diff --git a/Code/Mantid/MantidQt/CustomInterfaces/CMakeLists.txt b/Code/Mantid/MantidQt/CustomInterfaces/CMakeLists.txt
index 049063234c6d5815fde8011225e63647a8966e34..939d62cb6129e2def32e321affa99e7e113e0db0 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/CMakeLists.txt
+++ b/Code/Mantid/MantidQt/CustomInterfaces/CMakeLists.txt
@@ -1,37 +1,37 @@
set ( SRC_FILES
- src/ApplyCorr.cpp
- src/CalcCorr.cpp
- src/ConvFit.cpp
+ src/Indirect/ApplyCorr.cpp
+ src/Indirect/CalcCorr.cpp
+ src/Indirect/ConvFit.cpp
src/DirectConvertToEnergy.cpp
- src/Elwin.cpp
- src/Fury.cpp
- src/FuryFit.cpp
+ src/Indirect/Elwin.cpp
+ src/Indirect/Fury.cpp
+ src/Indirect/FuryFit.cpp
src/Homer.cpp
- src/IDATab.cpp
- src/IndirectBayes.cpp
- src/IndirectBayesTab.cpp
- src/IndirectCalibration.cpp
- src/IndirectConvertToEnergy.cpp
- src/IndirectDataAnalysis.cpp
- src/IndirectDataReduction.cpp
- src/IndirectDataReductionTab.cpp
- src/IndirectDiagnostics.cpp
- src/IndirectDiffractionReduction.cpp
- src/IndirectLoadILL.cpp
- src/IndirectMolDyn.cpp
- src/IndirectMoments.cpp
- src/IndirectSassena.cpp
- src/IndirectSimulation.cpp
- src/IndirectSimulationTab.cpp
- src/IndirectSqw.cpp
- src/IndirectSymmetrise.cpp
- src/IndirectTab.cpp
- src/IndirectTools.cpp
- src/IndirectToolsTab.cpp
- src/IndirectTransmission.cpp
- src/IndirectTransmissionCalc.cpp
- src/JumpFit.cpp
- src/MSDFit.cpp
+ src/Indirect/IDATab.cpp
+ src/Indirect/IndirectBayes.cpp
+ src/Indirect/IndirectBayesTab.cpp
+ src/Indirect/IndirectCalibration.cpp
+ src/Indirect/IndirectConvertToEnergy.cpp
+ src/Indirect/IndirectDataAnalysis.cpp
+ src/Indirect/IndirectDataReduction.cpp
+ src/Indirect/IndirectDataReductionTab.cpp
+ src/Indirect/IndirectDiagnostics.cpp
+ src/Indirect/IndirectDiffractionReduction.cpp
+ src/Indirect/IndirectLoadILL.cpp
+ src/Indirect/IndirectMolDyn.cpp
+ src/Indirect/IndirectMoments.cpp
+ src/Indirect/IndirectSassena.cpp
+ src/Indirect/IndirectSimulation.cpp
+ src/Indirect/IndirectSimulationTab.cpp
+ src/Indirect/IndirectSqw.cpp
+ src/Indirect/IndirectSymmetrise.cpp
+ src/Indirect/IndirectTab.cpp
+ src/Indirect/IndirectTools.cpp
+ src/Indirect/IndirectToolsTab.cpp
+ src/Indirect/IndirectTransmission.cpp
+ src/Indirect/IndirectTransmissionCalc.cpp
+ src/Indirect/JumpFit.cpp
+ src/Indirect/MSDFit.cpp
src/MantidEV.cpp
src/MantidEVWorker.cpp
src/MultiDatasetFit.cpp
@@ -54,19 +54,19 @@ set ( SRC_FILES
src/QReflTableModel.cpp
src/QtReflMainView.cpp
src/QtReflOptionsDialog.cpp
- src/Quasi.cpp
+ src/Indirect/Quasi.cpp
src/ReflCatalogSearcher.cpp
src/ReflLegacyTransferStrategy.cpp
src/ReflMainViewPresenter.cpp
src/ReflSearchModel.cpp
- src/ResNorm.cpp
+ src/Indirect/ResNorm.cpp
src/SANSAddFiles.cpp
src/SANSDiagnostics.cpp
src/SANSEventSlicing.cpp
src/SANSPlotSpecial.cpp
src/SANSRunWindow.cpp
src/StepScan.cpp
- src/Stretch.cpp
+ src/Indirect/Stretch.cpp
src/UserInputValidator.cpp
src/background.cpp
src/deltaECalc.cpp
@@ -74,43 +74,43 @@ set ( SRC_FILES
# Include files aren't required, but this makes them appear in Visual Studio
set ( INC_FILES
- inc/MantidQtCustomInterfaces/ApplyCorr.h
+ inc/MantidQtCustomInterfaces/Indirect/ApplyCorr.h
inc/MantidQtCustomInterfaces/Background.h
- inc/MantidQtCustomInterfaces/CalcCorr.h
- inc/MantidQtCustomInterfaces/ConvFit.h
+ inc/MantidQtCustomInterfaces/Indirect/CalcCorr.h
+ inc/MantidQtCustomInterfaces/Indirect/ConvFit.h
inc/MantidQtCustomInterfaces/DirectConvertToEnergy.h
inc/MantidQtCustomInterfaces/DllConfig.h
- inc/MantidQtCustomInterfaces/Elwin.h
- inc/MantidQtCustomInterfaces/Fury.h
- inc/MantidQtCustomInterfaces/FuryFit.h
+ inc/MantidQtCustomInterfaces/Indirect/Elwin.h
+ inc/MantidQtCustomInterfaces/Indirect/Fury.h
+ inc/MantidQtCustomInterfaces/Indirect/FuryFit.h
inc/MantidQtCustomInterfaces/Homer.h
- inc/MantidQtCustomInterfaces/IDATab.h
- inc/MantidQtCustomInterfaces/IndirectBayes.h
- inc/MantidQtCustomInterfaces/IndirectBayesTab.h
- inc/MantidQtCustomInterfaces/IndirectCalibration.h
- inc/MantidQtCustomInterfaces/IndirectConvertToEnergy.h
- inc/MantidQtCustomInterfaces/IndirectDataAnalysis.h
- inc/MantidQtCustomInterfaces/IndirectDataReduction.h
- inc/MantidQtCustomInterfaces/IndirectDataReductionTab.h
- inc/MantidQtCustomInterfaces/IndirectDiagnostics.h
- inc/MantidQtCustomInterfaces/IndirectDiffractionReduction.h
- inc/MantidQtCustomInterfaces/IndirectLoadILL.h
- inc/MantidQtCustomInterfaces/IndirectMolDyn.h
- inc/MantidQtCustomInterfaces/IndirectMoments.h
- inc/MantidQtCustomInterfaces/IndirectSassena.h
- inc/MantidQtCustomInterfaces/IndirectSimulation.h
- inc/MantidQtCustomInterfaces/IndirectSimulationTab.h
- inc/MantidQtCustomInterfaces/IndirectSqw.h
- inc/MantidQtCustomInterfaces/IndirectSymmetrise.h
- inc/MantidQtCustomInterfaces/IndirectTransmission.h
- inc/MantidQtCustomInterfaces/IndirectTransmissionCalc.h
- inc/MantidQtCustomInterfaces/IndirectTools.h
- inc/MantidQtCustomInterfaces/IndirectToolsTab.h
- inc/MantidQtCustomInterfaces/IndirectTab.h
+ inc/MantidQtCustomInterfaces/Indirect/IDATab.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectBayes.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectBayesTab.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectCalibration.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectConvertToEnergy.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectDataAnalysis.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectDataReduction.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectDataReductionTab.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectDiagnostics.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectDiffractionReduction.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectLoadILL.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectMolDyn.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectMoments.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectSassena.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectSimulation.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectSimulationTab.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectSqw.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectSymmetrise.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectTransmission.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectTransmissionCalc.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectTools.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectToolsTab.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectTab.h
inc/MantidQtCustomInterfaces/IReflPresenter.h
inc/MantidQtCustomInterfaces/IReflSearcher.h
- inc/MantidQtCustomInterfaces/JumpFit.h
- inc/MantidQtCustomInterfaces/MSDFit.h
+ inc/MantidQtCustomInterfaces/Indirect/JumpFit.h
+ inc/MantidQtCustomInterfaces/Indirect/MSDFit.h
inc/MantidQtCustomInterfaces/MantidEV.h
inc/MantidQtCustomInterfaces/MantidEVWorker.h
inc/MantidQtCustomInterfaces/MultiDatasetFit.h
@@ -144,15 +144,15 @@ set ( INC_FILES
inc/MantidQtCustomInterfaces/QReflTableModel.h
inc/MantidQtCustomInterfaces/QtReflMainView.h
inc/MantidQtCustomInterfaces/QtReflOptionsDialog.h
- inc/MantidQtCustomInterfaces/Quasi.h
- inc/MantidQtCustomInterfaces/ResNorm.h
+ inc/MantidQtCustomInterfaces/Indirect/Quasi.h
+ inc/MantidQtCustomInterfaces/Indirect/ResNorm.h
inc/MantidQtCustomInterfaces/SANSAddFiles.h
inc/MantidQtCustomInterfaces/SANSDiagnostics.h
inc/MantidQtCustomInterfaces/SANSEventSlicing.h
inc/MantidQtCustomInterfaces/SANSPlotSpecial.h
inc/MantidQtCustomInterfaces/SANSRunWindow.h
inc/MantidQtCustomInterfaces/StepScan.h
- inc/MantidQtCustomInterfaces/Stretch.h
+ inc/MantidQtCustomInterfaces/Indirect/Stretch.h
inc/MantidQtCustomInterfaces/Updateable.h
inc/MantidQtCustomInterfaces/UserInputValidator.h
inc/MantidQtCustomInterfaces/deltaECalc.h
@@ -161,39 +161,39 @@ set ( INC_FILES
set ( SRC_UNITY_IGNORE_FILES )
set ( MOC_FILES inc/MantidQtCustomInterfaces/Background.h
- inc/MantidQtCustomInterfaces/ApplyCorr.h
- inc/MantidQtCustomInterfaces/CalcCorr.h
- inc/MantidQtCustomInterfaces/ConvFit.h
+ inc/MantidQtCustomInterfaces/Indirect/ApplyCorr.h
+ inc/MantidQtCustomInterfaces/Indirect/CalcCorr.h
+ inc/MantidQtCustomInterfaces/Indirect/ConvFit.h
inc/MantidQtCustomInterfaces/DirectConvertToEnergy.h
- inc/MantidQtCustomInterfaces/Elwin.h
- inc/MantidQtCustomInterfaces/Fury.h
- inc/MantidQtCustomInterfaces/FuryFit.h
+ inc/MantidQtCustomInterfaces/Indirect/Elwin.h
+ inc/MantidQtCustomInterfaces/Indirect/Fury.h
+ inc/MantidQtCustomInterfaces/Indirect/FuryFit.h
inc/MantidQtCustomInterfaces/Homer.h
- inc/MantidQtCustomInterfaces/IDATab.h
- inc/MantidQtCustomInterfaces/IndirectBayes.h
- inc/MantidQtCustomInterfaces/IndirectBayesTab.h
- inc/MantidQtCustomInterfaces/IndirectCalibration.h
- inc/MantidQtCustomInterfaces/IndirectConvertToEnergy.h
- inc/MantidQtCustomInterfaces/IndirectDataAnalysis.h
- inc/MantidQtCustomInterfaces/IndirectDataReduction.h
- inc/MantidQtCustomInterfaces/IndirectDataReductionTab.h
- inc/MantidQtCustomInterfaces/IndirectDiagnostics.h
- inc/MantidQtCustomInterfaces/IndirectDiffractionReduction.h
- inc/MantidQtCustomInterfaces/IndirectLoadILL.h
