diff --git a/CMakeLists.txt b/CMakeLists.txt
index ec4e36e39c..28a8e82730 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -73,16 +73,6 @@ file(RELATIVE_PATH relDir
 set(CMAKE_INSTALL_RPATH ${base} ${base}/${relDir})
 
 include(BuildType)
-include(LinkerSetup)
-include(FindFFTW)
-include(CompilerCache)
-include(ECMEnableSanitizers)
-include(Dependencies)
-if(CMAKE_SYSTEM_NAME MATCHES "Darwin")
-    include(MacOSBundle)
-endif()
-
-use_compiler_cache()
 
 if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/.git AND NOT EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/.git/hooks/pre-commit)
     message(WARNING
@@ -91,37 +81,6 @@ if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/.git AND NOT EXISTS ${CMAKE_CURRENT_SOURCE
         "and then run `pre-commit install` from the ${CMAKE_CURRENT_SOURCE_DIR} directory.")
 endif()
 
-add_library(mrtrix-common INTERFACE)
-add_library(mrtrix::common ALIAS mrtrix-common)
-target_compile_definitions(mrtrix-common INTERFACE
-    MRTRIX_BUILD_TYPE="${CMAKE_BUILD_TYPE}"
-    $<$<PLATFORM_ID:Windows>:MRTRIX_WINDOWS>
-    $<$<PLATFORM_ID:Darwin>:MRTRIX_MACOSX>
-    $<$<PLATFORM_ID:FreeBSD>:MRTRIX_FREEBSD>
-)
-
-if(MRTRIX_STL_DEBUGGING AND NOT CMAKE_BUILD_TYPE STREQUAL "Debug")
-    message(STATUS "Enabling STL debug mode")
-    target_compile_definitions(mrtrix-common INTERFACE
-        $<$<CXX_COMPILER_ID:MSVC>:_ITERATOR_DEBUG_LEVEL=1>
-        $<$<CXX_COMPILER_ID:GNU>:_GLIBCXX_DEBUG _GLIBCXX_DEBUG_PEDANTIC>
-        $<$<CXX_COMPILER_ID:Clang>:_LIBCPP_DEBUG=1>
-    )
-endif()
-
-if(MRTRIX_WARNINGS_AS_ERRORS)
-    message(STATUS "Enabling warnings as errors")
-    target_compile_options(mrtrix-common INTERFACE
-        $<$<CXX_COMPILER_ID:MSVC>:/WX>
-        $<$<CXX_COMPILER_ID:GNU,Clang>:-Werror>
-    )
-endif()
-
-# Allow compilation of big object of files in debug mode on MINGW
-if(MINGW AND CMAKE_BUILD_TYPE MATCHES "Debug")
-    target_compile_options(mrtrix-common INTERFACE -Wa,-mbig-obj)
-endif()
-
 
 if(MRTRIX_STRIP_CONDA AND DEFINED ENV{CONDA_PREFIX})
     message(WARNING "CONDA_PREFIX is set to ${CONDA_PREFIX}, adding conda diretories to CMAKE_IGNORE_PATH to avoid conflicts.\n"
@@ -145,11 +104,9 @@ if(COMPILER_PATH MATCHES "fsl/bin" OR LINKER_PATH MATCHES "fsl/bin")
     )
 endif()
 
-add_subdirectory(cmd)
-add_subdirectory(core)
+add_subdirectory(cpp)
 add_subdirectory(python)
 add_subdirectory(share)
-add_subdirectory(src)
 
 if(PROJECT_IS_TOP_LEVEL AND MRTRIX_BUILD_TESTS)
     add_subdirectory(testing)
diff --git a/cmake/MacOSBundle.cmake b/cmake/MacOSBundle.cmake
index 42bb702a7d..aa10bf9f94 100644
--- a/cmake/MacOSBundle.cmake
+++ b/cmake/MacOSBundle.cmake
@@ -1,7 +1,7 @@
 function(set_bundle_properties executable_name)
-    set(icon_files ${CMAKE_CURRENT_SOURCE_DIR}/../icons/macos/${executable_name}.icns)
+    set(icon_files ${PROJECT_SOURCE_DIR}/icons/macos/${executable_name}.icns)
     if(${executable_name} STREQUAL "mrview")
-        list(APPEND icon_files ${CMAKE_CURRENT_SOURCE_DIR}/../icons/macos/mrview_doc.icns)
+        list(APPEND icon_files ${PROJECT_SOURCE_DIR}/icons/macos/mrview_doc.icns)
     endif()
 
     string(TIMESTAMP CURRENT_YEAR "%Y")
@@ -10,14 +10,15 @@ function(set_bundle_properties executable_name)
     target_sources(${executable_name} PRIVATE ${icon_files})
     set_target_properties(${executable_name} PROPERTIES
         MACOSX_BUNDLE TRUE
-        MACOSX_BUNDLE_INFO_PLIST "${CMAKE_CURRENT_SOURCE_DIR}/../packaging/macos/bundle/${executable_name}.plist.in"
+        MACOSX_BUNDLE_INFO_PLIST "${PROJECT_SOURCE_DIR}/packaging/macos/bundle/${executable_name}.plist.in"
         RESOURCE "${icon_files}"
         INSTALL_RPATH "@executable_path/../../../../lib"
     )
 endfunction()
 
 function(install_bundle_wrapper_scripts executable_name)
-    set(wrapper_script ${CMAKE_CURRENT_SOURCE_DIR}/../packaging/macos/bundle/wrapper_launcher.sh.in)
+    message(STATUS "CURRENT_LIST_DIR: ${CMAKE_CURRENT_LIST_DIR}")
+    set(wrapper_script ${PROJECT_SOURCE_DIR}/packaging/macos/bundle/wrapper_launcher.sh.in)
     configure_file(${wrapper_script} ${PROJECT_BINARY_DIR}/bin/${executable_name}
         FILE_PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
         @ONLY
diff --git a/cpp/CMakeLists.txt b/cpp/CMakeLists.txt
new file mode 100644
index 0000000000..b9750d7dca
--- /dev/null
+++ b/cpp/CMakeLists.txt
@@ -0,0 +1,40 @@
+include(LinkerSetup)
+include(FindFFTW)
+include(ECMEnableSanitizers)
+include(Dependencies)
+include(CompilerCache)
+use_compiler_cache()
+
+add_library(mrtrix-common INTERFACE)
+add_library(mrtrix::common ALIAS mrtrix-common)
+target_compile_definitions(mrtrix-common INTERFACE
+    MRTRIX_BUILD_TYPE="${CMAKE_BUILD_TYPE}"
+    $<$<PLATFORM_ID:Windows>:MRTRIX_WINDOWS>
+    $<$<PLATFORM_ID:Darwin>:MRTRIX_MACOSX>
+    $<$<PLATFORM_ID:FreeBSD>:MRTRIX_FREEBSD>
+)
+
+if(MRTRIX_STL_DEBUGGING AND NOT CMAKE_BUILD_TYPE STREQUAL "Debug")
+    message(STATUS "Enabling STL debug mode")
+    target_compile_definitions(mrtrix-common INTERFACE
+        $<$<CXX_COMPILER_ID:MSVC>:_ITERATOR_DEBUG_LEVEL=1>
+        $<$<CXX_COMPILER_ID:GNU>:_GLIBCXX_DEBUG _GLIBCXX_DEBUG_PEDANTIC>
+        $<$<CXX_COMPILER_ID:Clang>:_LIBCPP_DEBUG=1>
+    )
+endif()
+
+if(MRTRIX_WARNINGS_AS_ERRORS)
+    message(STATUS "Enabling warnings as errors")
+    target_compile_options(mrtrix-common INTERFACE
+        $<$<CXX_COMPILER_ID:MSVC>:/WX>
+        $<$<CXX_COMPILER_ID:GNU,Clang>:-Werror>
+    )
+endif()
+
+# Allow compilation of big object of files in debug mode on MINGW
+if(MINGW AND CMAKE_BUILD_TYPE MATCHES "Debug")
+    target_compile_options(mrtrix-common INTERFACE -Wa,-mbig-obj)
+endif()
+
+add_subdirectory(lib)
+add_subdirectory(cmd)
diff --git a/cmd/5tt2gmwmi.cpp b/cpp/cmd/5tt2gmwmi.cpp
similarity index 100%
rename from cmd/5tt2gmwmi.cpp
rename to cpp/cmd/5tt2gmwmi.cpp
diff --git a/cmd/5tt2vis.cpp b/cpp/cmd/5tt2vis.cpp
similarity index 100%
rename from cmd/5tt2vis.cpp
rename to cpp/cmd/5tt2vis.cpp
diff --git a/cmd/5ttcheck.cpp b/cpp/cmd/5ttcheck.cpp
similarity index 100%
rename from cmd/5ttcheck.cpp
rename to cpp/cmd/5ttcheck.cpp
diff --git a/cmd/5ttedit.cpp b/cpp/cmd/5ttedit.cpp
similarity index 100%
rename from cmd/5ttedit.cpp
rename to cpp/cmd/5ttedit.cpp
diff --git a/cmd/CMakeLists.txt b/cpp/cmd/CMakeLists.txt
similarity index 94%
rename from cmd/CMakeLists.txt
rename to cpp/cmd/CMakeLists.txt
index e6ede5619b..849abe5b54 100644
--- a/cmd/CMakeLists.txt
+++ b/cpp/cmd/CMakeLists.txt
@@ -1,3 +1,7 @@
+if(CMAKE_SYSTEM_NAME MATCHES "Darwin")
+    include(MacOSBundle)
+endif()
+
 set(GUI_CMD_SRCS mrview.cpp shview.cpp)
 
 file(GLOB HEADLESS_CMD_SRCS *.cpp)
@@ -8,7 +12,7 @@ endforeach(CMD)
 if(MRTRIX_USE_PCH)
     file(GENERATE OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/pch_cmd.cpp CONTENT "int main(){}")
     add_executable(pch_cmd ${CMAKE_CURRENT_BINARY_DIR}/pch_cmd.cpp)
-    target_include_directories(pch_cmd PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/../core)
+    target_include_directories(pch_cmd PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/../lib/core)
     target_link_libraries(pch_cmd PRIVATE Eigen3::Eigen half::half mrtrix::common)
     target_precompile_headers(pch_cmd PRIVATE
         [["app.h"]]
@@ -27,7 +31,7 @@ function(add_cmd CMD_SRC IS_GUI)
     add_executable(${CMD_NAME} ${CMD_SRC})
     target_link_libraries(${CMD_NAME} PRIVATE
         $<IF:$<BOOL:${IS_GUI}>,mrtrix::gui,mrtrix::headless>
-        mrtrix::exec-version-lib
+        mrtrix::cmd-version-lib
     )
     set_target_properties(${CMD_NAME} PROPERTIES
         LINK_DEPENDS_NO_SHARED true
diff --git a/cmd/afdconnectivity.cpp b/cpp/cmd/afdconnectivity.cpp
similarity index 99%
rename from cmd/afdconnectivity.cpp
rename to cpp/cmd/afdconnectivity.cpp
index 617a242679..5d0023d63d 100644
--- a/cmd/afdconnectivity.cpp
+++ b/cpp/cmd/afdconnectivity.cpp
@@ -23,7 +23,7 @@
 #include "dwi/tractography/mapping/mapping.h"
 #include "dwi/tractography/properties.h"
 #include "memory.h"
-#include "version.h"
+#include "mrtrix_version.h"
 
