Refs #4814. Fix system tests.

Extract shouldn't clear the parameter map flags (broke SANS tests) and
ExtractMask/MaskDetectors doesn't seem to give the right answer when
used with detector IDs. Switched to using MaskWorkspace directly

Code/Mantid/Framework/Algorithms/src/ExtractMask.cpp

@@ -77,7 +77,6 @@ namespace Mantid
       MatrixWorkspace_sptr outputWS(maskWS);
       WorkspaceFactory::Instance().initializeFromParent(inputWS, outputWS, false);
       outputWS->setTitle(inputWS->getTitle());
-      outputWS->getInstrument()->getParameterMap()->clearParametersByName("masked"); // turn off the mask bit
 
       bool inputWSIsSpecial(false);
       {

Code/Mantid/Framework/DataHandling/src/MaskDetectors.cpp

@@ -273,7 +273,7 @@ void MaskDetectors::appendToIndexListFromMaskWS(std::vector<size_t>& indexList,
   for (int64_t i = startIndex; i <= endIndex; ++i)
   {
 
-    if( maskedWorkspace->dataY(i)[0] > 0.5 && existingIndices.count(i) == 0 )
+    if( maskedWorkspace->dataY(i-startIndex)[0] > 0.5 && existingIndices.count(i) == 0 )
     {
       indexList.push_back(i);
     }

Code/Mantid/scripts/Inelastic/diagnostics.py

@@ -143,12 +143,9 @@ def diagnose(white_int, **kwargs):
 def add_masking(input_ws, mask_ws, start_index=None, end_index=None):
     """
     Mask the Detectors on the input workspace that are masked 
-    on the mask_ws. Avoids a current bug in using MaskDetectors with a MaskedWorkspace in a loop 
+    on the mask_ws. 
     """
-    #MaskDetectors(input_ws, MaskedWorkspace=mask_ws, StartWorkspaceIndex=start_index, EndWorkspaceIndex=end_index)
-    masked = ExtractMasking(mask_ws, '__tmp')
-    MaskDetectors(input_ws, DetectorList=masked.getPropertyValue("DetectorList"))
-    DeleteWorkspace(masked.workspace())
+    MaskDetectors(input_ws, MaskedWorkspace=mask_ws, StartWorkspaceIndex=start_index, EndWorkspaceIndex=end_index)
 
 #-------------------------------------------------------------------------------