- inc/MantidQtCustomInterfaces/IndirectMolDyn.h
- inc/MantidQtCustomInterfaces/IndirectMoments.h
- inc/MantidQtCustomInterfaces/IndirectSassena.h
- inc/MantidQtCustomInterfaces/IndirectSimulation.h
- inc/MantidQtCustomInterfaces/IndirectSimulationTab.h
- inc/MantidQtCustomInterfaces/IndirectSqw.h
- inc/MantidQtCustomInterfaces/IndirectSymmetrise.h
- inc/MantidQtCustomInterfaces/IndirectTransmission.h
- inc/MantidQtCustomInterfaces/IndirectTransmissionCalc.h
- inc/MantidQtCustomInterfaces/IndirectTools.h
- inc/MantidQtCustomInterfaces/IndirectToolsTab.h
- inc/MantidQtCustomInterfaces/IndirectTab.h
- inc/MantidQtCustomInterfaces/JumpFit.h
- inc/MantidQtCustomInterfaces/MSDFit.h
+ inc/MantidQtCustomInterfaces/Indirect/IDATab.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectBayes.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectBayesTab.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectCalibration.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectConvertToEnergy.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectDataAnalysis.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectDataReduction.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectDataReductionTab.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectDiagnostics.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectDiffractionReduction.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectLoadILL.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectMolDyn.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectMoments.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectSassena.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectSimulation.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectSimulationTab.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectSqw.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectSymmetrise.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectTransmission.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectTransmissionCalc.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectTools.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectToolsTab.h
+ inc/MantidQtCustomInterfaces/Indirect/IndirectTab.h
+ inc/MantidQtCustomInterfaces/Indirect/JumpFit.h
+ inc/MantidQtCustomInterfaces/Indirect/MSDFit.h
inc/MantidQtCustomInterfaces/MultiDatasetFit.h
inc/MantidQtCustomInterfaces/Muon/ALCBaselineModellingPresenter.h
inc/MantidQtCustomInterfaces/Muon/ALCBaselineModellingView.h
@@ -214,46 +214,46 @@ set ( MOC_FILES inc/MantidQtCustomInterfaces/Background.h
inc/MantidQtCustomInterfaces/QReflTableModel.h
inc/MantidQtCustomInterfaces/QtReflMainView.h
inc/MantidQtCustomInterfaces/QtReflOptionsDialog.h
- inc/MantidQtCustomInterfaces/Quasi.h
- inc/MantidQtCustomInterfaces/ResNorm.h
+ inc/MantidQtCustomInterfaces/Indirect/Quasi.h
+ inc/MantidQtCustomInterfaces/Indirect/ResNorm.h
inc/MantidQtCustomInterfaces/SANSAddFiles.h
inc/MantidQtCustomInterfaces/SANSPlotSpecial.h
inc/MantidQtCustomInterfaces/SANSRunWindow.h
inc/MantidQtCustomInterfaces/SANSEventSlicing.h
inc/MantidQtCustomInterfaces/SANSDiagnostics.h
- inc/MantidQtCustomInterfaces/Stretch.h
+ inc/MantidQtCustomInterfaces/Indirect/Stretch.h
inc/MantidQtCustomInterfaces/MantidEV.h
inc/MantidQtCustomInterfaces/StepScan.h
)
set ( UI_FILES inc/MantidQtCustomInterfaces/AddWorkspace.ui
inc/MantidQtCustomInterfaces/DirectConvertToEnergy.ui
- inc/MantidQtCustomInterfaces/IndirectBayes.ui
- inc/MantidQtCustomInterfaces/IndirectDataAnalysis.ui
- inc/MantidQtCustomInterfaces/IndirectDataReduction.ui
- inc/MantidQtCustomInterfaces/IndirectDiffractionReduction.ui
- inc/MantidQtCustomInterfaces/IndirectLoadILL.ui
- inc/MantidQtCustomInterfaces/IndirectMolDyn.ui
- inc/MantidQtCustomInterfaces/IndirectSassena.ui
- inc/MantidQtCustomInterfaces/IndirectSimulation.ui
- inc/MantidQtCustomInterfaces/IndirectTools.ui
- inc/MantidQtCustomInterfaces/IndirectTransmissionCalc.ui
- inc/MantidQtCustomInterfaces/JumpFit.ui
+ inc/MantidQtCustomInterfaces/Indirect/IndirectBayes.ui
+ inc/MantidQtCustomInterfaces/Indirect/IndirectDataAnalysis.ui
+ inc/MantidQtCustomInterfaces/Indirect/IndirectDataReduction.ui
+ inc/MantidQtCustomInterfaces/Indirect/IndirectDiffractionReduction.ui
+ inc/MantidQtCustomInterfaces/Indirect/IndirectLoadILL.ui
+ inc/MantidQtCustomInterfaces/Indirect/IndirectMolDyn.ui
+ inc/MantidQtCustomInterfaces/Indirect/IndirectSassena.ui
+ inc/MantidQtCustomInterfaces/Indirect/IndirectSimulation.ui
+ inc/MantidQtCustomInterfaces/Indirect/IndirectTools.ui
+ inc/MantidQtCustomInterfaces/Indirect/IndirectTransmissionCalc.ui
+ inc/MantidQtCustomInterfaces/Indirect/JumpFit.ui
inc/MantidQtCustomInterfaces/MultiDatasetFit.ui
inc/MantidQtCustomInterfaces/Muon/ALCBaselineModellingView.ui
inc/MantidQtCustomInterfaces/Muon/ALCDataLoadingView.ui
inc/MantidQtCustomInterfaces/Muon/ALCInterface.ui
inc/MantidQtCustomInterfaces/Muon/ALCPeakFittingView.ui
inc/MantidQtCustomInterfaces/Muon/MuonAnalysis.ui
- inc/MantidQtCustomInterfaces/Quasi.ui
+ inc/MantidQtCustomInterfaces/Indirect/Quasi.ui
inc/MantidQtCustomInterfaces/ReflMainWidget.ui
inc/MantidQtCustomInterfaces/ReflOptionsDialog.ui
inc/MantidQtCustomInterfaces/ReflWindow.ui
- inc/MantidQtCustomInterfaces/ResNorm.ui
+ inc/MantidQtCustomInterfaces/Indirect/ResNorm.ui
inc/MantidQtCustomInterfaces/SANSPlotSpecial.ui
inc/MantidQtCustomInterfaces/SANSRunWindow.ui
inc/MantidQtCustomInterfaces/SANSEventSlicing.ui
- inc/MantidQtCustomInterfaces/Stretch.ui
+ inc/MantidQtCustomInterfaces/Indirect/Stretch.ui
inc/MantidQtCustomInterfaces/MantidEV.ui
inc/MantidQtCustomInterfaces/StepScan.ui
inc/MantidQtCustomInterfaces/EditLocalParameterDialog.ui
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ApplyCorr.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/ApplyCorr.h
similarity index 96%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ApplyCorr.h
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/ApplyCorr.h
index 8549dfa10175e87149c98d7ea1051f841b37e51c..1a6f5ed49a678b843d848762b035463180966135 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ApplyCorr.h
+++ b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/ApplyCorr.h
@@ -2,7 +2,7 @@
#define MANTIDQTCUSTOMINTERFACESIDA_APPLYCORR_H_
#include "MantidAPI/MatrixWorkspace.h"
-#include "MantidQtCustomInterfaces/IDATab.h"
+#include "IDATab.h"
namespace MantidQt
{
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/CalcCorr.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/CalcCorr.h
similarity index 94%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/CalcCorr.h
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/CalcCorr.h
index 1c56fd8fefcca653c62a6c6dc067363ad4a8c2d2..9845fa67d11b153e85afae01f0785a206c511536 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/CalcCorr.h
+++ b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/CalcCorr.h
@@ -1,7 +1,7 @@
#ifndef MANTIDQTCUSTOMINTERFACESIDA_CALCCORR_H_
#define MANTIDQTCUSTOMINTERFACESIDA_CALCCORR_H_
-#include "MantidQtCustomInterfaces/IDATab.h"
+#include "IDATab.h"
namespace MantidQt
{
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ConvFit.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/ConvFit.h
similarity index 97%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ConvFit.h
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/ConvFit.h
index 7a3b8fe60abfc79561f9d1e5baf476a3103f28e9..c396eae1bee0819da47d077bf5a5987be37de30e 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ConvFit.h
+++ b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/ConvFit.h
@@ -1,7 +1,7 @@
#ifndef MANTIDQTCUSTOMINTERFACESIDA_CONVFIT_H_
#define MANTIDQTCUSTOMINTERFACESIDA_CONVFIT_H_
-#include "MantidQtCustomInterfaces/IDATab.h"
+#include "IDATab.h"
#include "MantidAPI/MatrixWorkspace.h"
#include "MantidAPI/CompositeFunction.h"
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Elwin.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/Elwin.h
similarity index 95%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Elwin.h
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/Elwin.h
index b3e70b9750edf4e66a1bbfde2434e207a62ecdd2..7e860508075e0434563c7fd32e9389fe38156410 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Elwin.h
+++ b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/Elwin.h
@@ -2,7 +2,7 @@
#define MANTIDQTCUSTOMINTERFACESIDA_ELWIN_H_
#include "MantidAPI/MatrixWorkspace.h"
-#include "MantidQtCustomInterfaces/IDATab.h"
+#include "MantidQtCustomInterfaces/Indirect/IDATab.h"
namespace MantidQt
{
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Fury.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/Fury.h
similarity index 95%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Fury.h
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/Fury.h
index eb63d5f6066366bb3b9bd4433c26a91ae22399b1..3de4cc76674079e1c57f7d8496a694277d11407b 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Fury.h
+++ b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/Fury.h
@@ -1,7 +1,7 @@
#ifndef MANTIDQTCUSTOMINTERFACESIDA_FURY_H_