 using namespace MR;
 using namespace MR::DWI;
diff --git a/cmd/amp2response.cpp b/cpp/cmd/amp2response.cpp
similarity index 100%
rename from cmd/amp2response.cpp
rename to cpp/cmd/amp2response.cpp
diff --git a/cmd/amp2sh.cpp b/cpp/cmd/amp2sh.cpp
similarity index 100%
rename from cmd/amp2sh.cpp
rename to cpp/cmd/amp2sh.cpp
diff --git a/cmd/connectome2tck.cpp b/cpp/cmd/connectome2tck.cpp
similarity index 100%
rename from cmd/connectome2tck.cpp
rename to cpp/cmd/connectome2tck.cpp
diff --git a/cmd/connectomeedit.cpp b/cpp/cmd/connectomeedit.cpp
similarity index 100%
rename from cmd/connectomeedit.cpp
rename to cpp/cmd/connectomeedit.cpp
diff --git a/cmd/connectomestats.cpp b/cpp/cmd/connectomestats.cpp
similarity index 100%
rename from cmd/connectomestats.cpp
rename to cpp/cmd/connectomestats.cpp
diff --git a/cmd/dcmedit.cpp b/cpp/cmd/dcmedit.cpp
similarity index 100%
rename from cmd/dcmedit.cpp
rename to cpp/cmd/dcmedit.cpp
diff --git a/cmd/dcminfo.cpp b/cpp/cmd/dcminfo.cpp
similarity index 100%
rename from cmd/dcminfo.cpp
rename to cpp/cmd/dcminfo.cpp
diff --git a/cmd/dirflip.cpp b/cpp/cmd/dirflip.cpp
similarity index 100%
rename from cmd/dirflip.cpp
rename to cpp/cmd/dirflip.cpp
diff --git a/cmd/dirgen.cpp b/cpp/cmd/dirgen.cpp
similarity index 100%
rename from cmd/dirgen.cpp
rename to cpp/cmd/dirgen.cpp
diff --git a/cmd/dirmerge.cpp b/cpp/cmd/dirmerge.cpp
similarity index 100%
rename from cmd/dirmerge.cpp
rename to cpp/cmd/dirmerge.cpp
diff --git a/cmd/dirorder.cpp b/cpp/cmd/dirorder.cpp
similarity index 100%
rename from cmd/dirorder.cpp
rename to cpp/cmd/dirorder.cpp
diff --git a/cmd/dirrotate.cpp b/cpp/cmd/dirrotate.cpp
similarity index 100%
rename from cmd/dirrotate.cpp
rename to cpp/cmd/dirrotate.cpp
diff --git a/cmd/dirsplit.cpp b/cpp/cmd/dirsplit.cpp
similarity index 100%
rename from cmd/dirsplit.cpp
rename to cpp/cmd/dirsplit.cpp
diff --git a/cmd/dirstat.cpp b/cpp/cmd/dirstat.cpp
similarity index 100%
rename from cmd/dirstat.cpp
rename to cpp/cmd/dirstat.cpp
diff --git a/cmd/dwi2adc.cpp b/cpp/cmd/dwi2adc.cpp
similarity index 100%
rename from cmd/dwi2adc.cpp
rename to cpp/cmd/dwi2adc.cpp
diff --git a/cmd/dwi2fod.cpp b/cpp/cmd/dwi2fod.cpp
similarity index 100%
rename from cmd/dwi2fod.cpp
rename to cpp/cmd/dwi2fod.cpp
diff --git a/cmd/dwi2tensor.cpp b/cpp/cmd/dwi2tensor.cpp
similarity index 100%
rename from cmd/dwi2tensor.cpp
rename to cpp/cmd/dwi2tensor.cpp
diff --git a/cmd/dwidenoise.cpp b/cpp/cmd/dwidenoise.cpp
similarity index 100%
rename from cmd/dwidenoise.cpp
rename to cpp/cmd/dwidenoise.cpp
diff --git a/cmd/dwiextract.cpp b/cpp/cmd/dwiextract.cpp
similarity index 100%
rename from cmd/dwiextract.cpp
rename to cpp/cmd/dwiextract.cpp
diff --git a/cmd/fixel2peaks.cpp b/cpp/cmd/fixel2peaks.cpp
similarity index 100%
rename from cmd/fixel2peaks.cpp
rename to cpp/cmd/fixel2peaks.cpp
diff --git a/cmd/fixel2sh.cpp b/cpp/cmd/fixel2sh.cpp
similarity index 100%
rename from cmd/fixel2sh.cpp
rename to cpp/cmd/fixel2sh.cpp
diff --git a/cmd/fixel2tsf.cpp b/cpp/cmd/fixel2tsf.cpp
similarity index 100%
rename from cmd/fixel2tsf.cpp
rename to cpp/cmd/fixel2tsf.cpp
diff --git a/cmd/fixel2voxel.cpp b/cpp/cmd/fixel2voxel.cpp
similarity index 100%
rename from cmd/fixel2voxel.cpp
rename to cpp/cmd/fixel2voxel.cpp
diff --git a/cmd/fixelcfestats.cpp b/cpp/cmd/fixelcfestats.cpp
similarity index 100%
rename from cmd/fixelcfestats.cpp
rename to cpp/cmd/fixelcfestats.cpp
diff --git a/cmd/fixelconnectivity.cpp b/cpp/cmd/fixelconnectivity.cpp
similarity index 100%
rename from cmd/fixelconnectivity.cpp
rename to cpp/cmd/fixelconnectivity.cpp
diff --git a/cmd/fixelconvert.cpp b/cpp/cmd/fixelconvert.cpp
similarity index 100%
rename from cmd/fixelconvert.cpp
rename to cpp/cmd/fixelconvert.cpp
diff --git a/cmd/fixelcorrespondence.cpp b/cpp/cmd/fixelcorrespondence.cpp
similarity index 100%
rename from cmd/fixelcorrespondence.cpp
rename to cpp/cmd/fixelcorrespondence.cpp
diff --git a/cmd/fixelcrop.cpp b/cpp/cmd/fixelcrop.cpp
similarity index 100%
rename from cmd/fixelcrop.cpp
rename to cpp/cmd/fixelcrop.cpp
diff --git a/cmd/fixelfilter.cpp b/cpp/cmd/fixelfilter.cpp
similarity index 100%
rename from cmd/fixelfilter.cpp
rename to cpp/cmd/fixelfilter.cpp
diff --git a/cmd/fixelreorient.cpp b/cpp/cmd/fixelreorient.cpp
similarity index 100%
rename from cmd/fixelreorient.cpp
rename to cpp/cmd/fixelreorient.cpp
diff --git a/cmd/fod2dec.cpp b/cpp/cmd/fod2dec.cpp
similarity index 100%
rename from cmd/fod2dec.cpp
rename to cpp/cmd/fod2dec.cpp
diff --git a/cmd/fod2fixel.cpp b/cpp/cmd/fod2fixel.cpp
similarity index 100%
rename from cmd/fod2fixel.cpp
rename to cpp/cmd/fod2fixel.cpp
diff --git a/cmd/label2colour.cpp b/cpp/cmd/label2colour.cpp
similarity index 100%
rename from cmd/label2colour.cpp
rename to cpp/cmd/label2colour.cpp
diff --git a/cmd/label2mesh.cpp b/cpp/cmd/label2mesh.cpp
similarity index 100%
rename from cmd/label2mesh.cpp
rename to cpp/cmd/label2mesh.cpp
diff --git a/cmd/labelconvert.cpp b/cpp/cmd/labelconvert.cpp
similarity index 100%
rename from cmd/labelconvert.cpp
rename to cpp/cmd/labelconvert.cpp
diff --git a/cmd/labelstats.cpp b/cpp/cmd/labelstats.cpp
similarity index 100%
rename from cmd/labelstats.cpp
rename to cpp/cmd/labelstats.cpp
diff --git a/cmd/maskdump.cpp b/cpp/cmd/maskdump.cpp
similarity index 100%
rename from cmd/maskdump.cpp
rename to cpp/cmd/maskdump.cpp
diff --git a/cmd/maskfilter.cpp b/cpp/cmd/maskfilter.cpp
similarity index 100%
rename from cmd/maskfilter.cpp
rename to cpp/cmd/maskfilter.cpp
diff --git a/cmd/mesh2voxel.cpp b/cpp/cmd/mesh2voxel.cpp
similarity index 100%
rename from cmd/mesh2voxel.cpp
rename to cpp/cmd/mesh2voxel.cpp
diff --git a/cmd/meshconvert.cpp b/cpp/cmd/meshconvert.cpp
similarity index 100%
rename from cmd/meshconvert.cpp
rename to cpp/cmd/meshconvert.cpp
diff --git a/cmd/meshfilter.cpp b/cpp/cmd/meshfilter.cpp
similarity index 100%
rename from cmd/meshfilter.cpp
rename to cpp/cmd/meshfilter.cpp
diff --git a/cmd/mraverageheader.cpp b/cpp/cmd/mraverageheader.cpp
similarity index 100%
rename from cmd/mraverageheader.cpp
rename to cpp/cmd/mraverageheader.cpp
diff --git a/cmd/mrcalc.cpp b/cpp/cmd/mrcalc.cpp
similarity index 100%
rename from cmd/mrcalc.cpp
rename to cpp/cmd/mrcalc.cpp
diff --git a/cmd/mrcat.cpp b/cpp/cmd/mrcat.cpp
similarity index 100%
rename from cmd/mrcat.cpp
rename to cpp/cmd/mrcat.cpp
diff --git a/cmd/mrcentroid.cpp b/cpp/cmd/mrcentroid.cpp
similarity index 100%
rename from cmd/mrcentroid.cpp
rename to cpp/cmd/mrcentroid.cpp
diff --git a/cmd/mrcheckerboardmask.cpp b/cpp/cmd/mrcheckerboardmask.cpp
similarity index 100%
rename from cmd/mrcheckerboardmask.cpp
rename to cpp/cmd/mrcheckerboardmask.cpp
diff --git a/cmd/mrclusterstats.cpp b/cpp/cmd/mrclusterstats.cpp
similarity index 100%
rename from cmd/mrclusterstats.cpp
rename to cpp/cmd/mrclusterstats.cpp
diff --git a/cmd/mrcolour.cpp b/cpp/cmd/mrcolour.cpp
similarity index 100%
rename from cmd/mrcolour.cpp
rename to cpp/cmd/mrcolour.cpp
diff --git a/cmd/mrconvert.cpp b/cpp/cmd/mrconvert.cpp
similarity index 100%
rename from cmd/mrconvert.cpp
rename to cpp/cmd/mrconvert.cpp
diff --git a/cmd/mrdegibbs.cpp b/cpp/cmd/mrdegibbs.cpp
similarity index 100%
rename from cmd/mrdegibbs.cpp
rename to cpp/cmd/mrdegibbs.cpp
diff --git a/cmd/mrdump.cpp b/cpp/cmd/mrdump.cpp
similarity index 100%
rename from cmd/mrdump.cpp
rename to cpp/cmd/mrdump.cpp
diff --git a/cmd/mredit.cpp b/cpp/cmd/mredit.cpp
similarity index 100%
rename from cmd/mredit.cpp
rename to cpp/cmd/mredit.cpp
diff --git a/cmd/mrfilter.cpp b/cpp/cmd/mrfilter.cpp
similarity index 100%
rename from cmd/mrfilter.cpp
rename to cpp/cmd/mrfilter.cpp
diff --git a/cmd/mrgrid.cpp b/cpp/cmd/mrgrid.cpp
similarity index 100%
rename from cmd/mrgrid.cpp
rename to cpp/cmd/mrgrid.cpp
diff --git a/cmd/mrhistmatch.cpp b/cpp/cmd/mrhistmatch.cpp
similarity index 100%
rename from cmd/mrhistmatch.cpp
rename to cpp/cmd/mrhistmatch.cpp
diff --git a/cmd/mrhistogram.cpp b/cpp/cmd/mrhistogram.cpp
similarity index 100%
rename from cmd/mrhistogram.cpp
rename to cpp/cmd/mrhistogram.cpp
diff --git a/cmd/mrinfo.cpp b/cpp/cmd/mrinfo.cpp
similarity index 100%
rename from cmd/mrinfo.cpp
rename to cpp/cmd/mrinfo.cpp
diff --git a/cmd/mrmath.cpp b/cpp/cmd/mrmath.cpp
similarity index 100%
rename from cmd/mrmath.cpp
rename to cpp/cmd/mrmath.cpp
diff --git a/cmd/mrmetric.cpp b/cpp/cmd/mrmetric.cpp
similarity index 100%
rename from cmd/mrmetric.cpp
rename to cpp/cmd/mrmetric.cpp
diff --git a/cmd/mrregister.cpp b/cpp/cmd/mrregister.cpp
similarity index 100%
rename from cmd/mrregister.cpp
rename to cpp/cmd/mrregister.cpp
diff --git a/cmd/mrstats.cpp b/cpp/cmd/mrstats.cpp
similarity index 100%
rename from cmd/mrstats.cpp
rename to cpp/cmd/mrstats.cpp
diff --git a/cmd/mrthreshold.cpp b/cpp/cmd/mrthreshold.cpp
similarity index 100%
rename from cmd/mrthreshold.cpp
rename to cpp/cmd/mrthreshold.cpp
diff --git a/cmd/mrtransform.cpp b/cpp/cmd/mrtransform.cpp
similarity index 100%
rename from cmd/mrtransform.cpp
rename to cpp/cmd/mrtransform.cpp
diff --git a/cmd/mrview.cpp b/cpp/cmd/mrview.cpp
similarity index 100%
rename from cmd/mrview.cpp
rename to cpp/cmd/mrview.cpp
diff --git a/cmd/mtnormalise.cpp b/cpp/cmd/mtnormalise.cpp
similarity index 100%
rename from cmd/mtnormalise.cpp
rename to cpp/cmd/mtnormalise.cpp
diff --git a/cmd/peaks2amp.cpp b/cpp/cmd/peaks2amp.cpp
similarity index 100%
rename from cmd/peaks2amp.cpp
rename to cpp/cmd/peaks2amp.cpp
diff --git a/cmd/peaks2fixel.cpp b/cpp/cmd/peaks2fixel.cpp
similarity index 100%
rename from cmd/peaks2fixel.cpp
rename to cpp/cmd/peaks2fixel.cpp
diff --git a/cmd/sh2amp.cpp b/cpp/cmd/sh2amp.cpp
similarity index 100%
rename from cmd/sh2amp.cpp
rename to cpp/cmd/sh2amp.cpp
diff --git a/cmd/sh2peaks.cpp b/cpp/cmd/sh2peaks.cpp
similarity index 100%
rename from cmd/sh2peaks.cpp
rename to cpp/cmd/sh2peaks.cpp
diff --git a/cmd/sh2power.cpp b/cpp/cmd/sh2power.cpp
similarity index 100%
rename from cmd/sh2power.cpp
rename to cpp/cmd/sh2power.cpp
diff --git a/cmd/sh2response.cpp b/cpp/cmd/sh2response.cpp
similarity index 100%
rename from cmd/sh2response.cpp
rename to cpp/cmd/sh2response.cpp
diff --git a/cmd/shbasis.cpp b/cpp/cmd/shbasis.cpp
similarity index 100%
rename from cmd/shbasis.cpp
rename to cpp/cmd/shbasis.cpp
diff --git a/cmd/shconv.cpp b/cpp/cmd/shconv.cpp
similarity index 100%
rename from cmd/shconv.cpp
rename to cpp/cmd/shconv.cpp
diff --git a/cmd/shview.cpp b/cpp/cmd/shview.cpp
similarity index 100%
rename from cmd/shview.cpp
rename to cpp/cmd/shview.cpp
diff --git a/cmd/tck2connectome.cpp b/cpp/cmd/tck2connectome.cpp
similarity index 100%
rename from cmd/tck2connectome.cpp
rename to cpp/cmd/tck2connectome.cpp
diff --git a/cmd/tck2fixel.cpp b/cpp/cmd/tck2fixel.cpp
similarity index 100%
rename from cmd/tck2fixel.cpp
rename to cpp/cmd/tck2fixel.cpp
diff --git a/cmd/tckconvert.cpp b/cpp/cmd/tckconvert.cpp
similarity index 100%
rename from cmd/tckconvert.cpp
rename to cpp/cmd/tckconvert.cpp
diff --git a/cmd/tckdfc.cpp b/cpp/cmd/tckdfc.cpp
similarity index 100%
rename from cmd/tckdfc.cpp
rename to cpp/cmd/tckdfc.cpp
diff --git a/cmd/tckedit.cpp b/cpp/cmd/tckedit.cpp
similarity index 100%
rename from cmd/tckedit.cpp
rename to cpp/cmd/tckedit.cpp
diff --git a/cmd/tckgen.cpp b/cpp/cmd/tckgen.cpp
similarity index 100%
rename from cmd/tckgen.cpp
rename to cpp/cmd/tckgen.cpp
diff --git a/cmd/tckglobal.cpp b/cpp/cmd/tckglobal.cpp
similarity index 100%
rename from cmd/tckglobal.cpp
rename to cpp/cmd/tckglobal.cpp
diff --git a/cmd/tckinfo.cpp b/cpp/cmd/tckinfo.cpp
similarity index 100%
rename from cmd/tckinfo.cpp
rename to cpp/cmd/tckinfo.cpp
diff --git a/cmd/tckmap.cpp b/cpp/cmd/tckmap.cpp
similarity index 100%
rename from cmd/tckmap.cpp
rename to cpp/cmd/tckmap.cpp
diff --git a/cmd/tckresample.cpp b/cpp/cmd/tckresample.cpp
similarity index 100%
rename from cmd/tckresample.cpp
rename to cpp/cmd/tckresample.cpp
diff --git a/cmd/tcksample.cpp b/cpp/cmd/tcksample.cpp
similarity index 100%
rename from cmd/tcksample.cpp
rename to cpp/cmd/tcksample.cpp
diff --git a/cmd/tcksift.cpp b/cpp/cmd/tcksift.cpp
similarity index 100%
rename from cmd/tcksift.cpp
rename to cpp/cmd/tcksift.cpp
diff --git a/cmd/tcksift2.cpp b/cpp/cmd/tcksift2.cpp
similarity index 100%
rename from cmd/tcksift2.cpp
rename to cpp/cmd/tcksift2.cpp
diff --git a/cmd/tckstats.cpp b/cpp/cmd/tckstats.cpp
similarity index 100%
rename from cmd/tckstats.cpp
rename to cpp/cmd/tckstats.cpp
diff --git a/cmd/tcktransform.cpp b/cpp/cmd/tcktransform.cpp
similarity index 100%
rename from cmd/tcktransform.cpp
rename to cpp/cmd/tcktransform.cpp
diff --git a/cmd/tensor2metric.cpp b/cpp/cmd/tensor2metric.cpp
similarity index 100%
rename from cmd/tensor2metric.cpp
rename to cpp/cmd/tensor2metric.cpp
diff --git a/cmd/transformcalc.cpp b/cpp/cmd/transformcalc.cpp
similarity index 100%
rename from cmd/transformcalc.cpp
rename to cpp/cmd/transformcalc.cpp
diff --git a/cmd/transformcompose.cpp b/cpp/cmd/transformcompose.cpp
similarity index 100%
rename from cmd/transformcompose.cpp
rename to cpp/cmd/transformcompose.cpp
diff --git a/cmd/transformconvert.cpp b/cpp/cmd/transformconvert.cpp
similarity index 100%
rename from cmd/transformconvert.cpp
rename to cpp/cmd/transformconvert.cpp
diff --git a/cmd/tsfdivide.cpp b/cpp/cmd/tsfdivide.cpp
similarity index 100%
rename from cmd/tsfdivide.cpp
rename to cpp/cmd/tsfdivide.cpp
diff --git a/cmd/tsfinfo.cpp b/cpp/cmd/tsfinfo.cpp
similarity index 100%
rename from cmd/tsfinfo.cpp
rename to cpp/cmd/tsfinfo.cpp
diff --git a/cmd/tsfmult.cpp b/cpp/cmd/tsfmult.cpp
similarity index 100%
rename from cmd/tsfmult.cpp
rename to cpp/cmd/tsfmult.cpp
diff --git a/cmd/tsfsmooth.cpp b/cpp/cmd/tsfsmooth.cpp
similarity index 100%
rename from cmd/tsfsmooth.cpp
rename to cpp/cmd/tsfsmooth.cpp
diff --git a/cmd/tsfthreshold.cpp b/cpp/cmd/tsfthreshold.cpp
similarity index 100%
rename from cmd/tsfthreshold.cpp
rename to cpp/cmd/tsfthreshold.cpp
diff --git a/cmd/tsfvalidate.cpp b/cpp/cmd/tsfvalidate.cpp
similarity index 100%
rename from cmd/tsfvalidate.cpp
rename to cpp/cmd/tsfvalidate.cpp
diff --git a/cmd/vectorstats.cpp b/cpp/cmd/vectorstats.cpp
similarity index 100%
rename from cmd/vectorstats.cpp
rename to cpp/cmd/vectorstats.cpp
diff --git a/cmd/voxel2fixel.cpp b/cpp/cmd/voxel2fixel.cpp
similarity index 100%
rename from cmd/voxel2fixel.cpp
rename to cpp/cmd/voxel2fixel.cpp
diff --git a/cmd/voxel2mesh.cpp b/cpp/cmd/voxel2mesh.cpp
similarity index 100%
rename from cmd/voxel2mesh.cpp
rename to cpp/cmd/voxel2mesh.cpp
diff --git a/cmd/warp2metric.cpp b/cpp/cmd/warp2metric.cpp
similarity index 100%
rename from cmd/warp2metric.cpp
rename to cpp/cmd/warp2metric.cpp
diff --git a/cmd/warpconvert.cpp b/cpp/cmd/warpconvert.cpp
similarity index 100%
rename from cmd/warpconvert.cpp
rename to cpp/cmd/warpconvert.cpp
diff --git a/cmd/warpcorrect.cpp b/cpp/cmd/warpcorrect.cpp
similarity index 100%
rename from cmd/warpcorrect.cpp
rename to cpp/cmd/warpcorrect.cpp
diff --git a/cmd/warpinit.cpp b/cpp/cmd/warpinit.cpp
similarity index 100%
rename from cmd/warpinit.cpp
rename to cpp/cmd/warpinit.cpp
diff --git a/cmd/warpinvert.cpp b/cpp/cmd/warpinvert.cpp
similarity index 100%
rename from cmd/warpinvert.cpp
rename to cpp/cmd/warpinvert.cpp
diff --git a/src/CMakeLists.txt b/cpp/lib/CMakeLists.txt
similarity index 50%
rename from src/CMakeLists.txt
rename to cpp/lib/CMakeLists.txt
index 55c51f5ecd..77dad15cff 100644
--- a/src/CMakeLists.txt
+++ b/cpp/lib/CMakeLists.txt
@@ -1,3 +1,23 @@
+include(CheckSymbolExists)
+find_package(ZLIB REQUIRED)
+find_package(FFTW REQUIRED)
+find_package(Git QUIET)
+find_package(Threads REQUIRED)
+find_package(PNG QUIET)
+if(PNG_FOUND)
+    message(STATUS "Found PNG: ${PNG_LIBRARIES}")
+endif()
+
+# Check to see if we can use lgamma_r() function in custom Math::betaincreg()
+# The function is defined under _REENTRANT on some systems (e.g. MacOS)
+list(APPEND CMAKE_REQUIRED_DEFINITIONS -D_REENTRANT)
+check_symbol_exists(lgamma_r "math.h" MRTRIX_HAVE_LGAMMA_R)
+list(REMOVE_AT CMAKE_REQUIRED_DEFINITIONS -1)
+
+if(NOT MRTRIX_HAVE_LGAMMA_R)
+    message(STATUS "No lgamma_r() function found; statistical inference may have poorer multi-threading performance")
+endif()
+
 file(GLOB_RECURSE HEADLESS_SOURCES *.h *.cpp)
 list(FILTER HEADLESS_SOURCES EXCLUDE REGEX "gui/.*")
 
