diff --git a/.gitignore b/.gitignore
index 28853c5930f01543b5f669a47501b74ed00bcf3f..8f718aea18f8228889f4966d3e05d98422a63c57 100644
--- a/.gitignore
+++ b/.gitignore
@@ -167,3 +167,12 @@ Desktop.ini
 .tags_sorted_by_file
 
 Code/Mantid/Vates/VatesSimpleGui/ViewWidgets/inc/MantidVatesSimpleGuiViewWidgets/LibHelper.h
+
+
+# Make sure Third_Party doesn't get checked into the main repository
+Third_Party/
+# Common out-of-source build directory names. Usually, these should go in your .git/info/exclude
+win64/
+dbg/
+rel/
+
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 38df198a97db1c49acce959a0c1f7df3fa6af9a5..eb0616ea5b0154213add9fd9ca00e1a84f9227e4 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -211,13 +211,13 @@ endif ()
 ###########################################################################
 
 # N.B. INBUNDLE variable is empty except on Mac (set in DarwinSetup.cmake)
-install ( DIRECTORY Installers/colormaps/ DESTINATION ${INBUNDLE}colormaps PATTERN ".svn" EXCLUDE )
+install ( DIRECTORY installers/colormaps/ DESTINATION ${INBUNDLE}colormaps PATTERN ".svn" EXCLUDE )
 
 # Install the files (.desktop and icon) to create a menu item, but only if installing to /opt/Mantid
 if ( ${CMAKE_SYSTEM_NAME} STREQUAL "Linux" AND CMAKE_INSTALL_PREFIX STREQUAL "/opt/Mantid" )
-  install ( FILES ${CMAKE_CURRENT_SOURCE_DIR}/Installers/LinuxInstaller/mantidplot.desktop
+  install ( FILES ${CMAKE_CURRENT_SOURCE_DIR}/installers/LinuxInstaller/mantidplot.desktop
             DESTINATION /usr/share/applications )
-  install ( FILES ${CMAKE_CURRENT_SOURCE_DIR}/Images/MantidPlot_Icon_32offset.png
+  install ( FILES ${CMAKE_CURRENT_SOURCE_DIR}/images/MantidPlot_Icon_32offset.png
             DESTINATION /usr/share/pixmaps
             RENAME mantidplot.png )
 endif()
@@ -236,7 +236,7 @@ if ( ENABLE_CPACK )
     include ( CPackCommon )
 
     # Mac package settings
-    set ( CPACK_RESOURCE_FILE_LICENSE ${CMAKE_SOURCE_DIR}/Installers/WinInstaller/License.txt )
+    set ( CPACK_RESOURCE_FILE_LICENSE ${CMAKE_SOURCE_DIR}/installers/WinInstaller/License.txt )
 
     IF ( ${CMAKE_SYSTEM_NAME} STREQUAL "Linux" )
       include ( CPackLinuxSetup )
diff --git a/Code/.gitignore b/Code/.gitignore
deleted file mode 100644
index 3cde1d4d3a193a8d37e3f83586cb55a21506cd07..0000000000000000000000000000000000000000
--- a/Code/.gitignore
+++ /dev/null
@@ -1,7 +0,0 @@
-# Make sure Third_Party doesn't get checked into the main repository
-Third_Party/
-# Common out-of-source build directory names. Usually, these should go in your .git/info/exclude
-win64/
-dbg/
-rel/
-
diff --git a/Framework/DataHandling/src/DownloadInstrument.cpp b/Framework/DataHandling/src/DownloadInstrument.cpp
index 77f6428fce69cd4d8c3fe0ecdd7d0ccb8938459b..608b35f190fae3d94f0a368b871c8e75d7086c4f 100644
--- a/Framework/DataHandling/src/DownloadInstrument.cpp
+++ b/Framework/DataHandling/src/DownloadInstrument.cpp
@@ -147,8 +147,8 @@ DownloadInstrument::StringToStringMap DownloadInstrument::processRepository() {
         "this should point to the location of the instrument "
         "directory in the github API "
         "e.g. "
-        "https://api.github.com/repos/mantidproject/mantid/contents/Code/"
-        "Mantid/instrument.");
+        "https://api.github.com/repos/mantidproject/mantid/contents/"
+        "instrument.");
   }
   StringToStringMap fileMap;
   try {
diff --git a/Framework/DataHandling/test/DownloadInstrumentTest.h b/Framework/DataHandling/test/DownloadInstrumentTest.h
index 1fe7a3e0d7504ad09dc84cb06c81b56959765140..587b9fe1e47fa6d085dcb43ab83413d70280e5bd 100644
--- a/Framework/DataHandling/test/DownloadInstrumentTest.h
+++ b/Framework/DataHandling/test/DownloadInstrumentTest.h
@@ -43,7 +43,7 @@ private:
           "[\n"
           "  {\n"
           "    \"name\": \"NewFile.xml\",\n"
-          "    \"path\": \"Code/Mantid/instrument/NewFile.xml\",\n"
+          "    \"path\": \"instrument/NewFile.xml\",\n"
           "    \"sha\": \"Xaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa\",\n"
           "    \"size\": 60,\n"
           "    \"url\": \"https://www.mantidproject.org/invalid\",\n"
@@ -58,7 +58,7 @@ private:
           "  },\n"
           "  {\n"
           "    \"name\": \"UpdatableFile.xml\",\n"
-          "    \"path\": \"Code/Mantid/instrument/UpdatableFile.xml\",\n"
+          "    \"path\": \"instrument/UpdatableFile.xml\",\n"
           "    \"sha\": \"d66ba0a04290093d83d41901048068d495d41764\",\n"
           "    \"size\": 106141,\n"
           "    \"url\": \"https://www.mantidproject.org/invalid\",\n"
diff --git a/Framework/Doxygen/CMakeLists.txt b/Framework/Doxygen/CMakeLists.txt
index 5fa5bb562ea196c2058099f79fd43bf5f2d6ae8f..4f2fb3c026c3c1084319fe1e4e5b6022875ece48 100644
--- a/Framework/Doxygen/CMakeLists.txt
+++ b/Framework/Doxygen/CMakeLists.txt
@@ -40,8 +40,8 @@ if(DOXYGEN_FOUND)
 
   # configure doxygen
   add_custom_command ( OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/../../doxygen/html/Mantid_Logo_Transparent.png
-                       COMMAND ${CMAKE_COMMAND} ARGS -E copy_if_different  ${CMAKE_SOURCE_DIR}/Images/Mantid_Logo_Transparent.png ${CMAKE_CURRENT_BINARY_DIR}/../../doxygen/html/Mantid_Logo_Transparent.png
-		       DEPENDS  ${CMAKE_SOURCE_DIR}/Images/Mantid_Logo_Transparent.png
+                       COMMAND ${CMAKE_COMMAND} ARGS -E copy_if_different  ${CMAKE_SOURCE_DIR}/images/Mantid_Logo_Transparent.png ${CMAKE_CURRENT_BINARY_DIR}/../../doxygen/html/Mantid_Logo_Transparent.png
+		       DEPENDS  ${CMAKE_SOURCE_DIR}/images/Mantid_Logo_Transparent.png
                      )
   configure_file(${CMAKE_CURRENT_SOURCE_DIR}/Mantid_template.doxyfile
                  ${CMAKE_CURRENT_BINARY_DIR}/Mantid.doxyfile @ONLY)
diff --git a/Framework/Kernel/CMakeLists.txt b/Framework/Kernel/CMakeLists.txt
index 9da415f1b2dafc31f30b37aaf8cad02b99f4b8fd..f287fcf5d4723d4133366e3cce6681b96be0ae6e 100644
--- a/Framework/Kernel/CMakeLists.txt
+++ b/Framework/Kernel/CMakeLists.txt
@@ -489,7 +489,7 @@ set ( CHECK_FOR_NEW_MANTID_VERSION "0" )
 set ( ENABLE_USAGE_REPORTS "0" )
 set ( PYTHONPLUGIN_DIRS "${MANTID_ROOT}/Framework/PythonInterface/plugins" )
 set ( DATADIRS ${ExternalData_BINARY_ROOT}/Testing/Data/UnitTest;${ExternalData_BINARY_ROOT}/Testing/Data/DocTest;${MANTID_ROOT}/instrument )
-set ( COLORMAPS_FOLDER ${MANTID_ROOT}/Installers/colormaps/ )
+set ( COLORMAPS_FOLDER ${MANTID_ROOT}/installers/colormaps/ )
 set ( MANTIDPUBLISHER "http://upload.mantidproject.org/scriptrepository?debug=1" )
 set ( HTML_ROOT ${DOCS_BUILDDIR}/html )
 
diff --git a/Framework/Properties/Mantid.properties.template b/Framework/Properties/Mantid.properties.template
index e400eaa8e67d6cbea9e41f8b8abf44e097f517d7..27e669d1d7ff7c2297397b120797a006c97aa4b6 100644
--- a/Framework/Properties/Mantid.properties.template
+++ b/Framework/Properties/Mantid.properties.template
@@ -40,7 +40,7 @@ instrumentDefinition.directory = @MANTID_ROOT@/instrument
 
 # Whether to check for updated instrument definitions on startup of Mantid
 UpdateInstrumentDefinitions.OnStartup = @UPDATE_INSTRUMENT_DEFINTITIONS@
-UpdateInstrumentDefinitions.URL = https://api.github.com/repos/mantidproject/mantid/contents/Code/Mantid/instrument
+UpdateInstrumentDefinitions.URL = https://api.github.com/repos/mantidproject/mantid/contents/instrument
 