#define MANTIDQTCUSTOMINTERFACESIDA_FURY_H_
-#include "MantidQtCustomInterfaces/IDATab.h"
+#include "IDATab.h"
namespace MantidQt
{
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/FuryFit.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/FuryFit.h
similarity index 97%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/FuryFit.h
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/FuryFit.h
index 2d30bde7ff6c2eb1c5e40fbd37460b9bdc3e8847..c11edb0f0cbadcba3d9f9225501494f7679161eb 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/FuryFit.h
+++ b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/FuryFit.h
@@ -1,7 +1,7 @@
#ifndef MANTIDQTCUSTOMINTERFACESIDA_FURYFIT_H_
#define MANTIDQTCUSTOMINTERFACESIDA_FURYFIT_H_
-#include "MantidQtCustomInterfaces/IDATab.h"
+#include "IDATab.h"
#include "MantidAPI/CompositeFunction.h"
#include "MantidAPI/MatrixWorkspace.h"
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IDATab.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IDATab.h
similarity index 96%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IDATab.h
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IDATab.h
index 0370f251f7177fa6a375decd6f92fde5dc6d36e7..3349a0d61683e19181870d7c47e3e3f0f47d0728 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IDATab.h
+++ b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IDATab.h
@@ -3,8 +3,8 @@
#include "MantidAPI/AlgorithmManager.h"
#include "MantidAPI/MatrixWorkspace.h"
-#include "MantidQtCustomInterfaces/IndirectDataAnalysis.h"
-#include "MantidQtCustomInterfaces/IndirectTab.h"
+#include "IndirectDataAnalysis.h"
+#include "IndirectTab.h"
class QwtPlotCurve;
class QwtPlot;
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectBayes.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectBayes.h
similarity index 98%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectBayes.h
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectBayes.h
index 149be80b71993e344ddecfeea8effeb9a847a7b5..83cdc666b5dac642bdb350522db601109761a988 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectBayes.h
+++ b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectBayes.h
@@ -6,7 +6,7 @@
//----------------------
#include "ui_IndirectBayes.h"
#include "MantidQtAPI/UserSubWindow.h"
-#include "MantidQtCustomInterfaces/IndirectBayesTab.h"
+#include "IndirectBayesTab.h"
#include <Poco/NObserver.h>
#include "MantidKernel/ConfigService.h"
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectBayes.ui b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectBayes.ui
similarity index 100%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectBayes.ui
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectBayes.ui
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectBayesTab.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectBayesTab.h
similarity index 98%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectBayesTab.h
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectBayesTab.h
index 3f073e758bbd687366960b215a783ffb101926ed..b0e55dd30fd0e0b59c02b69b4be59b8a1a87f486 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectBayesTab.h
+++ b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectBayesTab.h
@@ -2,7 +2,7 @@
#define MANTID_CUSTOMINTERFACES_INDIRECTBAYESTAB_H_
#include "MantidAPI/MatrixWorkspace.h"
-#include "MantidQtCustomInterfaces/IndirectTab.h"
+#include "IndirectTab.h"
#include "MantidQtMantidWidgets/RangeSelector.h"
#include "MantidQtAPI/AlgorithmRunner.h"
#include "MantidQtAPI/QwtWorkspaceSpectrumData.h"
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectCalibration.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectCalibration.h
similarity index 97%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectCalibration.h
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectCalibration.h
index 69496515579748503f64880c660cc6e756d68d36..c14ec0a22ba8f620182322f3973295827359cda2 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectCalibration.h
+++ b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectCalibration.h
@@ -1,7 +1,7 @@
#ifndef MANTIDQTCUSTOMINTERFACES_INDIRECTCALIBRATION_H_
#define MANTIDQTCUSTOMINTERFACES_INDIRECTCALIBRATION_H_
-#include "MantidQtCustomInterfaces/IndirectDataReductionTab.h"
+#include "IndirectDataReductionTab.h"
#include "MantidKernel/System.h"
#include "MantidQtCustomInterfaces/UserInputValidator.h"
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectConvertToEnergy.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectConvertToEnergy.h
similarity index 98%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectConvertToEnergy.h
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectConvertToEnergy.h
index e09ab59bc350f4761ae67722cf82d2c13759ef97..5c430ced51fb7999ca537f710864e7836966bd6c 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectConvertToEnergy.h
+++ b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectConvertToEnergy.h
@@ -1,7 +1,7 @@
#ifndef MANTIDQTCUSTOMINTERFACES_INDIRECTCONVERTTOENERGY_H_
#define MANTIDQTCUSTOMINTERFACES_INDIRECTCONVERTTOENERGY_H_
-#include "MantidQtCustomInterfaces/IndirectDataReductionTab.h"
+#include "IndirectDataReductionTab.h"
#include "MantidKernel/System.h"
#include "MantidQtCustomInterfaces/Background.h"
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectDataAnalysis.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectDataAnalysis.h
similarity index 98%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectDataAnalysis.h
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectDataAnalysis.h
index c1d283acdeaafebdd328edba271f0b65cbfc0880..c7233144d7e0d9025cc5cb31908438e98659db32 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectDataAnalysis.h
+++ b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectDataAnalysis.h
@@ -6,7 +6,7 @@
//----------------------
#include "ui_IndirectDataAnalysis.h"
#include "MantidQtAPI/UserSubWindow.h"
-#include "MantidQtCustomInterfaces/IndirectTab.h"
+#include "IndirectTab.h"
#include <Poco/NObserver.h>
#include "MantidKernel/ConfigService.h"
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectDataAnalysis.ui b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectDataAnalysis.ui
similarity index 100%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectDataAnalysis.ui
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectDataAnalysis.ui
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectDataReduction.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectDataReduction.h
similarity index 98%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectDataReduction.h
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectDataReduction.h
index 79eb954a858f6da31e36adcaac7143068e11a883..0f3219bbbe129c3fac73a9c68e7edd4e4504fcfb 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectDataReduction.h
+++ b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectDataReduction.h
@@ -8,7 +8,7 @@
#include "MantidQtAPI/AlgorithmRunner.h"
#include "MantidQtAPI/UserSubWindow.h"
-#include "MantidQtCustomInterfaces/IndirectDataReductionTab.h"
+#include "IndirectDataReductionTab.h"
#include <qwt_plot.h>
#include <qwt_plot_curve.h>
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectDataReduction.ui b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectDataReduction.ui
similarity index 100%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectDataReduction.ui
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectDataReduction.ui
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectDataReductionTab.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectDataReductionTab.h
similarity index 96%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectDataReductionTab.h
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectDataReductionTab.h
index 10079fcd9290803293e267e1dbb3b252df53c3f1..bd9af5f20f5cb9b6901121a6c758bb80e553eea3 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectDataReductionTab.h
+++ b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectDataReductionTab.h
@@ -8,8 +8,8 @@
#include "MantidQtAPI/BatchAlgorithmRunner.h"
#include "MantidQtAPI/PythonRunner.h"
#include "MantidQtAPI/QwtWorkspaceSpectrumData.h"
-#include "MantidQtCustomInterfaces/IndirectDataReduction.h"
-#include "MantidQtCustomInterfaces/IndirectTab.h"
+#include "IndirectDataReduction.h"
+#include "IndirectTab.h"
#include "MantidQtMantidWidgets/RangeSelector.h"
#include <QDoubleValidator>
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectDiagnostics.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectDiagnostics.h
similarity index 97%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectDiagnostics.h
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectDiagnostics.h
index c58d8f69300e98f88a48b6f1e7964646a624bbb5..72b6dcc0609fa00d36fac2c3a26964a3bd3d0c40 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectDiagnostics.h
+++ b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectDiagnostics.h
@@ -1,7 +1,7 @@
#ifndef MANTIDQTCUSTOMINTERFACES_INDIRECTDIAGNOSTICS_H_