@@ -6,10 +26,10 @@ file(GLOB_RECURSE GUI_SOURCES gui/*.h gui/*.cpp)
 if(MRTRIX_BUILD_GUI)
     if(MRTRIX_USE_QT5)
         find_package(Qt5 COMPONENTS Core Gui Widgets OpenGL Network REQUIRED)
-        qt5_add_resources(RCC_SOURCES ${CMAKE_CURRENT_SOURCE_DIR}/../icons/icons.qrc)
+        qt5_add_resources(RCC_SOURCES ${PROJECT_SOURCE_DIR}/icons/icons.qrc)
     else()
         find_package(Qt6 COMPONENTS Core Gui Widgets OpenGL Network OpenGLWidgets REQUIRED)
-        qt6_add_resources(RCC_SOURCES ${CMAKE_CURRENT_SOURCE_DIR}/../icons/icons.qrc)
+        qt6_add_resources(RCC_SOURCES ${PROJECT_SOURCE_DIR}/icons/icons.qrc)
     endif()
     # Explicitly log Qt's location since it's not done automatically by the FindQt module
     message(STATUS "Qt${QT_MAJOR_VERSION}_DIR is set to: ${Qt${QT_MAJOR_VERSION}_DIR}")
@@ -21,24 +41,44 @@ endif()
 find_package(Git QUIET)
 