 # Whether to check for newer mantid versions on startup
 CheckMantidVersion.OnStartup = @CHECK_FOR_NEW_MANTID_VERSION@
diff --git a/MantidPlot/CMakeLists.txt b/MantidPlot/CMakeLists.txt
index 394c3e256ef9647711234ad43b8607f3a400a211..2f77fbf6fbff3cfb6f376e8769eceaf5a4fbe96a 100644
--- a/MantidPlot/CMakeLists.txt
+++ b/MantidPlot/CMakeLists.txt
@@ -762,8 +762,8 @@ include_directories ( ${CMAKE_CURRENT_BINARY_DIR} )
 # Internal icon links
 ###########################################################################
 
-qt4_add_resources ( RES_FILES ${PROJECT_SOURCE_DIR}/Images/images.qrc )
-qt4_add_resources ( RES_FILES ${PROJECT_SOURCE_DIR}/Images//fonts/fonts.qrc )
+qt4_add_resources ( RES_FILES ${PROJECT_SOURCE_DIR}/images/images.qrc )
+qt4_add_resources ( RES_FILES ${PROJECT_SOURCE_DIR}/images//fonts/fonts.qrc )
 qt4_add_resources ( RES_FILES ${CMAKE_CURRENT_SOURCE_DIR}/icons/icons.qrc )
 qt4_add_resources ( RES_FILES ${PROJECT_SOURCE_DIR}/MantidQt/SliceViewer/icons/SliceViewerIcons.qrc )
 qt4_add_resources ( RES_FILES ${PROJECT_SOURCE_DIR}/MantidQt/CustomInterfaces/icons/CustomInterfacesIcons.qrc )
@@ -821,7 +821,7 @@ if( WIN32 )
 endif( WIN32 )
 
 if ( APPLE )
-  set ( MANTID_RC_FILE ${CMAKE_SOURCE_DIR}/Images/MantidPlot.icns )
+  set ( MANTID_RC_FILE ${CMAKE_SOURCE_DIR}/images/MantidPlot.icns )
   set_source_files_properties(MANTID_RC_FILE PROPERTIES MACOSX_PACKAGE_LOCATION Resources)
 endif ()
 
@@ -935,7 +935,7 @@ if( APPLE )
     set ( MAC_BUNDLE_IDENTIFIER "" )
   endif()
 
-  configure_file ( ${CMAKE_CURRENT_SOURCE_DIR}/../Installers/MacInstaller/Info.plist.in
+  configure_file ( ${CMAKE_CURRENT_SOURCE_DIR}/../installers/MacInstaller/Info.plist.in
                    ${CMAKE_CURRENT_BINARY_DIR}/Info.plist
                    @ONLY )
 
diff --git a/MantidPlot/src/ApplicationWindow.cpp b/MantidPlot/src/ApplicationWindow.cpp
index 6e4d19ca956d800095fc2029bfbc2fde73d57cb8..d9455438c81ff03c2f0516cc79f00b0934b5c201 100644
--- a/MantidPlot/src/ApplicationWindow.cpp
+++ b/MantidPlot/src/ApplicationWindow.cpp
@@ -2627,7 +2627,7 @@ Matrix *ApplicationWindow::importImage(const QString &fileName) {
   QString fn = fileName;
   if (fn.isEmpty()) {
     QList<QByteArray> list = QImageReader::supportedImageFormats();
-    QString filter = tr("Images") + " (", aux1, aux2;
+    QString filter = tr("images") + " (", aux1, aux2;
     for (int i = 0; i < (int)list.count(); i++) {
       aux1 = " *." + list[i] + " ";
       aux2 += " *." + list[i] + ";;";
@@ -2668,7 +2668,7 @@ Matrix *ApplicationWindow::importImage(const QString &fileName) {
 
 void ApplicationWindow::loadImage() {
   QList<QByteArray> list = QImageReader::supportedImageFormats();
-  QString filter = tr("Images") + " (", aux1, aux2;
+  QString filter = tr("images") + " (", aux1, aux2;
   for (int i = 0; i < (int)list.count(); i++) {
     aux1 = " *." + list[i] + " ";
     aux2 += " *." + list[i] + ";;";
@@ -5041,13 +5041,13 @@ void ApplicationWindow::readSettings() {
   fitPluginsPath = settings.value("/FitPlugins", "fitPlugins").toString();
   templatesDir = settings.value("/TemplatesDir", appPath).toString();
   asciiDirPath = settings.value("/ASCII", appPath).toString();
-  imagesDirPath = settings.value("/Images", appPath).toString();
+  imagesDirPath = settings.value("/images", appPath).toString();
 #else
   fitPluginsPath =
       settings.value("/FitPlugins", "/usr/lib/MantidPlot/plugins").toString();
   templatesDir = settings.value("/TemplatesDir", QDir::homePath()).toString();
   asciiDirPath = settings.value("/ASCII", QDir::homePath()).toString();
-  imagesDirPath = settings.value("/Images", QDir::homePath()).toString();
+  imagesDirPath = settings.value("/images", QDir::homePath()).toString();
   workingDir = settings.value("/WorkingDir", QDir::homePath()).toString();
 #endif
   scriptsDirPath = settings.value("/ScriptsDir", appPath).toString();
@@ -5552,7 +5552,7 @@ void ApplicationWindow::saveSettings() {
   settings.setValue("/HelpFile", helpFilePath);
   settings.setValue("/FitPlugins", fitPluginsPath);
   settings.setValue("/ASCII", asciiDirPath);
-  settings.setValue("/Images", imagesDirPath);
+  settings.setValue("/images", imagesDirPath);
   settings.setValue("/ScriptsDir", scriptsDirPath);
   settings.setValue("/FitModelsDir", fitModelsPath);
   settings.setValue("/CustomActionsDir", customActionsDirPath);
@@ -8312,7 +8312,7 @@ void ApplicationWindow::addImage() {
     return;
 