#define MANTIDQTCUSTOMINTERFACES_INDIRECTDIAGNOSTICS_H_
-#include "MantidQtCustomInterfaces/IndirectDataReductionTab.h"
+#include "IndirectDataReductionTab.h"
#include "MantidAPI/MatrixWorkspace.h"
#include "MantidKernel/System.h"
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectDiffractionReduction.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectDiffractionReduction.h
similarity index 100%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectDiffractionReduction.h
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectDiffractionReduction.h
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectDiffractionReduction.ui b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectDiffractionReduction.ui
similarity index 100%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectDiffractionReduction.ui
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectDiffractionReduction.ui
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectLoadILL.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectLoadILL.h
similarity index 94%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectLoadILL.h
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectLoadILL.h
index a29fcea2d348ee98a25a2bd93df2f384bf929750..9fed1e099c0fd0cc8879475edb964f449a849c32 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectLoadILL.h
+++ b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectLoadILL.h
@@ -2,7 +2,7 @@
#define MANTIDQTCUSTOMINTERFACES_INDIRECTLOADILL_H_
#include "ui_IndirectLoadILL.h"
-#include "MantidQtCustomInterfaces/IndirectToolsTab.h"
+#include "IndirectToolsTab.h"
#include "MantidAPI/ExperimentInfo.h"
#include <QComboBox>
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectLoadILL.ui b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectLoadILL.ui
similarity index 100%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectLoadILL.ui
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectLoadILL.ui
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectMolDyn.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectMolDyn.h
similarity index 92%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectMolDyn.h
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectMolDyn.h
index 000c1a164acdbe1d7a3f58a213198c865d93b044..49641a23e47119e5add3e42e4d419c04ec02b779 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectMolDyn.h
+++ b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectMolDyn.h
@@ -2,7 +2,7 @@
#define MANTIDQTCUSTOMINTERFACES_INDIRECTMOLDYN_H_
#include "ui_IndirectMolDyn.h"
-#include "MantidQtCustomInterfaces/IndirectSimulationTab.h"
+#include "IndirectSimulationTab.h"
namespace MantidQt
{
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectMolDyn.ui b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectMolDyn.ui
similarity index 100%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectMolDyn.ui
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectMolDyn.ui
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectMoments.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectMoments.h
similarity index 97%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectMoments.h
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectMoments.h
index c28b5cb44ac65201dd0aeaddd3bcab475a3356bd..8e6ce70f327843817d8db22e0b00774d8fa12ca2 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectMoments.h
+++ b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectMoments.h
@@ -1,7 +1,7 @@
#ifndef MANTID_CUSTOMINTERFACES_INDIRECTMOMENTS_H_
#define MANTID_CUSTOMINTERFACES_INDIRECTMOMENTS_H_
-#include "MantidQtCustomInterfaces/IndirectDataReductionTab.h"
+#include "IndirectDataReductionTab.h"
#include "MantidKernel/System.h"
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectSassena.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectSassena.h
similarity index 93%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectSassena.h
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectSassena.h
index dc373046b05aa1cd4e54ebab68f9321fcf367ec4..25837e522d688d66b2ccdc4a4e170293deacd7c2 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectSassena.h
+++ b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectSassena.h
@@ -2,7 +2,7 @@
#define MANTIDQTCUSTOMINTERFACES_INDIRECTSASSENA_H_
#include "ui_IndirectSassena.h"
-#include "MantidQtCustomInterfaces/IndirectSimulationTab.h"
+#include "IndirectSimulationTab.h"
namespace MantidQt
{
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectSassena.ui b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectSassena.ui
similarity index 100%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectSassena.ui
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectSassena.ui
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectSimulation.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectSimulation.h
similarity index 98%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectSimulation.h
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectSimulation.h
index 5ac204d0b15e27f852362b1b39a80d5cac4623e8..b41d06333333a6e05d2678e5ee8c52ca32fddd70 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectSimulation.h
+++ b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectSimulation.h
@@ -7,7 +7,7 @@
#include "ui_IndirectSimulation.h"
#include "MantidKernel/ConfigService.h"
#include "MantidQtAPI/UserSubWindow.h"
-#include "MantidQtCustomInterfaces/IndirectSimulationTab.h"
+#include "IndirectSimulationTab.h"
#include <Poco/NObserver.h>
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectSimulation.ui b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectSimulation.ui
similarity index 100%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectSimulation.ui
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectSimulation.ui
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectSimulationTab.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectSimulationTab.h
similarity index 97%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectSimulationTab.h
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectSimulationTab.h
index 5b29466890c7ab2dbf634605c4c01e99da1125a8..d2a1c1d51c26347485b3cce1c6d5a2c392133ee8 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectSimulationTab.h
+++ b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectSimulationTab.h
@@ -4,7 +4,7 @@
#include "MantidAPI/AlgorithmManager.h"
#include "MantidKernel/System.h"
#include "MantidQtAPI/AlgorithmRunner.h"
-#include "MantidQtCustomInterfaces/IndirectTab.h"
+#include "IndirectTab.h"
#include <QSettings>
#include <QWidget>
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectSqw.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectSqw.h
similarity index 96%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectSqw.h
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectSqw.h
index 8185f93f6191beacf227b89543ff8393f0341f02..c8a730e7479a05f96672380d56976b27ab81c46b 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectSqw.h
+++ b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectSqw.h
@@ -1,7 +1,7 @@
#ifndef MANTIDQTCUSTOMINTERFACES_INDIRECTSQW_H_
#define MANTIDQTCUSTOMINTERFACES_INDIRECTSQW_H_
-#include "MantidQtCustomInterfaces/IndirectDataReductionTab.h"
+#include "IndirectDataReductionTab.h"
#include "MantidKernel/System.h"
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectSymmetrise.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectSymmetrise.h
similarity index 97%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectSymmetrise.h
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectSymmetrise.h
index 2951a409215fb5a24eee0526cc71301a0b7337e8..c391d8f3806d8b037dc0b71bf4086abc59942e1f 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectSymmetrise.h
+++ b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectSymmetrise.h
@@ -1,7 +1,7 @@
#ifndef MANTIDQTCUSTOMINTERFACES_INDIRECTSYMMETRISE_H_
#define MANTIDQTCUSTOMINTERFACES_INDIRECTSYMMETRISE_H_
-#include "MantidQtCustomInterfaces/IndirectDataReductionTab.h"
+#include "IndirectDataReductionTab.h"
#include "MantidAPI/MatrixWorkspace.h"
#include "MantidKernel/System.h"
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectTab.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectTab.h
similarity index 100%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectTab.h
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectTab.h
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectTools.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectTools.h
similarity index 98%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectTools.h
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectTools.h
index 7acf833d1efc3da44ed1dceb11e1586a5ae4afef..664ce3f1c272afccba5a32743379d79eaf7375c4 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectTools.h
+++ b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectTools.h
@@ -7,7 +7,7 @@
#include "ui_IndirectTools.h"
#include "MantidKernel/ConfigService.h"