 # Create version target and library
-set(EXEC_VERSION_CPP ${CMAKE_CURRENT_BINARY_DIR}/exec_version.cpp)
+set(MRTRIX_VERSION_CPP ${CMAKE_CURRENT_BINARY_DIR}/mrtrix_version.cpp)
+set(CMD_VERSION_CPP ${CMAKE_CURRENT_BINARY_DIR}/cmd_version.cpp)
+
+add_custom_target(cmd-version-target ALL
+    COMMAND ${CMAKE_COMMAND}
+        -D GIT_EXECUTABLE=${GIT_EXECUTABLE}
+        -D MRTRIX_BASE_VERSION=${MRTRIX_BASE_VERSION}
+        -D DST=${CMD_VERSION_CPP}
+        -D SRC=${CMAKE_CURRENT_SOURCE_DIR}/cmd_version.cpp.in
+        -P ${PROJECT_SOURCE_DIR}/cmake/FindVersion.cmake
+    WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+    COMMENT "Generating cmd_version.cpp"
+    BYPRODUCTS ${CMD_VERSION_CPP}
+    VERBATIM
+)
 
-add_custom_target(exec-version-target ALL
+add_custom_target(mrtrix-version-target ALL
     COMMAND ${CMAKE_COMMAND}
         -D GIT_EXECUTABLE=${GIT_EXECUTABLE}
         -D MRTRIX_BASE_VERSION=${MRTRIX_BASE_VERSION}
-        -D DST=${EXEC_VERSION_CPP}
-        -D SRC=${CMAKE_CURRENT_SOURCE_DIR}/exec_version.cpp.in
-        -P ${CMAKE_CURRENT_SOURCE_DIR}/../cmake/FindVersion.cmake
+        -D DST=${MRTRIX_VERSION_CPP}
+        -D SRC=${CMAKE_CURRENT_SOURCE_DIR}/mrtrix_version.cpp.in
+        -P ${PROJECT_SOURCE_DIR}/cmake/FindVersion.cmake
     WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
-    COMMENT "Generating exec_version.cpp for executables"
-    BYPRODUCTS ${EXEC_VERSION_CPP}
+    COMMENT "Generating mrtrix_version.cpp"
+    BYPRODUCTS ${MRTRIX_VERSION_CPP}
     VERBATIM
 )
 
-add_library(mrtrix-exec-version-lib STATIC ${EXEC_VERSION_CPP})
-add_library(mrtrix::exec-version-lib ALIAS mrtrix-exec-version-lib)
-add_dependencies(mrtrix-exec-version-lib exec-version-target)
+add_library(mrtrix-version-lib STATIC ${MRTRIX_VERSION_CPP})
+add_library(mrtrix::version-lib ALIAS mrtrix-version-lib)
+add_dependencies(mrtrix-version-lib mrtrix-version-target)
+
+add_library(mrtrix-cmd-version-lib STATIC ${CMD_VERSION_CPP})
+add_library(mrtrix::cmd-version-lib ALIAS mrtrix-cmd-version-lib)
+target_include_directories(mrtrix-cmd-version-lib PRIVATE ${CMAKE_CURRENT_SOURCE_DIR})
+add_dependencies(mrtrix-cmd-version-lib cmd-version-target)
+
 
 if(MRTRIX_BUILD_NON_CORE_STATIC)
     set(MRTRIX_LIBRARY_TYPE STATIC)
@@ -50,12 +90,13 @@ add_library(mrtrix-headless ${MRTRIX_LIBRARY_TYPE} ${HEADLESS_SOURCES})
 add_library(mrtrix::headless ALIAS mrtrix-headless)
 
 
-target_include_directories(mrtrix-exec-version-lib PUBLIC
+target_include_directories(mrtrix-version-lib PUBLIC
     ${CMAKE_CURRENT_SOURCE_DIR}
 )
 
 target_include_directories(mrtrix-headless PUBLIC
     ${CMAKE_CURRENT_SOURCE_DIR}
+    ${CMAKE_CURRENT_SOURCE_DIR}/core
 )
 
 if(MRTRIX_USE_PCH)
@@ -66,8 +107,31 @@ if(MRTRIX_USE_PCH)
     )
 endif()
 
+target_compile_definitions(mrtrix-headless PUBLIC
+    MRTRIX_BASE_VERSION="${MRTRIX_BASE_VERSION}"
+    $<$<BOOL:${MRTRIX_HAVE_LGAMMA_R}>:MRTRIX_HAVE_LGAMMA_R>
+)
+
+if(APPLE AND MRTRIX_HAVE_LGAMMA_R)
+    target_compile_definitions(mrtrix-headless PRIVATE _REENTRANT)
+endif()
+
+if(PNG_FOUND)
+    target_compile_definitions(mrtrix-headless PUBLIC MRTRIX_PNG_SUPPORT)
+    target_link_libraries(mrtrix-headless PUBLIC PNG::PNG)
+else()
+    message(WARNING "libpng not found, disabling PNG support")
+endif()
+
 target_link_libraries(mrtrix-headless PUBLIC
-    mrtrix::core
+    Eigen3::Eigen
+    ZLIB::ZLIB
+    ${FFTW_LIBRARIES}
+    mrtrix::common
+    Threads::Threads
+    nlohmann_json::nlohmann_json
+    nifti::nifti
+    half::half
 )
 
 if(MRTRIX_BUILD_GUI)
diff --git a/src/exec_version.cpp.in b/cpp/lib/cmd_version.cpp.in
similarity index 87%
rename from src/exec_version.cpp.in
rename to cpp/lib/cmd_version.cpp.in
index a424de082d..8bbac002c4 100644
--- a/src/exec_version.cpp.in
+++ b/cpp/lib/cmd_version.cpp.in
@@ -1,8 +1,8 @@
-#include "exec_version.h"
+#include "cmd_version.h"
 