   QList<QByteArray> list = QImageReader::supportedImageFormats();
-  QString filter = tr("Images") + " (", aux1, aux2;
+  QString filter = tr("images") + " (", aux1, aux2;
   for (int i = 0; i < (int)list.count(); i++) {
     aux1 = " *." + list[i] + " ";
     aux2 += " *." + list[i] + ";;";
diff --git a/MantidPlot/src/CustomActionDialog.cpp b/MantidPlot/src/CustomActionDialog.cpp
index e6867cfc82653909435c530d2fdc298a43f8c94b..0ffe792247682d974fbf3c6af8338c200fa32c61 100644
--- a/MantidPlot/src/CustomActionDialog.cpp
+++ b/MantidPlot/src/CustomActionDialog.cpp
@@ -474,7 +474,7 @@ void CustomActionDialog::saveAction(QAction *action)
 void CustomActionDialog::chooseIcon()
 {
     QList<QByteArray> list = QImageReader::supportedImageFormats();
-	QString filter = tr("Images") + " (", aux1, aux2;
+	QString filter = tr("images") + " (", aux1, aux2;
 	for (int i=0; i<(int)list.count(); i++){
 		aux1 = " *." + list[i] + " ";
 		aux2 += " *." + list[i] + ";;";
diff --git a/MantidPlot/src/Mantid/FirstTimeSetup.ui b/MantidPlot/src/Mantid/FirstTimeSetup.ui
index f0f78aa923f7933b9176023d853d04cb6336b183..26598580d2b60a8b66754bd3436dff407cbf22b3 100644
--- a/MantidPlot/src/Mantid/FirstTimeSetup.ui
+++ b/MantidPlot/src/Mantid/FirstTimeSetup.ui
@@ -149,7 +149,7 @@ font-size: 28px</string>
             <string>Sample Datasets</string>
            </property>
            <property name="icon">
-            <iconset resource="../../../Images/images.qrc">
+            <iconset resource="../../../images/images.qrc">
              <normaloff>:/Icons/download-icon-48x48.png</normaloff>:/Icons/download-icon-48x48.png</iconset>
            </property>
            <property name="iconSize">
@@ -187,7 +187,7 @@ font-size: 28px</string>
             <string>Extending Mantid with Python</string>
            </property>
            <property name="icon">
-            <iconset resource="../../../Images/images.qrc">
+            <iconset resource="../../../images/images.qrc">
              <normaloff>:/Icons/Plugin-Python-icon-48x48.png</normaloff>:/Icons/Plugin-Python-icon-48x48.png</iconset>
            </property>
            <property name="iconSize">
@@ -222,7 +222,7 @@ font-size: 28px</string>
             <string>Python in Mantid</string>
            </property>
            <property name="icon">
-            <iconset resource="../../../Images/images.qrc">
+            <iconset resource="../../../images/images.qrc">
              <normaloff>:/Icons/Circle_cog_48x48.png</normaloff>:/Icons/Circle_cog_48x48.png</iconset>
            </property>
            <property name="iconSize">
@@ -257,7 +257,7 @@ font-size: 28px</string>
             <string>Introduction to Python</string>
            </property>
            <property name="icon">
-            <iconset resource="../../../Images/images.qrc">
+            <iconset resource="../../../images/images.qrc">
              <normaloff>:/Icons/Python-icon-48x48.png</normaloff>:/Icons/Python-icon-48x48.png</iconset>
            </property>
            <property name="iconSize">
@@ -292,7 +292,7 @@ font-size: 28px</string>
             <string>Mantid Introduction</string>
            </property>
            <property name="icon">
-            <iconset resource="../../../Images/images.qrc">
+            <iconset resource="../../../images/images.qrc">
              <normaloff>:/Icons/Misc-Tutorial-icon-48x48.png</normaloff>:/Icons/Misc-Tutorial-icon-48x48.png</iconset>
            </property>
            <property name="iconSize">
@@ -348,7 +348,7 @@ color: rgb(0, 0, 0);</string>
             <string>Release Notes</string>
            </property>
            <property name="icon">
-            <iconset resource="../../../Images/images.qrc">
+            <iconset resource="../../../images/images.qrc">
              <normaloff>:/Icons/Notepad-Bloc-notes-icon-48x48.png</normaloff>:/Icons/Notepad-Bloc-notes-icon-48x48.png</iconset>
            </property>
            <property name="iconSize">
@@ -827,8 +827,8 @@ color: rgb(25,125,25);</string>
   <tabstop>pbConfirm</tabstop>
  </tabstops>
  <resources>
-  <include location="../../../Images/images.qrc"/>
-  <include location="../../../Images/fonts/fonts.qrc"/>
+  <include location="../../../images/images.qrc"/>
+  <include location="../../../images/fonts/fonts.qrc"/>
  </resources>
  <connections/>
 </ui>
diff --git a/MantidPlot/src/Mantid/MantidAbout.ui b/MantidPlot/src/Mantid/MantidAbout.ui
index 59a96c393e155adac6e8c241a94fbd38edec9043..377c4bbf0d0aa58d6c2beecb6f6d3b4437b54eae 100644
--- a/MantidPlot/src/Mantid/MantidAbout.ui
+++ b/MantidPlot/src/Mantid/MantidAbout.ui
@@ -220,7 +220,7 @@
            <string/>
           </property>
           <property name="pixmap">
-           <pixmap>:/Logos/Images/ISIS Logo.gif</pixmap>
+           <pixmap>:/Logos/images/ISIS Logo.gif</pixmap>
           </property>
           <property name="scaledContents">
            <bool>true</bool>
@@ -245,7 +245,7 @@
            <string/>
           </property>
           <property name="pixmap">
-           <pixmap resource="../../../Images/images.qrc">:/Ornl_hfir_sns_logo_small.png</pixmap>
+           <pixmap resource="../../../images/images.qrc">:/Ornl_hfir_sns_logo_small.png</pixmap>
           </property>
           <property name="scaledContents">
            <bool>true</bool>
@@ -289,7 +289,7 @@
            <string/>
           </property>
           <property name="pixmap">
-           <pixmap resource="../../../Images/images.qrc">:/ISIS_Logo_Transparent.gif</pixmap>
+           <pixmap resource="../../../images/images.qrc">:/ISIS_Logo_Transparent.gif</pixmap>
           </property>
           <property name="scaledContents">
            <bool>false</bool>
@@ -320,7 +320,7 @@
            <string/>
           </property>
           <property name="pixmap">
-           <pixmap resource="../../../Images/images.qrc">:/ess_logo_transparent_small.png</pixmap>
+           <pixmap resource="../../../images/images.qrc">:/ess_logo_transparent_small.png</pixmap>
           </property>
           <property name="scaledContents">
            <bool>true</bool>
@@ -404,7 +404,7 @@
            <string/>
           </property>
           <property name="pixmap">
-           <pixmap resource="../../../Images/images.qrc">:/Tessella_Logo_Transparent.gif</pixmap>
+           <pixmap resource="../../../images/images.qrc">:/Tessella_Logo_Transparent.gif</pixmap>
           </property>
           <property name="scaledContents">
            <bool>true</bool>
@@ -478,7 +478,7 @@
         <string/>
        </property>
        <property name="pixmap">
-        <pixmap resource="../../../Images/images.qrc">:/Mantid_Logo_Transparent.png</pixmap>
+        <pixmap resource="../../../images/images.qrc">:/Mantid_Logo_Transparent.png</pixmap>
        </property>
        <property name="scaledContents">
         <bool>true</bool>
@@ -490,7 +490,7 @@
   </layout>
  </widget>
  <resources>
-  <include location="../../../Images/images.qrc"/>
+  <include location="../../../images/images.qrc"/>
  </resources>
  <connections>
   <connection>
diff --git a/MantidQt/API/CMakeLists.txt b/MantidQt/API/CMakeLists.txt
index b743c10d41d3ab4bb383c2e9216517bf71869a53..10a2e479febf052505ec1cdc6f14c71c563b7cad 100644
--- a/MantidQt/API/CMakeLists.txt
+++ b/MantidQt/API/CMakeLists.txt
@@ -149,7 +149,7 @@ target_link_libraries ( MantidQtAPI LINK_PRIVATE ${TCMALLOC_LIBRARIES_LINKTIME}
 # Windows: Generate a qt.conf file so that the dev build finds the qt
 # plugins in third party. Done in two steps to get it into the build
 # directory that is selected at build time.
-# This file is NOT packaged. See Installers/WinInstaller for the package
+# This file is NOT packaged. See installers/WinInstaller for the package
 # version.
 ###########################################################################
 if ( WIN32 )
diff --git a/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/MWRunFiles.ui b/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/MWRunFiles.ui
index 0e1cd0f8cea23a0f671d35458bcc08611748cb07..6edbb9057145dede6af2f9b6857fbfc818a05270 100644
--- a/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/MWRunFiles.ui
+++ b/MantidQt/MantidWidgets/inc/MantidQtMantidWidgets/MWRunFiles.ui
@@ -140,7 +140,7 @@
       <string/>
      </property>
      <property name="icon">
-      <iconset resource="../../../../Images/images.qrc">
+      <iconset resource="../../../../images/images.qrc">
        <normaloff>:/Icons/LoadFile.png</normaloff>:/Icons/LoadFile.png</iconset>
      </property>
     </widget>
@@ -180,7 +180,7 @@
   </action>
  </widget>
  <resources>
-  <include location="../../../../Images/images.qrc"/>
+  <include location="../../../../images/images.qrc"/>
  </resources>
  <connections>
   <connection>
diff --git a/MantidQt/SliceViewer/inc/MantidQtSliceViewer/PeaksWorkspaceWidget.ui b/MantidQt/SliceViewer/inc/MantidQtSliceViewer/PeaksWorkspaceWidget.ui
index 4e96f3d638618b89b9fa4ea98aa132edfb06a3f0..9a05a3076bed568c090efc96f218e787ffaf5c7a 100644
--- a/MantidQt/SliceViewer/inc/MantidQtSliceViewer/PeaksWorkspaceWidget.ui
+++ b/MantidQt/SliceViewer/inc/MantidQtSliceViewer/PeaksWorkspaceWidget.ui
@@ -186,7 +186,7 @@
           <string/>
          </property>
          <property name="icon">
-          <iconset resource="../../../../Images/images.qrc">
+          <iconset resource="../../../../images/images.qrc">
            <normaloff>:/PickTools/selection-peaks.png</normaloff>:/PickTools/selection-peaks.png</iconset>
          </property>
          <property name="checkable">
@@ -203,7 +203,7 @@
           <string/>
          </property>
          <property name="icon">
-          <iconset resource="../../../../Images/images.qrc">
+          <iconset resource="../../../../images/images.qrc">
            <normaloff>:/PickTools/eraser.png</normaloff>:/PickTools/eraser.png</iconset>
          </property>
          <property name="checkable">
@@ -354,7 +354,7 @@
   </layout>
  </widget>
  <resources>
-  <include location="../../../../Images/images.qrc"/>
+  <include location="../../../../images/images.qrc"/>
  </resources>
  <connections/>
 </ui>
diff --git a/buildconfig/CMake/DarwinSetup.cmake b/buildconfig/CMake/DarwinSetup.cmake
index be401f1f73519712edb72677a1a6ccc0048d6220..66c0ff0bbd473b1130cb0d5b74b1193d76c177de 100644
--- a/buildconfig/CMake/DarwinSetup.cmake
+++ b/buildconfig/CMake/DarwinSetup.cmake
@@ -198,13 +198,13 @@ endif ()
 install ( DIRECTORY ${QT_PLUGINS_DIR}/imageformats DESTINATION MantidPlot.app/Contents/Frameworks/plugins )
 install ( DIRECTORY ${QT_PLUGINS_DIR}/sqldrivers DESTINATION MantidPlot.app/Contents/Frameworks/plugins )
 
-install ( FILES ${CMAKE_SOURCE_DIR}/Images/MantidPlot.icns
-                ${CMAKE_SOURCE_DIR}/Installers/MacInstaller/qt.conf
+install ( FILES ${CMAKE_SOURCE_DIR}/images/MantidPlot.icns
+                ${CMAKE_SOURCE_DIR}/installers/MacInstaller/qt.conf
           DESTINATION MantidPlot.app/Contents/Resources/
 )
 