#include "MantidQtAPI/UserSubWindow.h"
-#include "MantidQtCustomInterfaces/IndirectToolsTab.h"
+#include "IndirectToolsTab.h"
#include <Poco/NObserver.h>
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectTools.ui b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectTools.ui
similarity index 100%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectTools.ui
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectTools.ui
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectToolsTab.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectToolsTab.h
similarity index 100%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectToolsTab.h
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectToolsTab.h
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectTransmission.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectTransmission.h
similarity index 96%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectTransmission.h
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectTransmission.h
index f0b69a70958493b0d3cd4efafc34573830f067e8..bc57dc29e72f38c767bd77e30b66741c37669009 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectTransmission.h
+++ b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectTransmission.h
@@ -1,7 +1,7 @@
#ifndef MANTID_CUSTOMINTERFACES_INDIRECTTRANSMISSION_H_
#define MANTID_CUSTOMINTERFACES_INDIRECTTRANSMISSION_H_
-#include "MantidQtCustomInterfaces/IndirectDataReductionTab.h"
+#include "IndirectDataReductionTab.h"
#include "MantidKernel/System.h"
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectTransmissionCalc.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectTransmissionCalc.h
similarity index 95%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectTransmissionCalc.h
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectTransmissionCalc.h
index c1b2b31011c81ad66fd551103e82a63d68cfc242..a52722639af2a7c05e81f9351dc3be58bbf4605c 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectTransmissionCalc.h
+++ b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectTransmissionCalc.h
@@ -2,7 +2,7 @@
#define MANTIDQTCUSTOMINTERFACES_INDIRECTTRANSMISSIONCALC_H_
#include "ui_IndirectTransmissionCalc.h"
-#include "MantidQtCustomInterfaces/IndirectToolsTab.h"
+#include "IndirectToolsTab.h"
#include "MantidAPI/ExperimentInfo.h"
#include <QComboBox>
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectTransmissionCalc.ui b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectTransmissionCalc.ui
similarity index 100%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectTransmissionCalc.ui
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/IndirectTransmissionCalc.ui
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/JumpFit.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/JumpFit.h
similarity index 96%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/JumpFit.h
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/JumpFit.h
index fbde3aabb08244ad484efcfa2122c89b0315c2b3..3f2b97506573387792ba70a7aa7d5888d4e04e49 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/JumpFit.h
+++ b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/JumpFit.h
@@ -2,7 +2,7 @@
#define MANTIDQTCUSTOMINTERFACES_JUMPFIT_H_
#include "ui_JumpFit.h"
-#include "MantidQtCustomInterfaces/IndirectBayesTab.h"
+#include "IndirectBayesTab.h"
namespace MantidQt
{
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/JumpFit.ui b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/JumpFit.ui
similarity index 100%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/JumpFit.ui
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/JumpFit.ui
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/MSDFit.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/MSDFit.h
similarity index 95%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/MSDFit.h
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/MSDFit.h
index fd0951849eee7f95a468d9adb7802601c8c348d8..bd23d836b3d47965e9d59932e5f9dc9cbec938fa 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/MSDFit.h
+++ b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/MSDFit.h
@@ -1,7 +1,7 @@
#ifndef MANTIDQTCUSTOMINTERFACESIDA_MSDFIT_H_
#define MANTIDQTCUSTOMINTERFACESIDA_MSDFIT_H_
-#include "MantidQtCustomInterfaces/IDATab.h"
+#include "IDATab.h"
namespace MantidQt
{
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Quasi.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/Quasi.h
similarity index 96%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Quasi.h
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/Quasi.h
index d7cd02ab6dc39e4512f3aa58d2ac20a4c6c23a0a..df94ec39c20ae342e975daf50be9a91c6c7c7759 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Quasi.h
+++ b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/Quasi.h
@@ -2,7 +2,7 @@
#define MANTIDQTCUSTOMINTERFACES_QUASI_H_
#include "ui_Quasi.h"
-#include "MantidQtCustomInterfaces/IndirectBayesTab.h"
+#include "IndirectBayesTab.h"
namespace MantidQt
{
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Quasi.ui b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/Quasi.ui
similarity index 100%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Quasi.ui
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/Quasi.ui
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ResNorm.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/ResNorm.h
similarity index 95%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ResNorm.h
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/ResNorm.h
index 66c0f03b7a160aed539078c32d2a1886680e02e9..1377de73f0236ba351ad46f4f9b478bc3e386d24 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ResNorm.h
+++ b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/ResNorm.h
@@ -2,7 +2,7 @@
#define MANTIDQTCUSTOMINTERFACES_RESNORM_H_
#include "ui_ResNorm.h"
-#include "MantidQtCustomInterfaces/IndirectBayesTab.h"
+#include "IndirectBayesTab.h"
namespace MantidQt
{
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ResNorm.ui b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/ResNorm.ui
similarity index 100%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/ResNorm.ui
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/ResNorm.ui
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Stretch.h b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/Stretch.h
similarity index 95%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Stretch.h
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/Stretch.h
index b35d2dec4adf671362fdf050aef896a53f247f84..6fbfdaea0c33d8fbf659dc82d0740c7cc45d0792 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Stretch.h
+++ b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/Stretch.h
@@ -2,7 +2,7 @@
#define MANTIDQTCUSTOMINTERFACES_STRETCH_H_
#include "ui_Stretch.h"
-#include "MantidQtCustomInterfaces/IndirectBayesTab.h"
+#include "IndirectBayesTab.h"
namespace MantidQt
{
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Stretch.ui b/Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/Stretch.ui
similarity index 100%
rename from Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Stretch.ui
rename to Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/Indirect/Stretch.ui
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/ApplyCorr.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/ApplyCorr.cpp
similarity index 99%
rename from Code/Mantid/MantidQt/CustomInterfaces/src/ApplyCorr.cpp
rename to Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/ApplyCorr.cpp
index 3b7de751945c73490f70bcd9c1b8e5db1d12727a..138fe1c3e9d98cb7b9e3f69b1aefb94ded671925 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/src/ApplyCorr.cpp
+++ b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/ApplyCorr.cpp
@@ -1,4 +1,4 @@
-#include "MantidQtCustomInterfaces/ApplyCorr.h"
+#include "MantidQtCustomInterfaces/Indirect/ApplyCorr.h"
#include "MantidAPI/AnalysisDataService.h"
#include "MantidAPI/TextAxis.h"
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/CalcCorr.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/CalcCorr.cpp
similarity index 99%
rename from Code/Mantid/MantidQt/CustomInterfaces/src/CalcCorr.cpp
rename to Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/CalcCorr.cpp
index 325451b7e798d7e634f141f6f081f8c4b2919117..ea58f2f06cb1d2c988b038a5922a173140926dba 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/src/CalcCorr.cpp
+++ b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/CalcCorr.cpp
@@ -1,5 +1,5 @@
#include "MantidAPI/AnalysisDataService.h"
-#include "MantidQtCustomInterfaces/CalcCorr.h"
+#include "MantidQtCustomInterfaces/Indirect/CalcCorr.h"
#include "MantidQtCustomInterfaces/UserInputValidator.h"
#include "MantidQtMantidWidgets/WorkspaceSelector.h"
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/ConvFit.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/ConvFit.cpp
similarity index 99%
rename from Code/Mantid/MantidQt/CustomInterfaces/src/ConvFit.cpp
rename to Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/ConvFit.cpp