 namespace MR {
   namespace App {
     extern const char* executable_uses_mrtrix_version;
     void set_executable_uses_mrtrix_version () { executable_uses_mrtrix_version = "@MRTRIX_VERSION@"; }
   }
-}
\ No newline at end of file
+}
diff --git a/src/exec_version.h b/cpp/lib/cmd_version.h
similarity index 100%
rename from src/exec_version.h
rename to cpp/lib/cmd_version.h
diff --git a/src/colourmap.cpp b/cpp/lib/colourmap.cpp
similarity index 100%
rename from src/colourmap.cpp
rename to cpp/lib/colourmap.cpp
diff --git a/src/colourmap.h b/cpp/lib/colourmap.h
similarity index 100%
rename from src/colourmap.h
rename to cpp/lib/colourmap.h
diff --git a/src/connectome/connectome.cpp b/cpp/lib/connectome/connectome.cpp
similarity index 100%
rename from src/connectome/connectome.cpp
rename to cpp/lib/connectome/connectome.cpp
diff --git a/src/connectome/connectome.h b/cpp/lib/connectome/connectome.h
similarity index 100%
rename from src/connectome/connectome.h
rename to cpp/lib/connectome/connectome.h
diff --git a/src/connectome/enhance.cpp b/cpp/lib/connectome/enhance.cpp
similarity index 100%
rename from src/connectome/enhance.cpp
rename to cpp/lib/connectome/enhance.cpp
diff --git a/src/connectome/enhance.h b/cpp/lib/connectome/enhance.h
similarity index 100%
rename from src/connectome/enhance.h
rename to cpp/lib/connectome/enhance.h
diff --git a/src/connectome/lut.cpp b/cpp/lib/connectome/lut.cpp
similarity index 100%
rename from src/connectome/lut.cpp
rename to cpp/lib/connectome/lut.cpp
diff --git a/src/connectome/lut.h b/cpp/lib/connectome/lut.h
similarity index 100%
rename from src/connectome/lut.h
rename to cpp/lib/connectome/lut.h
diff --git a/src/connectome/mat2vec.h b/cpp/lib/connectome/mat2vec.h
similarity index 100%
rename from src/connectome/mat2vec.h
rename to cpp/lib/connectome/mat2vec.h
diff --git a/core/CMakeLists.txt b/cpp/lib/core/CMakeLists.txt
similarity index 100%
rename from core/CMakeLists.txt
rename to cpp/lib/core/CMakeLists.txt
diff --git a/core/adapter/base.h b/cpp/lib/core/adapter/base.h
similarity index 100%
rename from core/adapter/base.h
rename to cpp/lib/core/adapter/base.h
diff --git a/core/adapter/extract.h b/cpp/lib/core/adapter/extract.h
similarity index 100%
rename from core/adapter/extract.h
rename to cpp/lib/core/adapter/extract.h
diff --git a/core/adapter/gaussian1D.h b/cpp/lib/core/adapter/gaussian1D.h
similarity index 100%
rename from core/adapter/gaussian1D.h
rename to cpp/lib/core/adapter/gaussian1D.h
diff --git a/core/adapter/gradient1D.h b/cpp/lib/core/adapter/gradient1D.h
similarity index 100%
rename from core/adapter/gradient1D.h
rename to cpp/lib/core/adapter/gradient1D.h
diff --git a/core/adapter/gradient3D.h b/cpp/lib/core/adapter/gradient3D.h
similarity index 100%
rename from core/adapter/gradient3D.h
rename to cpp/lib/core/adapter/gradient3D.h
diff --git a/core/adapter/jacobian.h b/cpp/lib/core/adapter/jacobian.h
similarity index 100%
rename from core/adapter/jacobian.h
rename to cpp/lib/core/adapter/jacobian.h
diff --git a/core/adapter/median.h b/cpp/lib/core/adapter/median.h
similarity index 100%
rename from core/adapter/median.h
rename to cpp/lib/core/adapter/median.h
diff --git a/core/adapter/neighbourhood3D.h b/cpp/lib/core/adapter/neighbourhood3D.h
similarity index 100%
rename from core/adapter/neighbourhood3D.h
rename to cpp/lib/core/adapter/neighbourhood3D.h
diff --git a/core/adapter/normalise3D.h b/cpp/lib/core/adapter/normalise3D.h
similarity index 100%
rename from core/adapter/normalise3D.h
rename to cpp/lib/core/adapter/normalise3D.h
diff --git a/core/adapter/permute_axes.h b/cpp/lib/core/adapter/permute_axes.h
similarity index 100%
rename from core/adapter/permute_axes.h
rename to cpp/lib/core/adapter/permute_axes.h
diff --git a/core/adapter/regrid.h b/cpp/lib/core/adapter/regrid.h
similarity index 100%
rename from core/adapter/regrid.h
rename to cpp/lib/core/adapter/regrid.h
diff --git a/core/adapter/replicate.h b/cpp/lib/core/adapter/replicate.h
similarity index 100%
rename from core/adapter/replicate.h
rename to cpp/lib/core/adapter/replicate.h
diff --git a/core/adapter/reslice.cpp b/cpp/lib/core/adapter/reslice.cpp
similarity index 100%
rename from core/adapter/reslice.cpp
rename to cpp/lib/core/adapter/reslice.cpp
diff --git a/core/adapter/reslice.h b/cpp/lib/core/adapter/reslice.h
similarity index 100%
rename from core/adapter/reslice.h
rename to cpp/lib/core/adapter/reslice.h
diff --git a/core/adapter/subset.h b/cpp/lib/core/adapter/subset.h
similarity index 100%
rename from core/adapter/subset.h
rename to cpp/lib/core/adapter/subset.h
diff --git a/core/adapter/warp.h b/cpp/lib/core/adapter/warp.h
similarity index 100%
rename from core/adapter/warp.h
rename to cpp/lib/core/adapter/warp.h
diff --git a/core/algo/copy.h b/cpp/lib/core/algo/copy.h
similarity index 100%
rename from core/algo/copy.h
rename to cpp/lib/core/algo/copy.h
diff --git a/core/algo/histogram.cpp b/cpp/lib/core/algo/histogram.cpp
similarity index 100%
rename from core/algo/histogram.cpp
rename to cpp/lib/core/algo/histogram.cpp
diff --git a/core/algo/histogram.h b/cpp/lib/core/algo/histogram.h
similarity index 100%
rename from core/algo/histogram.h
rename to cpp/lib/core/algo/histogram.h
diff --git a/core/algo/iterator.h b/cpp/lib/core/algo/iterator.h
similarity index 100%
rename from core/algo/iterator.h
rename to cpp/lib/core/algo/iterator.h
diff --git a/core/algo/loop.h b/cpp/lib/core/algo/loop.h
similarity index 100%
rename from core/algo/loop.h
rename to cpp/lib/core/algo/loop.h
diff --git a/core/algo/min_max.h b/cpp/lib/core/algo/min_max.h
similarity index 100%
rename from core/algo/min_max.h
rename to cpp/lib/core/algo/min_max.h
diff --git a/core/algo/neighbourhooditerator.h b/cpp/lib/core/algo/neighbourhooditerator.h
similarity index 100%
rename from core/algo/neighbourhooditerator.h
rename to cpp/lib/core/algo/neighbourhooditerator.h
diff --git a/core/algo/random_loop.h b/cpp/lib/core/algo/random_loop.h
similarity index 100%
rename from core/algo/random_loop.h
rename to cpp/lib/core/algo/random_loop.h
diff --git a/core/algo/random_threaded_loop.h b/cpp/lib/core/algo/random_threaded_loop.h
similarity index 100%
rename from core/algo/random_threaded_loop.h
rename to cpp/lib/core/algo/random_threaded_loop.h
diff --git a/core/algo/stochastic_threaded_loop.h b/cpp/lib/core/algo/stochastic_threaded_loop.h
similarity index 100%
rename from core/algo/stochastic_threaded_loop.h
rename to cpp/lib/core/algo/stochastic_threaded_loop.h
diff --git a/core/algo/threaded_copy.h b/cpp/lib/core/algo/threaded_copy.h
similarity index 100%
rename from core/algo/threaded_copy.h
rename to cpp/lib/core/algo/threaded_copy.h
diff --git a/core/algo/threaded_loop.h b/cpp/lib/core/algo/threaded_loop.h
similarity index 100%
rename from core/algo/threaded_loop.h
rename to cpp/lib/core/algo/threaded_loop.h
diff --git a/core/app.cpp b/cpp/lib/core/app.cpp
similarity index 100%
rename from core/app.cpp
rename to cpp/lib/core/app.cpp
diff --git a/core/app.h b/cpp/lib/core/app.h
similarity index 100%
rename from core/app.h
rename to cpp/lib/core/app.h
diff --git a/core/apply.h b/cpp/lib/core/apply.h
similarity index 100%
rename from core/apply.h
rename to cpp/lib/core/apply.h
diff --git a/core/axes.cpp b/cpp/lib/core/axes.cpp
similarity index 100%
rename from core/axes.cpp
rename to cpp/lib/core/axes.cpp
diff --git a/core/axes.h b/cpp/lib/core/axes.h
similarity index 100%
rename from core/axes.h
rename to cpp/lib/core/axes.h
diff --git a/core/cmdline_option.h b/cpp/lib/core/cmdline_option.h
similarity index 100%
rename from core/cmdline_option.h
rename to cpp/lib/core/cmdline_option.h
diff --git a/core/command.h b/cpp/lib/core/command.h
similarity index 99%
rename from core/command.h
rename to cpp/lib/core/command.h
index aec23d4415..5d4b9d44b6 100644
--- a/core/command.h
+++ b/cpp/lib/core/command.h
@@ -21,7 +21,7 @@
 #endif
 