-set ( CPACK_DMG_BACKGROUND_IMAGE ${CMAKE_SOURCE_DIR}/Images/osx-bundle-background.png )
-set ( CPACK_DMG_DS_STORE ${CMAKE_SOURCE_DIR}/Installers/MacInstaller/osx_DS_Store)
+set ( CPACK_DMG_BACKGROUND_IMAGE ${CMAKE_SOURCE_DIR}/images/osx-bundle-background.png )
+set ( CPACK_DMG_DS_STORE ${CMAKE_SOURCE_DIR}/installers/MacInstaller/osx_DS_Store)
 set ( MACOSX_BUNDLE_ICON_FILE MantidPlot.icns )
 
 string (REPLACE " " "" CPACK_SYSTEM_NAME ${OSX_CODENAME})
diff --git a/buildconfig/CMake/FindPylint.cmake b/buildconfig/CMake/FindPylint.cmake
index dcb4e94b659742f6549694b2e6e938544c98d709..e673732303caf059c3124ff4d677de6831009ca4 100644
--- a/buildconfig/CMake/FindPylint.cmake
+++ b/buildconfig/CMake/FindPylint.cmake
@@ -29,9 +29,9 @@ if ( PYLINT_EXECUTABLE )
     set ( PYLINT_VERSION "unknown" )
   endif()
   # Script to find all .py files and execute pylint
-  set ( PYLINT_RUNNER_SCRIPT ${CMAKE_SOURCE_DIR}/Tools/Pylint/run_pylint.py )
+  set ( PYLINT_RUNNER_SCRIPT ${CMAKE_SOURCE_DIR}/tools/Pylint/run_pylint.py )
   # Configuration file
-  set ( PYLINT_CFG_FILE ${CMAKE_SOURCE_DIR}/Tools/Pylint/pylint.cfg )
+  set ( PYLINT_CFG_FILE ${CMAKE_SOURCE_DIR}/tools/Pylint/pylint.cfg )
 endif ()
 
 include(FindPackageHandleStandardArgs)
diff --git a/buildconfig/CMake/MPISetup.cmake b/buildconfig/CMake/MPISetup.cmake
index bcc8602360efc199896fe176b4367d9726277fe9..66ca25c21acb71c8bc140656cba0fd2a6a5f3be6 100644
--- a/buildconfig/CMake/MPISetup.cmake
+++ b/buildconfig/CMake/MPISetup.cmake
@@ -42,7 +42,7 @@ set ( INSTALL_ROOT ${CMAKE_INSTALL_PREFIX} CACHE PATH "The location you intend t
 # Remove old module file
 execute_process ( COMMAND ${CMAKE_COMMAND} -E remove_directory ${CMAKE_BINARY_DIR}/modulefile )
 # Create new module file
-configure_file( ${CMAKE_CURRENT_SOURCE_DIR}/../Installers/LinuxInstaller/modulefile.template
+configure_file( ${CMAKE_CURRENT_SOURCE_DIR}/../installers/LinuxInstaller/modulefile.template
                 ${CMAKE_BINARY_DIR}/modulefile/${CPACK_PACKAGE_VERSION}
 )
 
diff --git a/buildconfig/CMake/WindowsNSIS.cmake b/buildconfig/CMake/WindowsNSIS.cmake
index b9a299a2ee61ff18653912072b3b6f0d708ded4a..82743b8031c35f1f6de0b1b11145beffcd71608f 100644
--- a/buildconfig/CMake/WindowsNSIS.cmake
+++ b/buildconfig/CMake/WindowsNSIS.cmake
@@ -11,9 +11,9 @@ set( CPACK_NSIS_DISPLAY_NAME "Mantid${CPACK_PACKAGE_SUFFIX}")
 set( CPACK_PACKAGE_NAME "mantid${CPACK_PACKAGE_SUFFIX}" )
 set( CPACK_PACKAGE_INSTALL_DIRECTORY "MantidInstall${CPACK_PACKAGE_SUFFIX}")
 set( CPACK_NSIS_INSTALL_ROOT "C:")
-set( CPACK_PACKAGE_ICON "${CMAKE_CURRENT_SOURCE_DIR}/Images\\\\MantidPlot_Icon_32offset.png" )
-set( CPACK_NSIS_MUI_ICON "${CMAKE_CURRENT_SOURCE_DIR}/Images\\\\MantidPlot_Icon_32offset.ico" )
-set( CPACK_NSIS_MUI_UNIICON "${CMAKE_CURRENT_SOURCE_DIR}/Images\\\\MantidPlot_Icon_32offset.ico" )
+set( CPACK_PACKAGE_ICON "${CMAKE_CURRENT_SOURCE_DIR}/images\\\\MantidPlot_Icon_32offset.png" )
+set( CPACK_NSIS_MUI_ICON "${CMAKE_CURRENT_SOURCE_DIR}/images\\\\MantidPlot_Icon_32offset.ico" )
+set( CPACK_NSIS_MUI_UNIICON "${CMAKE_CURRENT_SOURCE_DIR}/images\\\\MantidPlot_Icon_32offset.ico" )
 
 ###########################################################################
 # Deployment type - currently only works for Release!
@@ -120,7 +120,7 @@ endforeach()
 ###########################################################################
 # Qt Plugins + qt.conf file
 ###########################################################################
-install ( FILES ${CMAKE_CURRENT_SOURCE_DIR}/Installers/WinInstaller/qt.conf DESTINATION bin )
+install ( FILES ${CMAKE_CURRENT_SOURCE_DIR}/installers/WinInstaller/qt.conf DESTINATION bin )
 # imageformats
 set ( QT_PLUGINS_IMAGEFORMAT qgif4.dll qico4.dll qjpeg4.dll qmng4.dll qsvg4.dll qtga4.dll qtiff4.dll )
 foreach( DLL ${QT_PLUGINS_IMAGEFORMAT} )
@@ -143,7 +143,7 @@ install ( DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/Framework/Geometry/inc/MantidGeo
 install ( DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/Framework/API/inc/MantidAPI DESTINATION include
           PATTERN ".svn" EXCLUDE PATTERN ".git" EXCLUDE )
 # scons
-install ( DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/Installers/WinInstaller/scons-local/ DESTINATION scons-local
+install ( DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/installers/WinInstaller/scons-local/ DESTINATION scons-local
           PATTERN ".svn" EXCLUDE PATTERN ".git" EXCLUDE )
 # user algorithms
 install ( DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/Framework/UserAlgorithms/ DESTINATION UserAlgorithms FILES_MATCHING PATTERN "*.h" )
diff --git a/docs/conf.py.in b/docs/conf.py.in
index d320b5f4d9c4f17c738678ba7046719407db38da..4eb1cac59761bc9ab786ac711173372ca133b79c 100644
--- a/docs/conf.py.in
+++ b/docs/conf.py.in
@@ -124,7 +124,7 @@ html_title = ""
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-html_logo = os.path.relpath('@CMAKE_CURRENT_SOURCE_DIR@/../Images/Mantid_Logo_Transparent.png')
+html_logo = os.path.relpath('@CMAKE_CURRENT_SOURCE_DIR@/../images/Mantid_Logo_Transparent.png')
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
diff --git a/docs/source/algorithms/DownloadInstrument-v1.rst b/docs/source/algorithms/DownloadInstrument-v1.rst
index 051d20ce1045289b872c0dde2f9ab1479bf50461..04a1c5808d5c5838dbce4eb5eef855c7afd7d6e1 100644
--- a/docs/source/algorithms/DownloadInstrument-v1.rst
+++ b/docs/source/algorithms/DownloadInstrument-v1.rst
@@ -23,7 +23,7 @@ The code is configured using he following Mantid.Property, or Mantid.User.Proper
 UpdateInstrumentDefinitions.OnStartup = 1
    This controls wether this algorithm is run on startup of Mantid.  1 = Run on startup, 0 = don't.
 
-UpdateInstrumentDefinitions.URL = https://api.github.com/repos/mantidproject/mantid/contents/Code/Mantid/instrument
+UpdateInstrumentDefinitions.URL = https://api.github.com/repos/mantidproject/mantid/contents/instrument
    This stores the url used to access the contents of the Mantid Instrument Definition Repository.
 