index 81a70982483ff31a9d87831cf2d7e9f4bcb8514d..897185cd9abc58f3c8df6c560c637087a37bc53d 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/src/ConvFit.cpp
+++ b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/ConvFit.cpp
@@ -1,4 +1,4 @@
-#include "MantidQtCustomInterfaces/ConvFit.h"
+#include "MantidQtCustomInterfaces/Indirect/ConvFit.h"
#include "MantidQtCustomInterfaces/UserInputValidator.h"
#include "MantidQtMantidWidgets/RangeSelector.h"
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/Elwin.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/Elwin.cpp
similarity index 99%
rename from Code/Mantid/MantidQt/CustomInterfaces/src/Elwin.cpp
rename to Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/Elwin.cpp
index 919f78b054909dae24a8fb063079f69765564fcc..ac1443964f0977734b4eb780f32ef055c675a2a7 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/src/Elwin.cpp
+++ b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/Elwin.cpp
@@ -1,4 +1,4 @@
-#include "MantidQtCustomInterfaces/Elwin.h"
+#include "MantidQtCustomInterfaces/Indirect/Elwin.h"
#include "MantidQtCustomInterfaces/UserInputValidator.h"
#include "MantidQtMantidWidgets/RangeSelector.h"
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/Fury.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/Fury.cpp
similarity index 99%
rename from Code/Mantid/MantidQt/CustomInterfaces/src/Fury.cpp
rename to Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/Fury.cpp
index 8ae8c8e68187741e996fa82842874ff583d369b0..6598db8fc9d48a42245b4a4cffb5d48bb7eb0d0b 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/src/Fury.cpp
+++ b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/Fury.cpp
@@ -1,4 +1,4 @@
-#include "MantidQtCustomInterfaces/Fury.h"
+#include "MantidQtCustomInterfaces/Indirect/Fury.h"
#include "MantidQtCustomInterfaces/UserInputValidator.h"
#include "MantidQtMantidWidgets/RangeSelector.h"
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/FuryFit.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/FuryFit.cpp
similarity index 99%
rename from Code/Mantid/MantidQt/CustomInterfaces/src/FuryFit.cpp
rename to Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/FuryFit.cpp
index 6fab6fc6d2f6943895666418d91fc99b2245f552..d9e3a568d0190c9f0badf3866e86e951977a9c00 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/src/FuryFit.cpp
+++ b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/FuryFit.cpp
@@ -1,4 +1,4 @@
-#include "MantidQtCustomInterfaces/FuryFit.h"
+#include "MantidQtCustomInterfaces/Indirect/FuryFit.h"
#include "MantidQtCustomInterfaces/UserInputValidator.h"
#include "MantidQtMantidWidgets/RangeSelector.h"
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/IDATab.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IDATab.cpp
similarity index 98%
rename from Code/Mantid/MantidQt/CustomInterfaces/src/IDATab.cpp
rename to Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IDATab.cpp
index 587c2921c733ad9c456f09c28d6df40573ee7802..225408fc783d780eb9085b33a13e51fb16996081 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/src/IDATab.cpp
+++ b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IDATab.cpp
@@ -1,4 +1,4 @@
-#include "MantidQtCustomInterfaces/IDATab.h"
+#include "MantidQtCustomInterfaces/Indirect/IDATab.h"
#include "MantidAPI/MatrixWorkspace.h"
#include "MantidAPI/AnalysisDataService.h"
#include "boost/shared_ptr.hpp"
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectBayes.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectBayes.cpp
similarity index 93%
rename from Code/Mantid/MantidQt/CustomInterfaces/src/IndirectBayes.cpp
rename to Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectBayes.cpp
index 49db0e54f64a0f160019f02d901bd38d916aa1a5..2460528a5828f6bce9825bd686cdf16d01c005ab 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectBayes.cpp
+++ b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectBayes.cpp
@@ -1,9 +1,9 @@
#include "MantidQtAPI/ManageUserDirectories.h"
-#include "MantidQtCustomInterfaces/IndirectBayes.h"
-#include "MantidQtCustomInterfaces/JumpFit.h"
-#include "MantidQtCustomInterfaces/Quasi.h"
-#include "MantidQtCustomInterfaces/ResNorm.h"
-#include "MantidQtCustomInterfaces/Stretch.h"
+#include "MantidQtCustomInterfaces/Indirect/IndirectBayes.h"
+#include "MantidQtCustomInterfaces/Indirect/JumpFit.h"
+#include "MantidQtCustomInterfaces/Indirect/Quasi.h"
+#include "MantidQtCustomInterfaces/Indirect/ResNorm.h"
+#include "MantidQtCustomInterfaces/Indirect/Stretch.h"
#include <QDesktopServices>
#include <QUrl>
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectBayesTab.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectBayesTab.cpp
similarity index 98%
rename from Code/Mantid/MantidQt/CustomInterfaces/src/IndirectBayesTab.cpp
rename to Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectBayesTab.cpp
index 6ce219f719e2e279f674ee8fec37ad9db495eb5d..c87d289b062b281f6d07ee21983b5832e288293e 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectBayesTab.cpp
+++ b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectBayesTab.cpp
@@ -2,7 +2,7 @@
#include "MantidAPI/AnalysisDataService.h"
#include "MantidQtAPI/QwtWorkspaceSpectrumData.h"
#include "MantidQtAPI/UserSubWindow.h"
-#include "MantidQtCustomInterfaces/IndirectBayesTab.h"
+#include "MantidQtCustomInterfaces/Indirect/IndirectBayesTab.h"
using MantidQt::MantidWidgets::RangeSelector;
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectCalibration.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectCalibration.cpp
similarity index 99%
rename from Code/Mantid/MantidQt/CustomInterfaces/src/IndirectCalibration.cpp
rename to Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectCalibration.cpp
index 498b5fbc861719970ef64e289fb92c178d59aacb..c67673eb9a51052d6cb76c0075b7c545c994c583 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectCalibration.cpp
+++ b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectCalibration.cpp
@@ -1,4 +1,4 @@
-#include "MantidQtCustomInterfaces/IndirectCalibration.h"
+#include "MantidQtCustomInterfaces/Indirect/IndirectCalibration.h"
#include "MantidKernel/Logger.h"
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectConvertToEnergy.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectConvertToEnergy.cpp
similarity index 99%
rename from Code/Mantid/MantidQt/CustomInterfaces/src/IndirectConvertToEnergy.cpp
rename to Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectConvertToEnergy.cpp
index 15d765f96f8d6a3c3dd32eeabdf9d579dcaf075c..e55a58c742bf6db2ee8ac4e205720bb45feaab42 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectConvertToEnergy.cpp
+++ b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectConvertToEnergy.cpp
@@ -1,4 +1,4 @@
-#include "MantidQtCustomInterfaces/IndirectConvertToEnergy.h"
+#include "MantidQtCustomInterfaces/Indirect/IndirectConvertToEnergy.h"
#include "MantidQtCustomInterfaces/Background.h"
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectDataAnalysis.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectDataAnalysis.cpp
similarity index 92%
rename from Code/Mantid/MantidQt/CustomInterfaces/src/IndirectDataAnalysis.cpp
rename to Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectDataAnalysis.cpp
index 6ca177b45362d5226c6fbf96f814492c9d466ef4..c8debe579969e33d5ea3e7bd0384f51a968e112e 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectDataAnalysis.cpp
+++ b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectDataAnalysis.cpp
@@ -1,16 +1,16 @@
//----------------------
// Includes
//----------------------
-#include "MantidQtCustomInterfaces/IndirectDataAnalysis.h"
+#include "MantidQtCustomInterfaces/Indirect/IndirectDataAnalysis.h"
// IDATab subclasses:
-#include "MantidQtCustomInterfaces/Elwin.h"
-#include "MantidQtCustomInterfaces/MSDFit.h"
-#include "MantidQtCustomInterfaces/Fury.h"
-#include "MantidQtCustomInterfaces/FuryFit.h"
-#include "MantidQtCustomInterfaces/ConvFit.h"
-#include "MantidQtCustomInterfaces/CalcCorr.h"
-#include "MantidQtCustomInterfaces/ApplyCorr.h"
+#include "MantidQtCustomInterfaces/Indirect/Elwin.h"
+#include "MantidQtCustomInterfaces/Indirect/MSDFit.h"
+#include "MantidQtCustomInterfaces/Indirect/Fury.h"
+#include "MantidQtCustomInterfaces/Indirect/FuryFit.h"
+#include "MantidQtCustomInterfaces/Indirect/ConvFit.h"
+#include "MantidQtCustomInterfaces/Indirect/CalcCorr.h"
+#include "MantidQtCustomInterfaces/Indirect/ApplyCorr.h"
#include "MantidQtAPI/ManageUserDirectories.h"
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectDataReduction.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectDataReduction.cpp
similarity index 96%
rename from Code/Mantid/MantidQt/CustomInterfaces/src/IndirectDataReduction.cpp
rename to Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectDataReduction.cpp
index a77827f97c32fc2d95b003bce4cb621551183693..bc53306820a8a6b6216d47812eeed22fb31390ea 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectDataReduction.cpp
+++ b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectDataReduction.cpp