 #include "app.h"
-#include "exec_version.h"
+#include "cmd_version.h"
 #include "mrtrix.h"
 #ifdef MRTRIX_PROJECT
 namespace MR {
diff --git a/core/datatype.cpp b/cpp/lib/core/datatype.cpp
similarity index 100%
rename from core/datatype.cpp
rename to cpp/lib/core/datatype.cpp
diff --git a/core/datatype.h b/cpp/lib/core/datatype.h
similarity index 100%
rename from core/datatype.h
rename to cpp/lib/core/datatype.h
diff --git a/core/debug.h b/cpp/lib/core/debug.h
similarity index 100%
rename from core/debug.h
rename to cpp/lib/core/debug.h
diff --git a/core/dwi/gradient.cpp b/cpp/lib/core/dwi/gradient.cpp
similarity index 100%
rename from core/dwi/gradient.cpp
rename to cpp/lib/core/dwi/gradient.cpp
diff --git a/core/dwi/gradient.h b/cpp/lib/core/dwi/gradient.h
similarity index 100%
rename from core/dwi/gradient.h
rename to cpp/lib/core/dwi/gradient.h
diff --git a/core/dwi/shells.cpp b/cpp/lib/core/dwi/shells.cpp
similarity index 100%
rename from core/dwi/shells.cpp
rename to cpp/lib/core/dwi/shells.cpp
diff --git a/core/dwi/shells.h b/cpp/lib/core/dwi/shells.h
similarity index 100%
rename from core/dwi/shells.h
rename to cpp/lib/core/dwi/shells.h
diff --git a/core/eigen_plugins/array.h b/cpp/lib/core/eigen_plugins/array.h
similarity index 100%
rename from core/eigen_plugins/array.h
rename to cpp/lib/core/eigen_plugins/array.h
diff --git a/core/eigen_plugins/dense_base.h b/cpp/lib/core/eigen_plugins/dense_base.h
similarity index 100%
rename from core/eigen_plugins/dense_base.h
rename to cpp/lib/core/eigen_plugins/dense_base.h
diff --git a/core/eigen_plugins/matrix.h b/cpp/lib/core/eigen_plugins/matrix.h
similarity index 100%
rename from core/eigen_plugins/matrix.h
rename to cpp/lib/core/eigen_plugins/matrix.h
diff --git a/core/exception.cpp b/cpp/lib/core/exception.cpp
similarity index 100%
rename from core/exception.cpp
rename to cpp/lib/core/exception.cpp
diff --git a/core/exception.h b/cpp/lib/core/exception.h
similarity index 100%
rename from core/exception.h
rename to cpp/lib/core/exception.h
diff --git a/core/fetch_store.cpp b/cpp/lib/core/fetch_store.cpp
similarity index 100%
rename from core/fetch_store.cpp
rename to cpp/lib/core/fetch_store.cpp
diff --git a/core/fetch_store.h b/cpp/lib/core/fetch_store.h
similarity index 100%
rename from core/fetch_store.h
rename to cpp/lib/core/fetch_store.h
diff --git a/core/file/config.cpp b/cpp/lib/core/file/config.cpp
similarity index 100%
rename from core/file/config.cpp
rename to cpp/lib/core/file/config.cpp
diff --git a/core/file/config.h b/cpp/lib/core/file/config.h
similarity index 100%
rename from core/file/config.h
rename to cpp/lib/core/file/config.h
diff --git a/core/file/copy.h b/cpp/lib/core/file/copy.h
similarity index 100%
rename from core/file/copy.h
rename to cpp/lib/core/file/copy.h
diff --git a/core/file/dicom/csa_entry.h b/cpp/lib/core/file/dicom/csa_entry.h
similarity index 100%
rename from core/file/dicom/csa_entry.h
rename to cpp/lib/core/file/dicom/csa_entry.h
diff --git a/core/file/dicom/definitions.h b/cpp/lib/core/file/dicom/definitions.h
similarity index 100%
rename from core/file/dicom/definitions.h
rename to cpp/lib/core/file/dicom/definitions.h
diff --git a/core/file/dicom/dict.cpp b/cpp/lib/core/file/dicom/dict.cpp
similarity index 100%
rename from core/file/dicom/dict.cpp
rename to cpp/lib/core/file/dicom/dict.cpp
diff --git a/core/file/dicom/element.cpp b/cpp/lib/core/file/dicom/element.cpp
similarity index 100%
rename from core/file/dicom/element.cpp
rename to cpp/lib/core/file/dicom/element.cpp
diff --git a/core/file/dicom/element.h b/cpp/lib/core/file/dicom/element.h
similarity index 100%
rename from core/file/dicom/element.h
rename to cpp/lib/core/file/dicom/element.h
diff --git a/core/file/dicom/image.cpp b/cpp/lib/core/file/dicom/image.cpp
similarity index 100%
rename from core/file/dicom/image.cpp
rename to cpp/lib/core/file/dicom/image.cpp
diff --git a/core/file/dicom/image.h b/cpp/lib/core/file/dicom/image.h
similarity index 100%
rename from core/file/dicom/image.h
rename to cpp/lib/core/file/dicom/image.h
diff --git a/core/file/dicom/mapper.cpp b/cpp/lib/core/file/dicom/mapper.cpp
similarity index 100%
rename from core/file/dicom/mapper.cpp
rename to cpp/lib/core/file/dicom/mapper.cpp
diff --git a/core/file/dicom/mapper.h b/cpp/lib/core/file/dicom/mapper.h
similarity index 100%
rename from core/file/dicom/mapper.h
rename to cpp/lib/core/file/dicom/mapper.h
diff --git a/core/file/dicom/patient.cpp b/cpp/lib/core/file/dicom/patient.cpp
similarity index 100%
rename from core/file/dicom/patient.cpp
rename to cpp/lib/core/file/dicom/patient.cpp
diff --git a/core/file/dicom/patient.h b/cpp/lib/core/file/dicom/patient.h
similarity index 100%
rename from core/file/dicom/patient.h
rename to cpp/lib/core/file/dicom/patient.h
diff --git a/core/file/dicom/quick_scan.cpp b/cpp/lib/core/file/dicom/quick_scan.cpp
similarity index 100%
rename from core/file/dicom/quick_scan.cpp
rename to cpp/lib/core/file/dicom/quick_scan.cpp
diff --git a/core/file/dicom/quick_scan.h b/cpp/lib/core/file/dicom/quick_scan.h
similarity index 100%
rename from core/file/dicom/quick_scan.h
rename to cpp/lib/core/file/dicom/quick_scan.h
diff --git a/core/file/dicom/select_cmdline.cpp b/cpp/lib/core/file/dicom/select_cmdline.cpp
similarity index 100%
rename from core/file/dicom/select_cmdline.cpp
rename to cpp/lib/core/file/dicom/select_cmdline.cpp
diff --git a/core/file/dicom/series.cpp b/cpp/lib/core/file/dicom/series.cpp
similarity index 100%
rename from core/file/dicom/series.cpp
rename to cpp/lib/core/file/dicom/series.cpp
diff --git a/core/file/dicom/series.h b/cpp/lib/core/file/dicom/series.h
similarity index 100%
rename from core/file/dicom/series.h
rename to cpp/lib/core/file/dicom/series.h
diff --git a/core/file/dicom/study.cpp b/cpp/lib/core/file/dicom/study.cpp
similarity index 100%
rename from core/file/dicom/study.cpp
rename to cpp/lib/core/file/dicom/study.cpp
diff --git a/core/file/dicom/study.h b/cpp/lib/core/file/dicom/study.h
similarity index 100%
rename from core/file/dicom/study.h
rename to cpp/lib/core/file/dicom/study.h
diff --git a/core/file/dicom/tree.cpp b/cpp/lib/core/file/dicom/tree.cpp
similarity index 100%
rename from core/file/dicom/tree.cpp
rename to cpp/lib/core/file/dicom/tree.cpp
diff --git a/core/file/dicom/tree.h b/cpp/lib/core/file/dicom/tree.h
similarity index 100%
rename from core/file/dicom/tree.h
rename to cpp/lib/core/file/dicom/tree.h
diff --git a/core/file/entry.h b/cpp/lib/core/file/entry.h
similarity index 100%
rename from core/file/entry.h
rename to cpp/lib/core/file/entry.h
diff --git a/core/file/gz.h b/cpp/lib/core/file/gz.h
similarity index 100%
rename from core/file/gz.h
rename to cpp/lib/core/file/gz.h
diff --git a/core/file/json_utils.cpp b/cpp/lib/core/file/json_utils.cpp
similarity index 100%
rename from core/file/json_utils.cpp
rename to cpp/lib/core/file/json_utils.cpp
diff --git a/core/file/json_utils.h b/cpp/lib/core/file/json_utils.h
similarity index 100%
rename from core/file/json_utils.h
rename to cpp/lib/core/file/json_utils.h
diff --git a/core/file/key_value.cpp b/cpp/lib/core/file/key_value.cpp
similarity index 100%
rename from core/file/key_value.cpp
rename to cpp/lib/core/file/key_value.cpp
diff --git a/core/file/key_value.h b/cpp/lib/core/file/key_value.h
similarity index 100%
rename from core/file/key_value.h
rename to cpp/lib/core/file/key_value.h
diff --git a/core/file/matrix.h b/cpp/lib/core/file/matrix.h
similarity index 100%
rename from core/file/matrix.h
rename to cpp/lib/core/file/matrix.h
diff --git a/core/file/mgh.cpp b/cpp/lib/core/file/mgh.cpp
similarity index 100%
rename from core/file/mgh.cpp
rename to cpp/lib/core/file/mgh.cpp
diff --git a/core/file/mgh.h b/cpp/lib/core/file/mgh.h
similarity index 100%
rename from core/file/mgh.h
rename to cpp/lib/core/file/mgh.h
diff --git a/core/file/mmap.cpp b/cpp/lib/core/file/mmap.cpp
similarity index 100%
rename from core/file/mmap.cpp
rename to cpp/lib/core/file/mmap.cpp
diff --git a/core/file/mmap.h b/cpp/lib/core/file/mmap.h
similarity index 100%
rename from core/file/mmap.h
rename to cpp/lib/core/file/mmap.h
diff --git a/core/file/name_parser.cpp b/cpp/lib/core/file/name_parser.cpp
similarity index 100%
rename from core/file/name_parser.cpp
rename to cpp/lib/core/file/name_parser.cpp
diff --git a/core/file/name_parser.h b/cpp/lib/core/file/name_parser.h
similarity index 100%
rename from core/file/name_parser.h
rename to cpp/lib/core/file/name_parser.h
diff --git a/core/file/nifti_utils.cpp b/cpp/lib/core/file/nifti_utils.cpp
similarity index 100%
rename from core/file/nifti_utils.cpp
rename to cpp/lib/core/file/nifti_utils.cpp
diff --git a/core/file/nifti_utils.h b/cpp/lib/core/file/nifti_utils.h
similarity index 100%
rename from core/file/nifti_utils.h
rename to cpp/lib/core/file/nifti_utils.h
diff --git a/core/file/npy.cpp b/cpp/lib/core/file/npy.cpp
similarity index 100%
rename from core/file/npy.cpp
rename to cpp/lib/core/file/npy.cpp
diff --git a/core/file/npy.h b/cpp/lib/core/file/npy.h
similarity index 100%
rename from core/file/npy.h
rename to cpp/lib/core/file/npy.h
diff --git a/core/file/ofstream.cpp b/cpp/lib/core/file/ofstream.cpp
similarity index 100%
rename from core/file/ofstream.cpp
rename to cpp/lib/core/file/ofstream.cpp
diff --git a/core/file/ofstream.h b/cpp/lib/core/file/ofstream.h
similarity index 100%
rename from core/file/ofstream.h
rename to cpp/lib/core/file/ofstream.h
diff --git a/core/file/path.h b/cpp/lib/core/file/path.h
similarity index 100%
rename from core/file/path.h
rename to cpp/lib/core/file/path.h
diff --git a/core/file/png.cpp b/cpp/lib/core/file/png.cpp
similarity index 100%
rename from core/file/png.cpp
rename to cpp/lib/core/file/png.cpp
diff --git a/core/file/png.h b/cpp/lib/core/file/png.h
similarity index 100%
rename from core/file/png.h
rename to cpp/lib/core/file/png.h
diff --git a/core/file/pyconfig.h b/cpp/lib/core/file/pyconfig.h
similarity index 100%
rename from core/file/pyconfig.h
rename to cpp/lib/core/file/pyconfig.h
diff --git a/core/file/utils.cpp b/cpp/lib/core/file/utils.cpp
similarity index 100%
rename from core/file/utils.cpp
rename to cpp/lib/core/file/utils.cpp
diff --git a/core/file/utils.h b/cpp/lib/core/file/utils.h
similarity index 100%
rename from core/file/utils.h
rename to cpp/lib/core/file/utils.h
diff --git a/core/filter/base.h b/cpp/lib/core/filter/base.h
similarity index 100%
rename from core/filter/base.h
rename to cpp/lib/core/filter/base.h
diff --git a/core/filter/connected_components.cpp b/cpp/lib/core/filter/connected_components.cpp
similarity index 100%
rename from core/filter/connected_components.cpp
rename to cpp/lib/core/filter/connected_components.cpp
diff --git a/core/filter/connected_components.h b/cpp/lib/core/filter/connected_components.h
similarity index 100%
rename from core/filter/connected_components.h
rename to cpp/lib/core/filter/connected_components.h
diff --git a/core/filter/dilate.h b/cpp/lib/core/filter/dilate.h
similarity index 100%
rename from core/filter/dilate.h
rename to cpp/lib/core/filter/dilate.h
diff --git a/core/filter/erode.h b/cpp/lib/core/filter/erode.h
similarity index 100%
rename from core/filter/erode.h
rename to cpp/lib/core/filter/erode.h
diff --git a/core/filter/fill.h b/cpp/lib/core/filter/fill.h
similarity index 100%
rename from core/filter/fill.h
rename to cpp/lib/core/filter/fill.h
diff --git a/core/filter/gradient.h b/cpp/lib/core/filter/gradient.h
similarity index 100%
rename from core/filter/gradient.h
rename to cpp/lib/core/filter/gradient.h
diff --git a/core/filter/mask_clean.h b/cpp/lib/core/filter/mask_clean.h
similarity index 100%
rename from core/filter/mask_clean.h
rename to cpp/lib/core/filter/mask_clean.h
diff --git a/core/filter/median.h b/cpp/lib/core/filter/median.h
similarity index 100%
rename from core/filter/median.h
rename to cpp/lib/core/filter/median.h
diff --git a/core/filter/normalise.h b/cpp/lib/core/filter/normalise.h
similarity index 100%
rename from core/filter/normalise.h
rename to cpp/lib/core/filter/normalise.h
diff --git a/core/filter/optimal_threshold.h b/cpp/lib/core/filter/optimal_threshold.h
similarity index 100%
rename from core/filter/optimal_threshold.h
rename to cpp/lib/core/filter/optimal_threshold.h
diff --git a/core/filter/resize.h b/cpp/lib/core/filter/resize.h
similarity index 100%
rename from core/filter/resize.h
rename to cpp/lib/core/filter/resize.h
diff --git a/core/filter/reslice.h b/cpp/lib/core/filter/reslice.h
similarity index 100%
rename from core/filter/reslice.h
rename to cpp/lib/core/filter/reslice.h
diff --git a/core/filter/smooth.h b/cpp/lib/core/filter/smooth.h
similarity index 100%
rename from core/filter/smooth.h
rename to cpp/lib/core/filter/smooth.h
diff --git a/core/filter/warp.h b/cpp/lib/core/filter/warp.h
similarity index 100%
rename from core/filter/warp.h
rename to cpp/lib/core/filter/warp.h
diff --git a/core/filter/zclean.h b/cpp/lib/core/filter/zclean.h
similarity index 100%
rename from core/filter/zclean.h
rename to cpp/lib/core/filter/zclean.h
diff --git a/core/fixel/fixel.cpp b/cpp/lib/core/fixel/fixel.cpp
similarity index 97%
rename from core/fixel/fixel.cpp
rename to cpp/lib/core/fixel/fixel.cpp
index 74e75defe9..e5c8f9c085 100644
--- a/core/fixel/fixel.cpp
+++ b/cpp/lib/core/fixel/fixel.cpp
@@ -15,7 +15,7 @@
  */
 