 Output Messages
diff --git a/Images/Circle_cog_48x48.png b/images/Circle_cog_48x48.png
similarity index 100%
rename from Images/Circle_cog_48x48.png
rename to images/Circle_cog_48x48.png
diff --git a/Images/First_use_Background.pdn b/images/First_use_Background.pdn
similarity index 100%
rename from Images/First_use_Background.pdn
rename to images/First_use_Background.pdn
diff --git a/Images/First_use_Background.png b/images/First_use_Background.png
similarity index 100%
rename from Images/First_use_Background.png
rename to images/First_use_Background.png
diff --git a/Images/First_use_Background_black.pdn b/images/First_use_Background_black.pdn
similarity index 100%
rename from Images/First_use_Background_black.pdn
rename to images/First_use_Background_black.pdn
diff --git a/Images/First_use_Background_green.pdn b/images/First_use_Background_green.pdn
similarity index 100%
rename from Images/First_use_Background_green.pdn
rename to images/First_use_Background_green.pdn
diff --git a/Images/First_use_Background_green_beam.pdn b/images/First_use_Background_green_beam.pdn
similarity index 100%
rename from Images/First_use_Background_green_beam.pdn
rename to images/First_use_Background_green_beam.pdn
diff --git a/Images/First_use_Background_green_beam_black_logo.pdn b/images/First_use_Background_green_beam_black_logo.pdn
similarity index 100%
rename from Images/First_use_Background_green_beam_black_logo.pdn
rename to images/First_use_Background_green_beam_black_logo.pdn
diff --git a/Images/First_use_Background_mantis.pdn b/images/First_use_Background_mantis.pdn
similarity index 100%
rename from Images/First_use_Background_mantis.pdn
rename to images/First_use_Background_mantis.pdn
diff --git a/Images/First_use_Background_mantis_washout.pdn b/images/First_use_Background_mantis_washout.pdn
similarity index 100%
rename from Images/First_use_Background_mantis_washout.pdn
rename to images/First_use_Background_mantis_washout.pdn
diff --git a/Images/HFIR_logo_small.png b/images/HFIR_logo_small.png
similarity index 100%
rename from Images/HFIR_logo_small.png
rename to images/HFIR_logo_small.png
diff --git a/Images/ICatComboBackground.png b/images/ICatComboBackground.png
similarity index 100%
rename from Images/ICatComboBackground.png
rename to images/ICatComboBackground.png
diff --git a/Images/ICatComboVScrollbar.png b/images/ICatComboVScrollbar.png
similarity index 100%
rename from Images/ICatComboVScrollbar.png
rename to images/ICatComboVScrollbar.png
diff --git a/Images/ICatSearchBackGround.png b/images/ICatSearchBackGround.png
similarity index 100%
rename from Images/ICatSearchBackGround.png
rename to images/ICatSearchBackGround.png
diff --git a/Images/ICatSearchBackGround.qrc b/images/ICatSearchBackGround.qrc
similarity index 100%
rename from Images/ICatSearchBackGround.qrc
rename to images/ICatSearchBackGround.qrc
diff --git a/Images/ISIS_Logo_Transparent.gif b/images/ISIS_Logo_Transparent.gif
similarity index 100%
rename from Images/ISIS_Logo_Transparent.gif
rename to images/ISIS_Logo_Transparent.gif
diff --git a/Images/LoadFile.png b/images/LoadFile.png
similarity index 100%
rename from Images/LoadFile.png
rename to images/LoadFile.png
diff --git a/Images/MantidPlot.icns b/images/MantidPlot.icns
similarity index 100%
rename from Images/MantidPlot.icns
rename to images/MantidPlot.icns
diff --git a/Images/MantidPlot_Icon_32offset.ico b/images/MantidPlot_Icon_32offset.ico
similarity index 100%
rename from Images/MantidPlot_Icon_32offset.ico
rename to images/MantidPlot_Icon_32offset.ico
diff --git a/Images/MantidPlot_Icon_32offset.png b/images/MantidPlot_Icon_32offset.png
similarity index 100%
rename from Images/MantidPlot_Icon_32offset.png
rename to images/MantidPlot_Icon_32offset.png
diff --git a/Images/MantidPlot_Python_Icon_32x32.pdn b/images/MantidPlot_Python_Icon_32x32.pdn
similarity index 100%
rename from Images/MantidPlot_Python_Icon_32x32.pdn
rename to images/MantidPlot_Python_Icon_32x32.pdn
diff --git a/Images/MantidPlot_Python_Icon_32x32.png b/images/MantidPlot_Python_Icon_32x32.png
similarity index 100%
rename from Images/MantidPlot_Python_Icon_32x32.png
rename to images/MantidPlot_Python_Icon_32x32.png
diff --git a/Images/MantidSplashScreen.png b/images/MantidSplashScreen.png
similarity index 100%
rename from Images/MantidSplashScreen.png
rename to images/MantidSplashScreen.png
diff --git a/Images/Mantid_Logo_Forum.pdn b/images/Mantid_Logo_Forum.pdn
similarity index 100%
rename from Images/Mantid_Logo_Forum.pdn
rename to images/Mantid_Logo_Forum.pdn
diff --git a/Images/Mantid_Logo_Forum.png b/images/Mantid_Logo_Forum.png
similarity index 100%
rename from Images/Mantid_Logo_Forum.png
rename to images/Mantid_Logo_Forum.png
diff --git a/Images/Mantid_Logo_Transparent.png b/images/Mantid_Logo_Transparent.png
similarity index 100%
rename from Images/Mantid_Logo_Transparent.png
rename to images/Mantid_Logo_Transparent.png
diff --git a/Images/Mantid_Logo_Transparent_Cropped.png b/images/Mantid_Logo_Transparent_Cropped.png
similarity index 100%
rename from Images/Mantid_Logo_Transparent_Cropped.png
rename to images/Mantid_Logo_Transparent_Cropped.png
diff --git a/Images/Mantid_Logo_Transparent_for_dark_backgrounds.png b/images/Mantid_Logo_Transparent_for_dark_backgrounds.png
similarity index 100%
rename from Images/Mantid_Logo_Transparent_for_dark_backgrounds.png
rename to images/Mantid_Logo_Transparent_for_dark_backgrounds.png
diff --git a/Images/Misc-Tutorial-icon-32x32.png b/images/Misc-Tutorial-icon-32x32.png
similarity index 100%
rename from Images/Misc-Tutorial-icon-32x32.png
rename to images/Misc-Tutorial-icon-32x32.png
diff --git a/Images/Misc-Tutorial-icon-48x48.png b/images/Misc-Tutorial-icon-48x48.png
similarity index 100%
rename from Images/Misc-Tutorial-icon-48x48.png
rename to images/Misc-Tutorial-icon-48x48.png
diff --git a/Images/Notepad-Bloc-notes-icon-32x32.png b/images/Notepad-Bloc-notes-icon-32x32.png
similarity index 100%
rename from Images/Notepad-Bloc-notes-icon-32x32.png
rename to images/Notepad-Bloc-notes-icon-32x32.png
diff --git a/Images/Notepad-Bloc-notes-icon-48x48.png b/images/Notepad-Bloc-notes-icon-48x48.png
similarity index 100%
rename from Images/Notepad-Bloc-notes-icon-48x48.png
rename to images/Notepad-Bloc-notes-icon-48x48.png
diff --git a/Images/Ornl_hfir_sns_logo_small.png b/images/Ornl_hfir_sns_logo_small.png
similarity index 100%
rename from Images/Ornl_hfir_sns_logo_small.png
rename to images/Ornl_hfir_sns_logo_small.png
diff --git a/Images/Plugin-Python-icon-32x32.png b/images/Plugin-Python-icon-32x32.png
similarity index 100%
rename from Images/Plugin-Python-icon-32x32.png
rename to images/Plugin-Python-icon-32x32.png
diff --git a/Images/Plugin-Python-icon-48x48.png b/images/Plugin-Python-icon-48x48.png
similarity index 100%
rename from Images/Plugin-Python-icon-48x48.png
rename to images/Plugin-Python-icon-48x48.png
diff --git a/Images/Plugin-icon-32x32.png b/images/Plugin-icon-32x32.png
similarity index 100%
rename from Images/Plugin-icon-32x32.png
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diff --git a/Images/Python-icon-16x16.png b/images/Python-icon-16x16.png
similarity index 100%
rename from Images/Python-icon-16x16.png
rename to images/Python-icon-16x16.png
diff --git a/Images/Python-icon-32x32.png b/images/Python-icon-32x32.png
similarity index 100%
rename from Images/Python-icon-32x32.png
rename to images/Python-icon-32x32.png
diff --git a/Images/Python-icon-48x48.png b/images/Python-icon-48x48.png
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rename to images/Python-icon-48x48.png
diff --git a/Images/README.txt b/images/README.txt
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diff --git a/Images/SNS_logo_trans_back.gif b/images/SNS_logo_trans_back.gif
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rename from Images/SNS_logo_trans_back.gif
rename to images/SNS_logo_trans_back.gif
diff --git a/Images/Tessella_Logo_Transparent.gif b/images/Tessella_Logo_Transparent.gif
similarity index 100%
rename from Images/Tessella_Logo_Transparent.gif
rename to images/Tessella_Logo_Transparent.gif
diff --git a/Images/data_replace.png b/images/data_replace.png
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rename from Images/data_replace.png
rename to images/data_replace.png
diff --git a/Images/dialog-ok.png b/images/dialog-ok.png
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rename from Images/dialog-ok.png
rename to images/dialog-ok.png
diff --git a/Images/document.png b/images/document.png
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rename from Images/document.png
rename to images/document.png
diff --git a/Images/download-icon-32x32.png b/images/download-icon-32x32.png
similarity index 100%
rename from Images/download-icon-32x32.png
rename to images/download-icon-32x32.png
diff --git a/Images/download-icon-48x48.png b/images/download-icon-48x48.png
similarity index 100%
rename from Images/download-icon-48x48.png
rename to images/download-icon-48x48.png
diff --git a/Images/download.png b/images/download.png
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rename from Images/download.png
rename to images/download.png
diff --git a/Images/emptytrash.png b/images/emptytrash.png
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rename from Images/emptytrash.png