@@ -1,20 +1,20 @@
//----------------------
// Includes
//----------------------
-#include "MantidQtCustomInterfaces/IndirectDataReduction.h"
+#include "MantidQtCustomInterfaces/Indirect/IndirectDataReduction.h"
#include "MantidAPI/AlgorithmManager.h"
#include "MantidAPI/AnalysisDataService.h"
#include "MantidAPI/ExperimentInfo.h"
#include "MantidKernel/ConfigService.h"
#include "MantidQtAPI/ManageUserDirectories.h"
-#include "MantidQtCustomInterfaces/IndirectCalibration.h"
-#include "MantidQtCustomInterfaces/IndirectConvertToEnergy.h"
-#include "MantidQtCustomInterfaces/IndirectDiagnostics.h"
-#include "MantidQtCustomInterfaces/IndirectMoments.h"
-#include "MantidQtCustomInterfaces/IndirectSqw.h"
-#include "MantidQtCustomInterfaces/IndirectSymmetrise.h"
-#include "MantidQtCustomInterfaces/IndirectTransmission.h"
+#include "MantidQtCustomInterfaces/Indirect/IndirectCalibration.h"
+#include "MantidQtCustomInterfaces/Indirect/IndirectConvertToEnergy.h"
+#include "MantidQtCustomInterfaces/Indirect/IndirectDiagnostics.h"
+#include "MantidQtCustomInterfaces/Indirect/IndirectMoments.h"
+#include "MantidQtCustomInterfaces/Indirect/IndirectSqw.h"
+#include "MantidQtCustomInterfaces/Indirect/IndirectSymmetrise.h"
+#include "MantidQtCustomInterfaces/Indirect/IndirectTransmission.h"
#include <QDesktopServices>
#include <QDir>
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectDataReductionTab.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectDataReductionTab.cpp
similarity index 99%
rename from Code/Mantid/MantidQt/CustomInterfaces/src/IndirectDataReductionTab.cpp
rename to Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectDataReductionTab.cpp
index b2013ec7468baf0e70899ef48554d3e12f9c0715..714864136dcb7cb241ecd88aa2bb28e2ed87c1ac 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectDataReductionTab.cpp
+++ b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectDataReductionTab.cpp
@@ -1,4 +1,4 @@
-#include "MantidQtCustomInterfaces/IndirectDataReductionTab.h"
+#include "MantidQtCustomInterfaces/Indirect/IndirectDataReductionTab.h"
#include "MantidAPI/AlgorithmManager.h"
#include "MantidKernel/Logger.h"
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectDiagnostics.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectDiagnostics.cpp
similarity index 99%
rename from Code/Mantid/MantidQt/CustomInterfaces/src/IndirectDiagnostics.cpp
rename to Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectDiagnostics.cpp
index f67c7e3a023f05ecb2a838b4f82c55890e4ea59b..308bed8c099c6b75b2ab48551b24aa608f39c9ad 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectDiagnostics.cpp
+++ b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectDiagnostics.cpp
@@ -1,4 +1,4 @@
-#include "MantidQtCustomInterfaces/IndirectDiagnostics.h"
+#include "MantidQtCustomInterfaces/Indirect/IndirectDiagnostics.h"
#include "MantidAPI/MatrixWorkspace.h"
#include "MantidKernel/Logger.h"
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectDiffractionReduction.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectDiffractionReduction.cpp
similarity index 99%
rename from Code/Mantid/MantidQt/CustomInterfaces/src/IndirectDiffractionReduction.cpp
rename to Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectDiffractionReduction.cpp
index db1faf3e8103b12a02b56ff954ebfb8ad5f3205b..c78a88e67c7c051b314597d3ba045e63ed2b6a07 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectDiffractionReduction.cpp
+++ b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectDiffractionReduction.cpp
@@ -1,7 +1,7 @@
//----------------------
// Includes
//----------------------
-#include "MantidQtCustomInterfaces/IndirectDiffractionReduction.h"
+#include "MantidQtCustomInterfaces/Indirect/IndirectDiffractionReduction.h"
#include "MantidQtAPI/ManageUserDirectories.h"
#include "MantidAPI/AlgorithmManager.h"
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectLoadILL.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectLoadILL.cpp
similarity index 98%
rename from Code/Mantid/MantidQt/CustomInterfaces/src/IndirectLoadILL.cpp
rename to Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectLoadILL.cpp
index 65692fbe9d41b3976184d6bf02cac2408220c254..a0a004f611a5d11e7ce5f0623581bf519335ef7c 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectLoadILL.cpp
+++ b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectLoadILL.cpp
@@ -3,7 +3,7 @@
#include "MantidAPI/MatrixWorkspace.h"
#include "MantidKernel/ConfigService.h"
#include "MantidKernel/FacilityInfo.h"
-#include "MantidQtCustomInterfaces/IndirectLoadILL.h"
+#include "MantidQtCustomInterfaces/Indirect/IndirectLoadILL.h"
#include <QFileInfo>
#include <QStringList>
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectMolDyn.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectMolDyn.cpp
similarity index 98%
rename from Code/Mantid/MantidQt/CustomInterfaces/src/IndirectMolDyn.cpp
rename to Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectMolDyn.cpp
index ed3b97c72d12ba915841b47762ab904fecf16877..53d90a12c739fb5cc0bfd9cb5514a6bc223c6660 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectMolDyn.cpp
+++ b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectMolDyn.cpp
@@ -1,4 +1,4 @@
-#include "MantidQtCustomInterfaces/IndirectMolDyn.h"
+#include "MantidQtCustomInterfaces/Indirect/IndirectMolDyn.h"
#include <QFileInfo>
#include <QString>
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectMoments.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectMoments.cpp
similarity index 99%
rename from Code/Mantid/MantidQt/CustomInterfaces/src/IndirectMoments.cpp
rename to Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectMoments.cpp
index 3c485433864ae4355afccb0326a281846484244e..75ddd23b90f4b4222b65cc47de83c0b837592e73 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectMoments.cpp
+++ b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectMoments.cpp
@@ -1,4 +1,4 @@
-#include "MantidQtCustomInterfaces/IndirectMoments.h"
+#include "MantidQtCustomInterfaces/Indirect/IndirectMoments.h"
#include "MantidQtCustomInterfaces/UserInputValidator.h"
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectSassena.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectSassena.cpp
similarity index 98%
rename from Code/Mantid/MantidQt/CustomInterfaces/src/IndirectSassena.cpp
rename to Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectSassena.cpp
index 457718358c6e126fba858834c0e50d667dd13669..ad7c83269025d46a3b1dab1d74967e154f6dd396 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectSassena.cpp
+++ b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectSassena.cpp
@@ -1,4 +1,4 @@
-#include "MantidQtCustomInterfaces/IndirectSassena.h"
+#include "MantidQtCustomInterfaces/Indirect/IndirectSassena.h"
#include <QFileInfo>
#include <QString>
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectSimulation.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectSimulation.cpp
similarity index 95%
rename from Code/Mantid/MantidQt/CustomInterfaces/src/IndirectSimulation.cpp
rename to Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectSimulation.cpp
index 649cdfa022b98c6f2a7729131d42c8b8d2b35dee..17386eaa3a0ec3d0d116d89423db8391a52aaad9 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectSimulation.cpp
+++ b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectSimulation.cpp
@@ -1,8 +1,8 @@
#include "MantidKernel/ConfigService.h"
#include "MantidQtAPI/ManageUserDirectories.h"
-#include "MantidQtCustomInterfaces/IndirectSimulation.h"
-#include "MantidQtCustomInterfaces/IndirectMolDyn.h"
-#include "MantidQtCustomInterfaces/IndirectSassena.h"
+#include "MantidQtCustomInterfaces/Indirect/IndirectSimulation.h"
+#include "MantidQtCustomInterfaces/Indirect/IndirectMolDyn.h"
+#include "MantidQtCustomInterfaces/Indirect/IndirectSassena.h"
#include <QDesktopServices>
#include <QUrl>
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectSimulationTab.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectSimulationTab.cpp
similarity index 92%
rename from Code/Mantid/MantidQt/CustomInterfaces/src/IndirectSimulationTab.cpp
rename to Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectSimulationTab.cpp
index 47d7cef49b874e7cf1675c0d122403c55ed328fd..d0f2a7f11cd2b08fea8daee5ba5b5f5917dcf607 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectSimulationTab.cpp
+++ b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectSimulationTab.cpp
@@ -1,5 +1,5 @@
#include "MantidQtAPI/UserSubWindow.h"
-#include "MantidQtCustomInterfaces/IndirectSimulationTab.h"
+#include "MantidQtCustomInterfaces/Indirect/IndirectSimulationTab.h"
using namespace Mantid::API;
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectSqw.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectSqw.cpp
similarity index 99%
rename from Code/Mantid/MantidQt/CustomInterfaces/src/IndirectSqw.cpp
rename to Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectSqw.cpp
index 3003c32c3af8aca44486570622024b369ae6a425..71ee2abab166086d4ac2e6979aa8947893489d91 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectSqw.cpp