 #include "fixel/fixel.h"
-#include "version.h"
+#include "mrtrix_version.h"
 
 namespace MR::Fixel {
 
diff --git a/core/fixel/fixel.h b/cpp/lib/core/fixel/fixel.h
similarity index 100%
rename from core/fixel/fixel.h
rename to cpp/lib/core/fixel/fixel.h
diff --git a/core/fixel/helpers.h b/cpp/lib/core/fixel/helpers.h
similarity index 100%
rename from core/fixel/helpers.h
rename to cpp/lib/core/fixel/helpers.h
diff --git a/core/fixel/legacy/fixel_metric.h b/cpp/lib/core/fixel/legacy/fixel_metric.h
similarity index 100%
rename from core/fixel/legacy/fixel_metric.h
rename to cpp/lib/core/fixel/legacy/fixel_metric.h
diff --git a/core/fixel/legacy/image.h b/cpp/lib/core/fixel/legacy/image.h
similarity index 100%
rename from core/fixel/legacy/image.h
rename to cpp/lib/core/fixel/legacy/image.h
diff --git a/core/fixel/legacy/keys.h b/cpp/lib/core/fixel/legacy/keys.h
similarity index 100%
rename from core/fixel/legacy/keys.h
rename to cpp/lib/core/fixel/legacy/keys.h
diff --git a/core/fixel/loop.h b/cpp/lib/core/fixel/loop.h
similarity index 100%
rename from core/fixel/loop.h
rename to cpp/lib/core/fixel/loop.h
diff --git a/core/formats/dicom.cpp b/cpp/lib/core/formats/dicom.cpp
similarity index 100%
rename from core/formats/dicom.cpp
rename to cpp/lib/core/formats/dicom.cpp
diff --git a/core/formats/list.cpp b/cpp/lib/core/formats/list.cpp
similarity index 100%
rename from core/formats/list.cpp
rename to cpp/lib/core/formats/list.cpp
diff --git a/core/formats/list.h b/cpp/lib/core/formats/list.h
similarity index 100%
rename from core/formats/list.h
rename to cpp/lib/core/formats/list.h
diff --git a/core/formats/mgh.cpp b/cpp/lib/core/formats/mgh.cpp
similarity index 100%
rename from core/formats/mgh.cpp
rename to cpp/lib/core/formats/mgh.cpp
diff --git a/core/formats/mgz.cpp b/cpp/lib/core/formats/mgz.cpp
similarity index 100%
rename from core/formats/mgz.cpp
rename to cpp/lib/core/formats/mgz.cpp
diff --git a/core/formats/mri.cpp b/cpp/lib/core/formats/mri.cpp
similarity index 100%
rename from core/formats/mri.cpp
rename to cpp/lib/core/formats/mri.cpp
diff --git a/core/formats/mrtrix.cpp b/cpp/lib/core/formats/mrtrix.cpp
similarity index 100%
rename from core/formats/mrtrix.cpp
rename to cpp/lib/core/formats/mrtrix.cpp
diff --git a/core/formats/mrtrix_gz.cpp b/cpp/lib/core/formats/mrtrix_gz.cpp
similarity index 100%
rename from core/formats/mrtrix_gz.cpp
rename to cpp/lib/core/formats/mrtrix_gz.cpp
diff --git a/core/formats/mrtrix_sparse_legacy.cpp b/cpp/lib/core/formats/mrtrix_sparse_legacy.cpp
similarity index 100%
rename from core/formats/mrtrix_sparse_legacy.cpp
rename to cpp/lib/core/formats/mrtrix_sparse_legacy.cpp
diff --git a/core/formats/mrtrix_utils.cpp b/cpp/lib/core/formats/mrtrix_utils.cpp
similarity index 100%
rename from core/formats/mrtrix_utils.cpp
rename to cpp/lib/core/formats/mrtrix_utils.cpp
diff --git a/core/formats/mrtrix_utils.h b/cpp/lib/core/formats/mrtrix_utils.h
similarity index 100%
rename from core/formats/mrtrix_utils.h
rename to cpp/lib/core/formats/mrtrix_utils.h
diff --git a/core/formats/nifti1.cpp b/cpp/lib/core/formats/nifti1.cpp
similarity index 100%
rename from core/formats/nifti1.cpp
rename to cpp/lib/core/formats/nifti1.cpp
diff --git a/core/formats/nifti1_gz.cpp b/cpp/lib/core/formats/nifti1_gz.cpp
similarity index 100%
rename from core/formats/nifti1_gz.cpp
rename to cpp/lib/core/formats/nifti1_gz.cpp
diff --git a/core/formats/nifti2.cpp b/cpp/lib/core/formats/nifti2.cpp
similarity index 100%
rename from core/formats/nifti2.cpp
rename to cpp/lib/core/formats/nifti2.cpp
diff --git a/core/formats/nifti2_gz.cpp b/cpp/lib/core/formats/nifti2_gz.cpp
similarity index 100%
rename from core/formats/nifti2_gz.cpp
rename to cpp/lib/core/formats/nifti2_gz.cpp
diff --git a/core/formats/par.cpp b/cpp/lib/core/formats/par.cpp
similarity index 100%
rename from core/formats/par.cpp
rename to cpp/lib/core/formats/par.cpp
diff --git a/core/formats/pipe.cpp b/cpp/lib/core/formats/pipe.cpp
similarity index 100%
rename from core/formats/pipe.cpp
rename to cpp/lib/core/formats/pipe.cpp
diff --git a/core/formats/png.cpp b/cpp/lib/core/formats/png.cpp
similarity index 100%
rename from core/formats/png.cpp
rename to cpp/lib/core/formats/png.cpp
diff --git a/core/formats/ram.cpp b/cpp/lib/core/formats/ram.cpp
similarity index 100%
rename from core/formats/ram.cpp
rename to cpp/lib/core/formats/ram.cpp
diff --git a/core/formats/xds.cpp b/cpp/lib/core/formats/xds.cpp
similarity index 100%
rename from core/formats/xds.cpp
rename to cpp/lib/core/formats/xds.cpp
diff --git a/core/half.h b/cpp/lib/core/half.h
similarity index 100%
rename from core/half.h
rename to cpp/lib/core/half.h
diff --git a/core/header.cpp b/cpp/lib/core/header.cpp
similarity index 100%
rename from core/header.cpp
rename to cpp/lib/core/header.cpp
diff --git a/core/header.h b/cpp/lib/core/header.h
similarity index 100%
rename from core/header.h
rename to cpp/lib/core/header.h
diff --git a/core/image.cpp b/cpp/lib/core/image.cpp
similarity index 100%
rename from core/image.cpp
rename to cpp/lib/core/image.cpp
diff --git a/core/image.h b/cpp/lib/core/image.h
similarity index 100%
rename from core/image.h
rename to cpp/lib/core/image.h
diff --git a/core/image_diff.h b/cpp/lib/core/image_diff.h
similarity index 100%
rename from core/image_diff.h
rename to cpp/lib/core/image_diff.h
diff --git a/core/image_helpers.h b/cpp/lib/core/image_helpers.h
similarity index 100%
rename from core/image_helpers.h
rename to cpp/lib/core/image_helpers.h
diff --git a/core/image_io/base.cpp b/cpp/lib/core/image_io/base.cpp
similarity index 100%
rename from core/image_io/base.cpp
rename to cpp/lib/core/image_io/base.cpp
diff --git a/core/image_io/base.h b/cpp/lib/core/image_io/base.h
similarity index 100%
rename from core/image_io/base.h
rename to cpp/lib/core/image_io/base.h
diff --git a/core/image_io/default.cpp b/cpp/lib/core/image_io/default.cpp
similarity index 100%
rename from core/image_io/default.cpp
rename to cpp/lib/core/image_io/default.cpp
diff --git a/core/image_io/default.h b/cpp/lib/core/image_io/default.h
similarity index 100%
rename from core/image_io/default.h
rename to cpp/lib/core/image_io/default.h
diff --git a/core/image_io/gz.cpp b/cpp/lib/core/image_io/gz.cpp
similarity index 100%
rename from core/image_io/gz.cpp
rename to cpp/lib/core/image_io/gz.cpp
diff --git a/core/image_io/gz.h b/cpp/lib/core/image_io/gz.h
similarity index 100%
rename from core/image_io/gz.h
rename to cpp/lib/core/image_io/gz.h
diff --git a/core/image_io/mosaic.cpp b/cpp/lib/core/image_io/mosaic.cpp
similarity index 100%
rename from core/image_io/mosaic.cpp
rename to cpp/lib/core/image_io/mosaic.cpp
diff --git a/core/image_io/mosaic.h b/cpp/lib/core/image_io/mosaic.h
similarity index 100%
rename from core/image_io/mosaic.h
rename to cpp/lib/core/image_io/mosaic.h
diff --git a/core/image_io/pipe.cpp b/cpp/lib/core/image_io/pipe.cpp
similarity index 100%
rename from core/image_io/pipe.cpp
rename to cpp/lib/core/image_io/pipe.cpp
diff --git a/core/image_io/pipe.h b/cpp/lib/core/image_io/pipe.h
similarity index 100%
rename from core/image_io/pipe.h
rename to cpp/lib/core/image_io/pipe.h
diff --git a/core/image_io/png.cpp b/cpp/lib/core/image_io/png.cpp
similarity index 100%
rename from core/image_io/png.cpp
rename to cpp/lib/core/image_io/png.cpp
diff --git a/core/image_io/png.h b/cpp/lib/core/image_io/png.h
similarity index 100%
rename from core/image_io/png.h
rename to cpp/lib/core/image_io/png.h
diff --git a/core/image_io/ram.cpp b/cpp/lib/core/image_io/ram.cpp
similarity index 100%
rename from core/image_io/ram.cpp
rename to cpp/lib/core/image_io/ram.cpp
diff --git a/core/image_io/ram.h b/cpp/lib/core/image_io/ram.h
similarity index 100%
rename from core/image_io/ram.h
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index 616c6eff14..053c1de7ea 100644
--- a/core/math/SH.cpp
+++ b/cpp/lib/core/math/SH.cpp
@@ -15,7 +15,7 @@
  */
 
 #include "math/SH.h"
-#include "version.h"
+#include "mrtrix_version.h"
 