rename to images/emptytrash.png
diff --git a/Images/eraser.png b/images/eraser.png
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rename from Images/eraser.png
rename to images/eraser.png
diff --git a/Images/ess_logo_transparent_small.png b/images/ess_logo_transparent_small.png
similarity index 100%
rename from Images/ess_logo_transparent_small.png
rename to images/ess_logo_transparent_small.png
diff --git a/Images/file_pdf.png b/images/file_pdf.png
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rename from Images/file_pdf.png
rename to images/file_pdf.png
diff --git a/Images/folder-remote.png b/images/folder-remote.png
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rename from Images/folder-remote.png
rename to images/folder-remote.png
diff --git a/Images/folder.png b/images/folder.png
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rename to images/folder.png
diff --git a/Images/fonts/Apache License.txt b/images/fonts/Apache License.txt
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rename from Images/fonts/Apache License.txt
rename to images/fonts/Apache License.txt
diff --git a/Images/fonts/MontserratAlternates-Bold.ttf b/images/fonts/MontserratAlternates-Bold.ttf
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rename from Images/fonts/MontserratAlternates-Bold.ttf
rename to images/fonts/MontserratAlternates-Bold.ttf
diff --git a/Images/fonts/MontserratAlternates-Regular.ttf b/images/fonts/MontserratAlternates-Regular.ttf
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rename from Images/fonts/MontserratAlternates-Regular.ttf
rename to images/fonts/MontserratAlternates-Regular.ttf
diff --git a/Images/fonts/OFL.txt b/images/fonts/OFL.txt
similarity index 100%
rename from Images/fonts/OFL.txt
rename to images/fonts/OFL.txt
diff --git a/Images/fonts/OpenSans-Bold.ttf b/images/fonts/OpenSans-Bold.ttf
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rename from Images/fonts/OpenSans-Bold.ttf
rename to images/fonts/OpenSans-Bold.ttf
diff --git a/Images/fonts/OpenSans-BoldItalic.ttf b/images/fonts/OpenSans-BoldItalic.ttf
similarity index 100%
rename from Images/fonts/OpenSans-BoldItalic.ttf
rename to images/fonts/OpenSans-BoldItalic.ttf
diff --git a/Images/fonts/OpenSans-ExtraBold.ttf b/images/fonts/OpenSans-ExtraBold.ttf
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rename from Images/fonts/OpenSans-ExtraBold.ttf
rename to images/fonts/OpenSans-ExtraBold.ttf
diff --git a/Images/fonts/OpenSans-ExtraBoldItalic.ttf b/images/fonts/OpenSans-ExtraBoldItalic.ttf
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rename from Images/fonts/OpenSans-ExtraBoldItalic.ttf
rename to images/fonts/OpenSans-ExtraBoldItalic.ttf
diff --git a/Images/fonts/OpenSans-Italic.ttf b/images/fonts/OpenSans-Italic.ttf
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rename from Images/fonts/OpenSans-Italic.ttf
rename to images/fonts/OpenSans-Italic.ttf
diff --git a/Images/fonts/OpenSans-Light.ttf b/images/fonts/OpenSans-Light.ttf
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rename from Images/fonts/OpenSans-Light.ttf
rename to images/fonts/OpenSans-Light.ttf
diff --git a/Images/fonts/OpenSans-LightItalic.ttf b/images/fonts/OpenSans-LightItalic.ttf
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rename from Images/fonts/OpenSans-LightItalic.ttf
rename to images/fonts/OpenSans-LightItalic.ttf
diff --git a/Images/fonts/OpenSans-Regular.ttf b/images/fonts/OpenSans-Regular.ttf
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rename to images/fonts/OpenSans-Regular.ttf
diff --git a/Images/fonts/OpenSans-Semibold.ttf b/images/fonts/OpenSans-Semibold.ttf
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rename to images/fonts/OpenSans-Semibold.ttf
diff --git a/Images/fonts/OpenSans-SemiboldItalic.ttf b/images/fonts/OpenSans-SemiboldItalic.ttf
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rename from Images/fonts/OpenSans-SemiboldItalic.ttf
rename to images/fonts/OpenSans-SemiboldItalic.ttf
diff --git a/Images/fonts/fonts.qrc b/images/fonts/fonts.qrc
similarity index 100%
rename from Images/fonts/fonts.qrc
rename to images/fonts/fonts.qrc
diff --git a/Images/fonts/pontano-sans.regular.ttf b/images/fonts/pontano-sans.regular.ttf
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rename from Images/fonts/pontano-sans.regular.ttf
rename to images/fonts/pontano-sans.regular.ttf
diff --git a/Images/history.png b/images/history.png
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rename from Images/history.png
rename to images/history.png
diff --git a/Images/history_off.png b/images/history_off.png
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diff --git a/Images/images.qrc b/images/images.qrc
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rename to images/images.qrc
diff --git a/Images/invalid.png b/images/invalid.png
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rename from Images/invalid.png
rename to images/invalid.png
diff --git a/Images/mantid.png b/images/mantid.png
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rename from Images/mantid.png
rename to images/mantid.png
diff --git a/Images/office-document.png b/images/office-document.png
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rename to images/office-document.png
diff --git a/Images/osx-bundle-background.png b/images/osx-bundle-background.png
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diff --git a/Images/panning.png b/images/panning.png
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rename to images/panning.png
diff --git a/Images/pvIcon.png b/images/pvIcon.png
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diff --git a/Images/replace.png b/images/replace.png
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diff --git a/Images/running_process.png b/images/running_process.png
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diff --git a/Images/selection-box-ring.png b/images/selection-box-ring.png
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rename from Installers/colormaps/BlueIn.map
rename to installers/colormaps/BlueIn.map
diff --git a/Installers/colormaps/BlueOut.map b/installers/colormaps/BlueOut.map
similarity index 100%
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rename to installers/colormaps/BlueOut.map
diff --git a/Installers/colormaps/BlueRed.map b/installers/colormaps/BlueRed.map
similarity index 100%
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diff --git a/Installers/colormaps/ColdFire.map b/installers/colormaps/ColdFire.map
similarity index 100%
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diff --git a/Installers/colormaps/Colors.map b/installers/colormaps/Colors.map
similarity index 100%
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diff --git a/Installers/colormaps/Cool.map b/installers/colormaps/Cool.map
similarity index 100%
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diff --git a/Installers/colormaps/Gamma1.map b/installers/colormaps/Gamma1.map
similarity index 100%
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diff --git a/Installers/colormaps/Gamma2.map b/installers/colormaps/Gamma2.map
similarity index 100%
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diff --git a/Installers/colormaps/GreenIn.map b/installers/colormaps/GreenIn.map
similarity index 100%
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similarity index 100%
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diff --git a/Installers/colormaps/GreenToWhite.map b/installers/colormaps/GreenToWhite.map
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diff --git a/Installers/colormaps/IDL-rainbow.map b/installers/colormaps/IDL-rainbow.map
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diff --git a/Installers/colormaps/Indigo.map b/installers/colormaps/Indigo.map
similarity index 100%
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diff --git a/Installers/colormaps/Jet.map b/installers/colormaps/Jet.map
similarity index 100%
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diff --git a/Installers/colormaps/Lace.map b/installers/colormaps/Lace.map
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diff --git a/Installers/colormaps/RBY.map b/installers/colormaps/RBY.map
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diff --git a/Installers/colormaps/RosePetals.map b/installers/colormaps/RosePetals.map
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diff --git a/Installers/colormaps/TouchOfBlues.map b/installers/colormaps/TouchOfBlues.map
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diff --git a/Installers/colormaps/Volcano.map b/installers/colormaps/Volcano.map
similarity index 100%
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diff --git a/Installers/colormaps/YellowToBlack.map b/installers/colormaps/YellowToBlack.map
similarity index 100%
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diff --git a/scripts/Examples/InstrumentView_Example.py b/scripts/Examples/InstrumentView_Example.py
index 0571ba5c39c2f81691e0e51ac8224086cf4e7840..8a1ac2bcb3514395e06c29855950c442748f9410 100644
--- a/scripts/Examples/InstrumentView_Example.py
+++ b/scripts/Examples/InstrumentView_Example.py
@@ -8,7 +8,7 @@ LoadRaw("LOQ48094.raw","LOQTest")
 
