRun._data_file.replace('\\','/'), 'Wrong data file: ' + loadRun._data_file)
+        self.assertTrue('Data/SystemTest/SANS2D/'+file_path in loadRun._data_file.replace('\\','/'), 'Wrong data file: ' + loadRun._data_file)
         self.assertEqual(loadRun.periods_in_file, periods_in_file)
         self.assertEqual(loadRun.wksp_name, ws_name)
         self.assertEqual(loadRun.shortrun_no, runnum)
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/SNSConvertToMDTest.py b/Code/Mantid/Testing/SystemTests/tests/analysis/SNSConvertToMDTest.py
index c711a1713874628fefda182c1fc078e636eb0876..4fd364d6f23fd8bf547b836c649c228e16159dbf 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/SNSConvertToMDTest.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/SNSConvertToMDTest.py
@@ -186,7 +186,6 @@ class SNSConvertToMDHistProjTest(stresstesting.MantidStressTest):
         return 2500
     
     def requiredFiles(self):
-        config.appendDataSearchDir("/home/builder/data/SystemTests/AnalysisTests/ReferenceResults/");
         files = [self.truth_file, DATA_FILE]
         return files	
     
diff --git a/Code/Mantid/Testing/SystemTests/tests/analysis/SpaceGroupFactoryTest.py b/Code/Mantid/Testing/SystemTests/tests/analysis/SpaceGroupFactoryTest.py
index b3a653e56f1edf8b38fc3921fa9ecc542fab56df..4f3065ff11efe1769f4d341d02f67f1b309e96a4 100644
--- a/Code/Mantid/Testing/SystemTests/tests/analysis/SpaceGroupFactoryTest.py
+++ b/Code/Mantid/Testing/SystemTests/tests/analysis/SpaceGroupFactoryTest.py
@@ -28,11 +28,12 @@ class SpaceGroupFactoryTest(stresstesting.MantidStressTest):
     self.assertTrue(groupOperations == referenceOperations, "Problem in space group " + str(group.number()) + " (" + symbol + ")")
 
   def loadReferenceData(self):
+    from mantid.api import FileFinder
     # Reference data.
     # Dictionary has a string set for each space group number.
     separatorMatcher = re.compile("(\d+)")
 
-    fileName = os.path.join(os.path.dirname(__file__), 'ReferenceResults','SpaceGroupSymmetryOperations.txt')
+    fileName = FileFinder.Instance().getFullPath('SpaceGroupSymmetryOperations.txt')
 
     print fileName