+++ b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectSqw.cpp
@@ -1,4 +1,4 @@
-#include "MantidQtCustomInterfaces/IndirectSqw.h"
+#include "MantidQtCustomInterfaces/Indirect/IndirectSqw.h"
#include "MantidQtCustomInterfaces/UserInputValidator.h"
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectSymmetrise.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectSymmetrise.cpp
similarity index 99%
rename from Code/Mantid/MantidQt/CustomInterfaces/src/IndirectSymmetrise.cpp
rename to Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectSymmetrise.cpp
index ce99f8dcb63d763d0048326a81b8ffd5b7c2d18c..0bbe9cad0859fddd944c744c322aaa5668626384 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectSymmetrise.cpp
+++ b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectSymmetrise.cpp
@@ -1,4 +1,4 @@
-#include "MantidQtCustomInterfaces/IndirectSymmetrise.h"
+#include "MantidQtCustomInterfaces/Indirect/IndirectSymmetrise.h"
#include "MantidAPI/MatrixWorkspace.h"
#include "MantidAPI/ITableWorkspace.h"
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectTab.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectTab.cpp
similarity index 99%
rename from Code/Mantid/MantidQt/CustomInterfaces/src/IndirectTab.cpp
rename to Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectTab.cpp
index 8940d782fcfcd8cbd73e72036e29599ebb5df435..6e2d5109c05fa42519beeebb141a4e1681dfa27b 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectTab.cpp
+++ b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectTab.cpp
@@ -1,4 +1,4 @@
-#include "MantidQtCustomInterfaces/IndirectTab.h"
+#include "MantidQtCustomInterfaces/Indirect/IndirectTab.h"
#include "MantidAPI/AlgorithmManager.h"
#include "MantidKernel/Logger.h"
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectTools.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectTools.cpp
similarity index 95%
rename from Code/Mantid/MantidQt/CustomInterfaces/src/IndirectTools.cpp
rename to Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectTools.cpp
index 23729ba8c0c252e083b006c8345db003160a9041..2b6fb85e5ae0d72be05dcf9bd4b2d778c8721cd6 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectTools.cpp
+++ b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectTools.cpp
@@ -1,8 +1,8 @@
#include "MantidKernel/ConfigService.h"
#include "MantidQtAPI/ManageUserDirectories.h"
-#include "MantidQtCustomInterfaces/IndirectTools.h"
-#include "MantidQtCustomInterfaces/IndirectTransmissionCalc.h"
-#include "MantidQtCustomInterfaces/IndirectLoadILL.h"
+#include "MantidQtCustomInterfaces/Indirect/IndirectTools.h"
+#include "MantidQtCustomInterfaces/Indirect/IndirectTransmissionCalc.h"
+#include "MantidQtCustomInterfaces/Indirect/IndirectLoadILL.h"
#include <QDesktopServices>
#include <QUrl>
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectToolsTab.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectToolsTab.cpp
similarity index 94%
rename from Code/Mantid/MantidQt/CustomInterfaces/src/IndirectToolsTab.cpp
rename to Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectToolsTab.cpp
index 768f9aafa86320f9e94ff22c2b127ba483d8689d..f1b1c007648021d3e2ae3894347ce912411dc8bb 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectToolsTab.cpp
+++ b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectToolsTab.cpp
@@ -1,5 +1,5 @@
#include "MantidQtAPI/UserSubWindow.h"
-#include "MantidQtCustomInterfaces/IndirectToolsTab.h"
+#include "MantidQtCustomInterfaces/Indirect/IndirectToolsTab.h"
namespace MantidQt
{
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectTransmission.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectTransmission.cpp
similarity index 98%
rename from Code/Mantid/MantidQt/CustomInterfaces/src/IndirectTransmission.cpp
rename to Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectTransmission.cpp
index 035353ab4c6cf2f4bd6564399e5fcf4e2b00b646..c1d4683fad2f90e97c853c9b60d4286b9ad9ce2b 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectTransmission.cpp
+++ b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectTransmission.cpp
@@ -1,4 +1,4 @@
-#include "MantidQtCustomInterfaces/IndirectTransmission.h"
+#include "MantidQtCustomInterfaces/Indirect/IndirectTransmission.h"
#include <QFileInfo>
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectTransmissionCalc.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectTransmissionCalc.cpp
similarity index 98%
rename from Code/Mantid/MantidQt/CustomInterfaces/src/IndirectTransmissionCalc.cpp
rename to Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectTransmissionCalc.cpp
index 1ff2c198a7f8c639e2dff770e97f0262d899071c..08b4c88e807cdd4421f45e61e7a3e40371f16629 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/src/IndirectTransmissionCalc.cpp
+++ b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/IndirectTransmissionCalc.cpp
@@ -2,7 +2,7 @@
#include "MantidAPI/ExperimentInfo.h"
#include "MantidAPI/MatrixWorkspace.h"
#include "MantidAPI/ITableWorkspace.h"
-#include "MantidQtCustomInterfaces/IndirectTransmissionCalc.h"
+#include "MantidQtCustomInterfaces/Indirect/IndirectTransmissionCalc.h"
#include "MantidQtCustomInterfaces/UserInputValidator.h"
#include <QTreeWidgetItem>
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/JumpFit.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/JumpFit.cpp
similarity index 99%
rename from Code/Mantid/MantidQt/CustomInterfaces/src/JumpFit.cpp
rename to Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/JumpFit.cpp
index 240174dc14ce4323a7b3278d0a062c0ce5f4aeed..6a093dcd26df8c22c493b1d8f975ede9f5c302f2 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/src/JumpFit.cpp
+++ b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/JumpFit.cpp
@@ -1,7 +1,7 @@
#include "MantidAPI/AlgorithmManager.h"
#include "MantidAPI/Run.h"
#include "MantidAPI/TextAxis.h"
-#include "MantidQtCustomInterfaces/JumpFit.h"
+#include "MantidQtCustomInterfaces/Indirect/JumpFit.h"
#include "MantidQtCustomInterfaces/UserInputValidator.h"
#include <string>
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/MSDFit.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/MSDFit.cpp
similarity index 99%
rename from Code/Mantid/MantidQt/CustomInterfaces/src/MSDFit.cpp
rename to Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/MSDFit.cpp
index 8ea5836e8c069fe18aa9215ba2b84bbf5f9323ad..fda5bdef0cfc27f5ef2fd9eee77e1d5ca74b7b33 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/src/MSDFit.cpp
+++ b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/MSDFit.cpp
@@ -1,6 +1,6 @@
#include "MantidAPI/AnalysisDataService.h"
#include "MantidAPI/WorkspaceGroup.h"
-#include "MantidQtCustomInterfaces/MSDFit.h"
+#include "MantidQtCustomInterfaces/Indirect/MSDFit.h"
#include "MantidQtCustomInterfaces/UserInputValidator.h"
#include "MantidQtMantidWidgets/RangeSelector.h"
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/Quasi.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/Quasi.cpp
similarity index 99%
rename from Code/Mantid/MantidQt/CustomInterfaces/src/Quasi.cpp
rename to Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/Quasi.cpp
index a27a8d564b0179caba27ce72d768220a3fb9394c..e70b4d3310feecf99dc2f6424bdc75a26eafd3a1 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/src/Quasi.cpp
+++ b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/Quasi.cpp
@@ -1,5 +1,5 @@
#include "MantidAPI/TextAxis.h"
-#include "MantidQtCustomInterfaces/Quasi.h"
+#include "MantidQtCustomInterfaces/Indirect/Quasi.h"
#include "MantidQtCustomInterfaces/UserInputValidator.h"
using namespace Mantid::API;
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/ResNorm.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/ResNorm.cpp
similarity index 99%
rename from Code/Mantid/MantidQt/CustomInterfaces/src/ResNorm.cpp
rename to Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/ResNorm.cpp
index 907609ff5ff37d08a6fbb41d492f9df0908b683b..a9ccfd47614baf84f202eebc878a012995cebcc8 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/src/ResNorm.cpp
+++ b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/ResNorm.cpp
@@ -1,4 +1,4 @@
-#include "MantidQtCustomInterfaces/ResNorm.h"
+#include "MantidQtCustomInterfaces/Indirect/ResNorm.h"
#include "MantidQtCustomInterfaces/UserInputValidator.h"
using namespace Mantid::API;
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/Stretch.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/Stretch.cpp
similarity index 99%
rename from Code/Mantid/MantidQt/CustomInterfaces/src/Stretch.cpp
rename to Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/Stretch.cpp
index 83f8217d2830da0d0ba47683e8df4f52755b1ed8..616c9ff852312a6a649073281bc2873a9a85d4d1 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/src/Stretch.cpp
+++ b/Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/Stretch.cpp
@@ -1,4 +1,4 @@
-#include "MantidQtCustomInterfaces/Stretch.h"
+#include "MantidQtCustomInterfaces/Indirect/Stretch.h"
#include "MantidQtCustomInterfaces/UserInputValidator.h"
namespace