 insView = getInstrumentView("LOQTest")
 
-#insView.changeColorMap("../../../repo/Code/Mantid/Installers/colormaps/Jet.map")   # Change to the correct path
+#insView.changeColorMap("../../../repo/installers/colormaps/Jet.map")   # Change to the correct path
 
 insView.setColorMapRange(0.,195)
 # Or can set a minimum and maximum separately
diff --git a/Tools/ArielToMantidXML/ARIEL/INES/bank.ass b/tools/ArielToMantidXML/ARIEL/INES/bank.ass
similarity index 100%
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similarity index 100%
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rename to tools/ArielToMantidXML/ARIEL/INES/monitor.dat
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similarity index 100%
rename from Tools/ArielToMantidXML/ARIEL/INES/scintillator.dat
rename to tools/ArielToMantidXML/ARIEL/INES/scintillator.dat
diff --git a/Tools/ArielToMantidXML/ARIEL/INES/tube.dat b/tools/ArielToMantidXML/ARIEL/INES/tube.dat
similarity index 100%
rename from Tools/ArielToMantidXML/ARIEL/INES/tube.dat
rename to tools/ArielToMantidXML/ARIEL/INES/tube.dat
diff --git a/Tools/ArielToMantidXML/ARIEL/POLARIS/Bank_90deg.ass b/tools/ArielToMantidXML/ARIEL/POLARIS/Bank_90deg.ass
similarity index 100%
rename from Tools/ArielToMantidXML/ARIEL/POLARIS/Bank_90deg.ass
rename to tools/ArielToMantidXML/ARIEL/POLARIS/Bank_90deg.ass
diff --git a/Tools/ArielToMantidXML/ARIEL/POLARIS/Bank_90deg.dat b/tools/ArielToMantidXML/ARIEL/POLARIS/Bank_90deg.dat
similarity index 100%
rename from Tools/ArielToMantidXML/ARIEL/POLARIS/Bank_90deg.dat
rename to tools/ArielToMantidXML/ARIEL/POLARIS/Bank_90deg.dat
diff --git a/Tools/ArielToMantidXML/ARIEL/POLARIS/Bank_back.ass b/tools/ArielToMantidXML/ARIEL/POLARIS/Bank_back.ass
similarity index 100%
rename from Tools/ArielToMantidXML/ARIEL/POLARIS/Bank_back.ass
rename to tools/ArielToMantidXML/ARIEL/POLARIS/Bank_back.ass
diff --git a/Tools/ArielToMantidXML/ARIEL/POLARIS/Bank_back.dat b/tools/ArielToMantidXML/ARIEL/POLARIS/Bank_back.dat
similarity index 100%
rename from Tools/ArielToMantidXML/ARIEL/POLARIS/Bank_back.dat
rename to tools/ArielToMantidXML/ARIEL/POLARIS/Bank_back.dat
diff --git a/Tools/ArielToMantidXML/ARIEL/POLARIS/Bank_lowang.ass b/tools/ArielToMantidXML/ARIEL/POLARIS/Bank_lowang.ass
similarity index 100%
rename from Tools/ArielToMantidXML/ARIEL/POLARIS/Bank_lowang.ass
rename to tools/ArielToMantidXML/ARIEL/POLARIS/Bank_lowang.ass
diff --git a/Tools/ArielToMantidXML/ARIEL/POLARIS/Bank_lowang.dat b/tools/ArielToMantidXML/ARIEL/POLARIS/Bank_lowang.dat
similarity index 100%
rename from Tools/ArielToMantidXML/ARIEL/POLARIS/Bank_lowang.dat
rename to tools/ArielToMantidXML/ARIEL/POLARIS/Bank_lowang.dat
diff --git a/Tools/ArielToMantidXML/ARIEL/POLARIS/Bank_verylow.ass b/tools/ArielToMantidXML/ARIEL/POLARIS/Bank_verylow.ass
similarity index 100%
rename from Tools/ArielToMantidXML/ARIEL/POLARIS/Bank_verylow.ass
rename to tools/ArielToMantidXML/ARIEL/POLARIS/Bank_verylow.ass
diff --git a/Tools/ArielToMantidXML/ARIEL/POLARIS/Bank_verylow.dat b/tools/ArielToMantidXML/ARIEL/POLARIS/Bank_verylow.dat
similarity index 100%
rename from Tools/ArielToMantidXML/ARIEL/POLARIS/Bank_verylow.dat
rename to tools/ArielToMantidXML/ARIEL/POLARIS/Bank_verylow.dat
diff --git a/Tools/ArielToMantidXML/ARIEL/POLARIS/Module_90deg.ass b/tools/ArielToMantidXML/ARIEL/POLARIS/Module_90deg.ass
similarity index 100%
rename from Tools/ArielToMantidXML/ARIEL/POLARIS/Module_90deg.ass
rename to tools/ArielToMantidXML/ARIEL/POLARIS/Module_90deg.ass
diff --git a/Tools/ArielToMantidXML/ARIEL/POLARIS/Module_90deg.dat b/tools/ArielToMantidXML/ARIEL/POLARIS/Module_90deg.dat
similarity index 100%
rename from Tools/ArielToMantidXML/ARIEL/POLARIS/Module_90deg.dat
rename to tools/ArielToMantidXML/ARIEL/POLARIS/Module_90deg.dat
diff --git a/Tools/ArielToMantidXML/ARIEL/POLARIS/Module_brick.ass b/tools/ArielToMantidXML/ARIEL/POLARIS/Module_brick.ass
similarity index 100%
rename from Tools/ArielToMantidXML/ARIEL/POLARIS/Module_brick.ass
rename to tools/ArielToMantidXML/ARIEL/POLARIS/Module_brick.ass
diff --git a/Tools/ArielToMantidXML/ARIEL/POLARIS/Module_brick.dat b/tools/ArielToMantidXML/ARIEL/POLARIS/Module_brick.dat
similarity index 100%
rename from Tools/ArielToMantidXML/ARIEL/POLARIS/Module_brick.dat
rename to tools/ArielToMantidXML/ARIEL/POLARIS/Module_brick.dat
diff --git a/Tools/ArielToMantidXML/ARIEL/POLARIS/Module_lowang.ass b/tools/ArielToMantidXML/ARIEL/POLARIS/Module_lowang.ass
similarity index 100%
rename from Tools/ArielToMantidXML/ARIEL/POLARIS/Module_lowang.ass
rename to tools/ArielToMantidXML/ARIEL/POLARIS/Module_lowang.ass
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similarity index 100%
rename from Tools/ArielToMantidXML/ARIEL/POLARIS/Module_verylow.ass
rename to tools/ArielToMantidXML/ARIEL/POLARIS/Module_verylow.ass
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similarity index 100%
rename from Tools/ArielToMantidXML/ARIEL/POLARIS/Module_verylow.dat
rename to tools/ArielToMantidXML/ARIEL/POLARIS/Module_verylow.dat
diff --git a/Tools/ArielToMantidXML/ARIEL/POLARIS/Polaris.ass b/tools/ArielToMantidXML/ARIEL/POLARIS/Polaris.ass
similarity index 100%
rename from Tools/ArielToMantidXML/ARIEL/POLARIS/Polaris.ass
rename to tools/ArielToMantidXML/ARIEL/POLARIS/Polaris.ass
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similarity index 100%
rename from Tools/ArielToMantidXML/ARIEL/POLARIS/Polaris.dat
rename to tools/ArielToMantidXML/ARIEL/POLARIS/Polaris.dat
diff --git a/Tools/ArielToMantidXML/ARIEL/POLARIS/Scintillator_90deg.dat b/tools/ArielToMantidXML/ARIEL/POLARIS/Scintillator_90deg.dat
similarity index 100%
rename from Tools/ArielToMantidXML/ARIEL/POLARIS/Scintillator_90deg.dat
rename to tools/ArielToMantidXML/ARIEL/POLARIS/Scintillator_90deg.dat
diff --git a/Tools/ArielToMantidXML/ARIEL/POLARIS/Scintillator_brick.dat b/tools/ArielToMantidXML/ARIEL/POLARIS/Scintillator_brick.dat
similarity index 100%
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rename to tools/ArielToMantidXML/ARIEL/POLARIS/Scintillator_brick.dat
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similarity index 100%
rename from Tools/ArielToMantidXML/ARIEL/POLARIS/Scintillator_verylow.dat
rename to tools/ArielToMantidXML/ARIEL/POLARIS/Scintillator_verylow.dat
diff --git a/Tools/ArielToMantidXML/ARIEL/POLARIS/Tube_140.dat b/tools/ArielToMantidXML/ARIEL/POLARIS/Tube_140.dat
similarity index 100%
rename from Tools/ArielToMantidXML/ARIEL/POLARIS/Tube_140.dat
rename to tools/ArielToMantidXML/ARIEL/POLARIS/Tube_140.dat
diff --git a/Tools/ArielToMantidXML/ARIEL/POLARIS/Tube_149.dat b/tools/ArielToMantidXML/ARIEL/POLARIS/Tube_149.dat
similarity index 100%
rename from Tools/ArielToMantidXML/ARIEL/POLARIS/Tube_149.dat
rename to tools/ArielToMantidXML/ARIEL/POLARIS/Tube_149.dat
diff --git a/Tools/ArielToMantidXML/ARIEL/POLARIS/Tube_158.dat b/tools/ArielToMantidXML/ARIEL/POLARIS/Tube_158.dat
similarity index 100%
rename from Tools/ArielToMantidXML/ARIEL/POLARIS/Tube_158.dat
rename to tools/ArielToMantidXML/ARIEL/POLARIS/Tube_158.dat
diff --git a/Tools/ArielToMantidXML/ARIEL/POLARIS/Tube_167.dat b/tools/ArielToMantidXML/ARIEL/POLARIS/Tube_167.dat
similarity index 100%
rename from Tools/ArielToMantidXML/ARIEL/POLARIS/Tube_167.dat
rename to tools/ArielToMantidXML/ARIEL/POLARIS/Tube_167.dat
diff --git a/Tools/ArielToMantidXML/ARIEL/POLARIS/Tube_175.dat b/tools/ArielToMantidXML/ARIEL/POLARIS/Tube_175.dat
similarity index 100%
rename from Tools/ArielToMantidXML/ARIEL/POLARIS/Tube_175.dat
rename to tools/ArielToMantidXML/ARIEL/POLARIS/Tube_175.dat
diff --git a/Tools/ArielToMantidXML/ARIEL/POLARIS/Tube_184.dat b/tools/ArielToMantidXML/ARIEL/POLARIS/Tube_184.dat
similarity index 100%
rename from Tools/ArielToMantidXML/ARIEL/POLARIS/Tube_184.dat
rename to tools/ArielToMantidXML/ARIEL/POLARIS/Tube_184.dat
diff --git a/Tools/ArielToMantidXML/ARIEL/POLARIS/Tube_193.dat b/tools/ArielToMantidXML/ARIEL/POLARIS/Tube_193.dat
similarity index 100%
rename from Tools/ArielToMantidXML/ARIEL/POLARIS/Tube_193.dat
rename to tools/ArielToMantidXML/ARIEL/POLARIS/Tube_193.dat
diff --git a/Tools/ArielToMantidXML/ARIEL/POLARIS/Tube_202.dat b/tools/ArielToMantidXML/ARIEL/POLARIS/Tube_202.dat
similarity index 100%
rename from Tools/ArielToMantidXML/ARIEL/POLARIS/Tube_202.dat
rename to tools/ArielToMantidXML/ARIEL/POLARIS/Tube_202.dat
diff --git a/Tools/ArielToMantidXML/ARIEL/POLARIS/Tube_211.dat b/tools/ArielToMantidXML/ARIEL/POLARIS/Tube_211.dat
similarity index 100%
rename from Tools/ArielToMantidXML/ARIEL/POLARIS/Tube_211.dat
rename to tools/ArielToMantidXML/ARIEL/POLARIS/Tube_211.dat
diff --git a/Tools/ArielToMantidXML/ARIEL/POLARIS/Tube_220.dat b/tools/ArielToMantidXML/ARIEL/POLARIS/Tube_220.dat
similarity index 100%
rename from Tools/ArielToMantidXML/ARIEL/POLARIS/Tube_220.dat
rename to tools/ArielToMantidXML/ARIEL/POLARIS/Tube_220.dat
diff --git a/Tools/ArielToMantidXML/ARIEL/POLARIS/Tube_229.dat b/tools/ArielToMantidXML/ARIEL/POLARIS/Tube_229.dat
similarity index 100%
rename from Tools/ArielToMantidXML/ARIEL/POLARIS/Tube_229.dat
rename to tools/ArielToMantidXML/ARIEL/POLARIS/Tube_229.dat
diff --git a/Tools/ArielToMantidXML/ARIEL/POLARIS/Tube_237.dat b/tools/ArielToMantidXML/ARIEL/POLARIS/Tube_237.dat
similarity index 100%
rename from Tools/ArielToMantidXML/ARIEL/POLARIS/Tube_237.dat
rename to tools/ArielToMantidXML/ARIEL/POLARIS/Tube_237.dat
diff --git a/Tools/ArielToMantidXML/ARIEL/POLARIS/Tube_246.dat b/tools/ArielToMantidXML/ARIEL/POLARIS/Tube_246.dat
similarity index 100%
rename from Tools/ArielToMantidXML/ARIEL/POLARIS/Tube_246.dat
rename to tools/ArielToMantidXML/ARIEL/POLARIS/Tube_246.dat
diff --git a/Tools/ArielToMantidXML/ARIEL/POLARIS/Tube_255.dat b/tools/ArielToMantidXML/ARIEL/POLARIS/Tube_255.dat
similarity index 100%
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rename to tools/ArielToMantidXML/ARIEL/POLARIS/Tube_255.dat
diff --git a/Tools/ArielToMantidXML/ARIEL/POLARIS/Tube_264.dat b/tools/ArielToMantidXML/ARIEL/POLARIS/Tube_264.dat
similarity index 100%
rename from Tools/ArielToMantidXML/ARIEL/POLARIS/Tube_264.dat
rename to tools/ArielToMantidXML/ARIEL/POLARIS/Tube_264.dat
diff --git a/Tools/ArielToMantidXML/ARIEL/POLARIS/Tube_273.dat b/tools/ArielToMantidXML/ARIEL/POLARIS/Tube_273.dat
similarity index 100%
rename from Tools/ArielToMantidXML/ARIEL/POLARIS/Tube_273.dat
rename to tools/ArielToMantidXML/ARIEL/POLARIS/Tube_273.dat
diff --git a/Tools/ArielToMantidXML/ARIEL/POLARIS/Tube_282.dat b/tools/ArielToMantidXML/ARIEL/POLARIS/Tube_282.dat
similarity index 100%
rename from Tools/ArielToMantidXML/ARIEL/POLARIS/Tube_282.dat
rename to tools/ArielToMantidXML/ARIEL/POLARIS/Tube_282.dat
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rename to tools/ArielToMantidXML/ARIEL/POLARIS/Tube_291.dat
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rename to tools/ArielToMantidXML/ARIEL/POLARIS/Tube_300.dat
diff --git a/Tools/ArielToMantidXML/ARIEL/POLARIS/Tube_lowang.dat b/tools/ArielToMantidXML/ARIEL/POLARIS/Tube_lowang.dat
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rename from Tools/ArielToMantidXML/ARIEL/POLARIS/Tube_lowang.dat
rename to tools/ArielToMantidXML/ARIEL/POLARIS/Tube_lowang.dat
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similarity index 100%
rename from Tools/ArielToMantidXML/ARIEL/POLARIS/detector.dat
rename to tools/ArielToMantidXML/ARIEL/POLARIS/detector.dat
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rename to tools/ArielToMantidXML/ARIEL/POLARIS/instrument.dat
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rename to tools/ArielToMantidXML/ARIEL/POLARIS/module_back.ass
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diff --git a/Tools/Workflow/git/.gitignore b/tools/Workflow/git/.gitignore
similarity index 100%
rename from Tools/Workflow/git/.gitignore
rename to tools/Workflow/git/.gitignore
diff --git a/Tools/Workflow/git/Makefile b/tools/Workflow/git/Makefile
similarity index 100%
rename from Tools/Workflow/git/Makefile
rename to tools/Workflow/git/Makefile
diff --git a/Tools/Workflow/git/README.md b/tools/Workflow/git/README.md
similarity index 100%
rename from Tools/Workflow/git/README.md
rename to tools/Workflow/git/README.md
diff --git a/Tools/Workflow/git/git-checkbuild b/tools/Workflow/git/git-checkbuild
similarity index 100%
rename from Tools/Workflow/git/git-checkbuild
rename to tools/Workflow/git/git-checkbuild
diff --git a/Tools/Workflow/git/git-finish b/tools/Workflow/git/git-finish
similarity index 100%
rename from Tools/Workflow/git/git-finish
rename to tools/Workflow/git/git-finish
diff --git a/Tools/Workflow/git/git-new b/tools/Workflow/git/git-new
similarity index 100%
rename from Tools/Workflow/git/git-new
rename to tools/Workflow/git/git-new
diff --git a/Tools/Workflow/git/git-publish b/tools/Workflow/git/git-publish
similarity index 100%
rename from Tools/Workflow/git/git-publish
rename to tools/Workflow/git/git-publish
diff --git a/Tools/Workflow/git/git-test b/tools/Workflow/git/git-test
similarity index 100%
rename from Tools/Workflow/git/git-test
rename to tools/Workflow/git/git-test
diff --git a/Tools/Workflow/git/gitworkflow-helpers b/tools/Workflow/git/gitworkflow-helpers
similarity index 100%
rename from Tools/Workflow/git/gitworkflow-helpers
rename to tools/Workflow/git/gitworkflow-helpers
diff --git a/Tools/Workflow/git/install_git_macros.bat b/tools/Workflow/git/install_git_macros.bat
similarity index 100%
rename from Tools/Workflow/git/install_git_macros.bat
rename to tools/Workflow/git/install_git_macros.bat
diff --git a/Tools/reports/facility-code-changes.py b/tools/reports/facility-code-changes.py
similarity index 100%
rename from Tools/reports/facility-code-changes.py
rename to tools/reports/facility-code-changes.py
diff --git a/Tools/reports/release-list.py b/tools/reports/release-list.py
similarity index 100%
rename from Tools/reports/release-list.py
rename to tools/reports/release-list.py
diff --git a/Tools/scripts/AddAlgorithmWikiLinksToText.py b/tools/scripts/AddAlgorithmWikiLinksToText.py
similarity index 100%
rename from Tools/scripts/AddAlgorithmWikiLinksToText.py
rename to tools/scripts/AddAlgorithmWikiLinksToText.py
diff --git a/Tools/scripts/ConvertBadAlgmLinks.py b/tools/scripts/ConvertBadAlgmLinks.py
similarity index 100%
rename from Tools/scripts/ConvertBadAlgmLinks.py
rename to tools/scripts/ConvertBadAlgmLinks.py
diff --git a/Tools/scripts/ConvertToRST/ConvertWikiPage.py b/tools/scripts/ConvertToRST/ConvertWikiPage.py
similarity index 98%
rename from Tools/scripts/ConvertToRST/ConvertWikiPage.py
rename to tools/scripts/ConvertToRST/ConvertWikiPage.py
index 618c066e923864977aee829330c5b004a296337c..696cb94f8c0c04968d309297b3ee10bea224d892 100644
--- a/Tools/scripts/ConvertToRST/ConvertWikiPage.py
+++ b/tools/scripts/ConvertToRST/ConvertWikiPage.py
@@ -2,7 +2,7 @@
 # Converts mediawiki pages to rst pages for sphinx.
 # run with -h for command line arguments
 #
-# sample command C:\MantidInstall\bin\python.exe C:/Mantid/Code/Tools/scripts/ConvertToRST/ConvertWikiPage.py
+# sample command C:\MantidInstall\bin\python.exe C:/Mantid/tools/scripts/ConvertToRST/ConvertWikiPage.py
 #                       -o C:/Mantid/Code/Mantid/docs/source/training/MBC_Displaying_data_Formatting.rst
 #
 # pandoc must be installed an in the path
diff --git a/Tools/scripts/CorrectConceptLinksinAlgPages.py b/tools/scripts/CorrectConceptLinksinAlgPages.py
similarity index 100%
rename from Tools/scripts/CorrectConceptLinksinAlgPages.py
rename to tools/scripts/CorrectConceptLinksinAlgPages.py
diff --git a/Tools/scripts/FindIncompleteAlgRSTPages.py b/tools/scripts/FindIncompleteAlgRSTPages.py
similarity index 100%
rename from Tools/scripts/FindIncompleteAlgRSTPages.py
rename to tools/scripts/FindIncompleteAlgRSTPages.py
diff --git a/Tools/scripts/TestWikiPython.py b/tools/scripts/TestWikiPython.py
similarity index 100%
rename from Tools/scripts/TestWikiPython.py
rename to tools/scripts/TestWikiPython.py
diff --git a/Tools/scripts/extractAlgorithmNames.py b/tools/scripts/extractAlgorithmNames.py
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rename from Tools/scripts/extractAlgorithmNames.py
rename to tools/scripts/extractAlgorithmNames.py
diff --git a/Tools/scripts/extractAuthorNamesFromGit.py b/tools/scripts/extractAuthorNamesFromGit.py
similarity index 100%
rename from Tools/scripts/extractAuthorNamesFromGit.py
rename to tools/scripts/extractAuthorNamesFromGit.py
diff --git a/Tools/skipped_systemtests.py b/tools/skipped_systemtests.py
similarity index 100%
rename from Tools/skipped_systemtests.py
rename to tools/skipped_systemtests.py