 namespace MR::Math::SH {
 
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rename to cpp/lib/gui/mrview/tool/odf/item.cpp
diff --git a/src/gui/mrview/tool/odf/item.h b/cpp/lib/gui/mrview/tool/odf/item.h
similarity index 100%
rename from src/gui/mrview/tool/odf/item.h
rename to cpp/lib/gui/mrview/tool/odf/item.h
diff --git a/src/gui/mrview/tool/odf/model.cpp b/cpp/lib/gui/mrview/tool/odf/model.cpp
similarity index 100%
rename from src/gui/mrview/tool/odf/model.cpp
rename to cpp/lib/gui/mrview/tool/odf/model.cpp
diff --git a/src/gui/mrview/tool/odf/model.h b/cpp/lib/gui/mrview/tool/odf/model.h
similarity index 100%
rename from src/gui/mrview/tool/odf/model.h
rename to cpp/lib/gui/mrview/tool/odf/model.h
diff --git a/src/gui/mrview/tool/odf/odf.cpp b/cpp/lib/gui/mrview/tool/odf/odf.cpp
similarity index 100%
rename from src/gui/mrview/tool/odf/odf.cpp
rename to cpp/lib/gui/mrview/tool/odf/odf.cpp
diff --git a/src/gui/mrview/tool/odf/odf.h b/cpp/lib/gui/mrview/tool/odf/odf.h
similarity index 100%
rename from src/gui/mrview/tool/odf/odf.h
rename to cpp/lib/gui/mrview/tool/odf/odf.h
diff --git a/src/gui/mrview/tool/odf/preview.cpp b/cpp/lib/gui/mrview/tool/odf/preview.cpp
similarity index 100%
rename from src/gui/mrview/tool/odf/preview.cpp
rename to cpp/lib/gui/mrview/tool/odf/preview.cpp
diff --git a/src/gui/mrview/tool/odf/preview.h b/cpp/lib/gui/mrview/tool/odf/preview.h
similarity index 100%
rename from src/gui/mrview/tool/odf/preview.h
rename to cpp/lib/gui/mrview/tool/odf/preview.h
diff --git a/src/gui/mrview/tool/odf/type.h b/cpp/lib/gui/mrview/tool/odf/type.h
similarity index 100%
rename from src/gui/mrview/tool/odf/type.h
rename to cpp/lib/gui/mrview/tool/odf/type.h
diff --git a/src/gui/mrview/tool/overlay.cpp b/cpp/lib/gui/mrview/tool/overlay.cpp
similarity index 100%
rename from src/gui/mrview/tool/overlay.cpp
rename to cpp/lib/gui/mrview/tool/overlay.cpp
diff --git a/src/gui/mrview/tool/overlay.h b/cpp/lib/gui/mrview/tool/overlay.h
similarity index 100%
rename from src/gui/mrview/tool/overlay.h
rename to cpp/lib/gui/mrview/tool/overlay.h
diff --git a/src/gui/mrview/tool/roi_editor/item.cpp b/cpp/lib/gui/mrview/tool/roi_editor/item.cpp
similarity index 100%
rename from src/gui/mrview/tool/roi_editor/item.cpp
rename to cpp/lib/gui/mrview/tool/roi_editor/item.cpp
diff --git a/src/gui/mrview/tool/roi_editor/item.h b/cpp/lib/gui/mrview/tool/roi_editor/item.h
similarity index 100%
rename from src/gui/mrview/tool/roi_editor/item.h
rename to cpp/lib/gui/mrview/tool/roi_editor/item.h
diff --git a/src/gui/mrview/tool/roi_editor/model.cpp b/cpp/lib/gui/mrview/tool/roi_editor/model.cpp
similarity index 100%
rename from src/gui/mrview/tool/roi_editor/model.cpp
rename to cpp/lib/gui/mrview/tool/roi_editor/model.cpp
diff --git a/src/gui/mrview/tool/roi_editor/model.h b/cpp/lib/gui/mrview/tool/roi_editor/model.h
similarity index 100%
rename from src/gui/mrview/tool/roi_editor/model.h
rename to cpp/lib/gui/mrview/tool/roi_editor/model.h
diff --git a/src/gui/mrview/tool/roi_editor/roi.cpp b/cpp/lib/gui/mrview/tool/roi_editor/roi.cpp
similarity index 100%
rename from src/gui/mrview/tool/roi_editor/roi.cpp
rename to cpp/lib/gui/mrview/tool/roi_editor/roi.cpp
diff --git a/src/gui/mrview/tool/roi_editor/roi.h b/cpp/lib/gui/mrview/tool/roi_editor/roi.h
similarity index 100%
rename from src/gui/mrview/tool/roi_editor/roi.h
rename to cpp/lib/gui/mrview/tool/roi_editor/roi.h
diff --git a/src/gui/mrview/tool/roi_editor/undoentry.cpp b/cpp/lib/gui/mrview/tool/roi_editor/undoentry.cpp
similarity index 100%
rename from src/gui/mrview/tool/roi_editor/undoentry.cpp
rename to cpp/lib/gui/mrview/tool/roi_editor/undoentry.cpp
diff --git a/src/gui/mrview/tool/roi_editor/undoentry.h b/cpp/lib/gui/mrview/tool/roi_editor/undoentry.h
similarity index 100%
rename from src/gui/mrview/tool/roi_editor/undoentry.h
rename to cpp/lib/gui/mrview/tool/roi_editor/undoentry.h
diff --git a/src/gui/mrview/tool/screen_capture.cpp b/cpp/lib/gui/mrview/tool/screen_capture.cpp
similarity index 100%
rename from src/gui/mrview/tool/screen_capture.cpp
rename to cpp/lib/gui/mrview/tool/screen_capture.cpp
diff --git a/src/gui/mrview/tool/screen_capture.h b/cpp/lib/gui/mrview/tool/screen_capture.h
similarity index 100%
rename from src/gui/mrview/tool/screen_capture.h
rename to cpp/lib/gui/mrview/tool/screen_capture.h
diff --git a/src/gui/mrview/tool/tractography/track_scalar_file.cpp b/cpp/lib/gui/mrview/tool/tractography/track_scalar_file.cpp
similarity index 100%
rename from src/gui/mrview/tool/tractography/track_scalar_file.cpp
rename to cpp/lib/gui/mrview/tool/tractography/track_scalar_file.cpp
diff --git a/src/gui/mrview/tool/tractography/track_scalar_file.h b/cpp/lib/gui/mrview/tool/tractography/track_scalar_file.h
similarity index 100%
rename from src/gui/mrview/tool/tractography/track_scalar_file.h
rename to cpp/lib/gui/mrview/tool/tractography/track_scalar_file.h
diff --git a/src/gui/mrview/tool/tractography/tractogram.cpp b/cpp/lib/gui/mrview/tool/tractography/tractogram.cpp
similarity index 100%
rename from src/gui/mrview/tool/tractography/tractogram.cpp
rename to cpp/lib/gui/mrview/tool/tractography/tractogram.cpp
diff --git a/src/gui/mrview/tool/tractography/tractogram.h b/cpp/lib/gui/mrview/tool/tractography/tractogram.h
similarity index 100%
rename from src/gui/mrview/tool/tractography/tractogram.h
rename to cpp/lib/gui/mrview/tool/tractography/tractogram.h
diff --git a/src/gui/mrview/tool/tractography/tractogram_enums.h b/cpp/lib/gui/mrview/tool/tractography/tractogram_enums.h
similarity index 100%
rename from src/gui/mrview/tool/tractography/tractogram_enums.h
rename to cpp/lib/gui/mrview/tool/tractography/tractogram_enums.h
diff --git a/src/gui/mrview/tool/tractography/tractography.cpp b/cpp/lib/gui/mrview/tool/tractography/tractography.cpp
similarity index 100%
rename from src/gui/mrview/tool/tractography/tractography.cpp
rename to cpp/lib/gui/mrview/tool/tractography/tractography.cpp
diff --git a/src/gui/mrview/tool/tractography/tractography.h b/cpp/lib/gui/mrview/tool/tractography/tractography.h
similarity index 100%
rename from src/gui/mrview/tool/tractography/tractography.h
rename to cpp/lib/gui/mrview/tool/tractography/tractography.h
diff --git a/src/gui/mrview/tool/transform.cpp b/cpp/lib/gui/mrview/tool/transform.cpp
similarity index 100%
rename from src/gui/mrview/tool/transform.cpp
rename to cpp/lib/gui/mrview/tool/transform.cpp
diff --git a/src/gui/mrview/tool/transform.h b/cpp/lib/gui/mrview/tool/transform.h
similarity index 100%
rename from src/gui/mrview/tool/transform.h
rename to cpp/lib/gui/mrview/tool/transform.h
diff --git a/src/gui/mrview/tool/view.cpp b/cpp/lib/gui/mrview/tool/view.cpp
similarity index 100%
rename from src/gui/mrview/tool/view.cpp
rename to cpp/lib/gui/mrview/tool/view.cpp
diff --git a/src/gui/mrview/tool/view.h b/cpp/lib/gui/mrview/tool/view.h
similarity index 100%
rename from src/gui/mrview/tool/view.h
rename to cpp/lib/gui/mrview/tool/view.h
diff --git a/src/gui/mrview/volume.cpp b/cpp/lib/gui/mrview/volume.cpp
similarity index 100%
rename from src/gui/mrview/volume.cpp
rename to cpp/lib/gui/mrview/volume.cpp
diff --git a/src/gui/mrview/volume.h b/cpp/lib/gui/mrview/volume.h
similarity index 100%
rename from src/gui/mrview/volume.h
rename to cpp/lib/gui/mrview/volume.h
diff --git a/src/gui/mrview/window.cpp b/cpp/lib/gui/mrview/window.cpp
similarity index 100%
rename from src/gui/mrview/window.cpp
rename to cpp/lib/gui/mrview/window.cpp
diff --git a/src/gui/mrview/window.h b/cpp/lib/gui/mrview/window.h
similarity index 100%
rename from src/gui/mrview/window.h
rename to cpp/lib/gui/mrview/window.h
diff --git a/src/gui/opengl/font.cpp b/cpp/lib/gui/opengl/font.cpp
similarity index 100%
rename from src/gui/opengl/font.cpp
rename to cpp/lib/gui/opengl/font.cpp
diff --git a/src/gui/opengl/font.h b/cpp/lib/gui/opengl/font.h
similarity index 100%
rename from src/gui/opengl/font.h
rename to cpp/lib/gui/opengl/font.h
diff --git a/src/gui/opengl/gl.cpp b/cpp/lib/gui/opengl/gl.cpp
similarity index 100%
rename from src/gui/opengl/gl.cpp
rename to cpp/lib/gui/opengl/gl.cpp
diff --git a/src/gui/opengl/gl.h b/cpp/lib/gui/opengl/gl.h
similarity index 100%
rename from src/gui/opengl/gl.h
rename to cpp/lib/gui/opengl/gl.h
diff --git a/src/gui/opengl/gl_core_3_3.cpp b/cpp/lib/gui/opengl/gl_core_3_3.cpp
similarity index 100%
rename from src/gui/opengl/gl_core_3_3.cpp
rename to cpp/lib/gui/opengl/gl_core_3_3.cpp
diff --git a/src/gui/opengl/gl_core_3_3.h b/cpp/lib/gui/opengl/gl_core_3_3.h
similarity index 100%
rename from src/gui/opengl/gl_core_3_3.h
rename to cpp/lib/gui/opengl/gl_core_3_3.h
diff --git a/src/gui/opengl/lighting.cpp b/cpp/lib/gui/opengl/lighting.cpp
similarity index 100%
rename from src/gui/opengl/lighting.cpp
rename to cpp/lib/gui/opengl/lighting.cpp
diff --git a/src/gui/opengl/lighting.h b/cpp/lib/gui/opengl/lighting.h
similarity index 100%
rename from src/gui/opengl/lighting.h
rename to cpp/lib/gui/opengl/lighting.h
diff --git a/src/gui/opengl/shader.cpp b/cpp/lib/gui/opengl/shader.cpp
similarity index 100%
rename from src/gui/opengl/shader.cpp
rename to cpp/lib/gui/opengl/shader.cpp
diff --git a/src/gui/opengl/shader.h b/cpp/lib/gui/opengl/shader.h
similarity index 100%
rename from src/gui/opengl/shader.h
rename to cpp/lib/gui/opengl/shader.h
diff --git a/src/gui/opengl/transformation.h b/cpp/lib/gui/opengl/transformation.h
similarity index 100%
rename from src/gui/opengl/transformation.h
rename to cpp/lib/gui/opengl/transformation.h
diff --git a/src/gui/projection.cpp b/cpp/lib/gui/projection.cpp
similarity index 100%
rename from src/gui/projection.cpp
rename to cpp/lib/gui/projection.cpp
diff --git a/src/gui/projection.h b/cpp/lib/gui/projection.h
similarity index 100%
rename from src/gui/projection.h
rename to cpp/lib/gui/projection.h
diff --git a/src/gui/shapes/cube.cpp b/cpp/lib/gui/shapes/cube.cpp
similarity index 100%
rename from src/gui/shapes/cube.cpp
rename to cpp/lib/gui/shapes/cube.cpp
diff --git a/src/gui/shapes/cube.h b/cpp/lib/gui/shapes/cube.h
similarity index 100%
rename from src/gui/shapes/cube.h
rename to cpp/lib/gui/shapes/cube.h
diff --git a/src/gui/shapes/cylinder.cpp b/cpp/lib/gui/shapes/cylinder.cpp
similarity index 100%
rename from src/gui/shapes/cylinder.cpp
rename to cpp/lib/gui/shapes/cylinder.cpp
diff --git a/src/gui/shapes/cylinder.h b/cpp/lib/gui/shapes/cylinder.h
similarity index 100%
rename from src/gui/shapes/cylinder.h
rename to cpp/lib/gui/shapes/cylinder.h
diff --git a/src/gui/shapes/halfsphere.cpp b/cpp/lib/gui/shapes/halfsphere.cpp
similarity index 100%
rename from src/gui/shapes/halfsphere.cpp
rename to cpp/lib/gui/shapes/halfsphere.cpp
diff --git a/src/gui/shapes/halfsphere.h b/cpp/lib/gui/shapes/halfsphere.h
similarity index 100%
rename from src/gui/shapes/halfsphere.h
rename to cpp/lib/gui/shapes/halfsphere.h
diff --git a/src/gui/shapes/sphere.cpp b/cpp/lib/gui/shapes/sphere.cpp
similarity index 100%
rename from src/gui/shapes/sphere.cpp
rename to cpp/lib/gui/shapes/sphere.cpp
diff --git a/src/gui/shapes/sphere.h b/cpp/lib/gui/shapes/sphere.h
similarity index 100%
rename from src/gui/shapes/sphere.h
rename to cpp/lib/gui/shapes/sphere.h
diff --git a/src/gui/shview/icons.h b/cpp/lib/gui/shview/icons.h
similarity index 100%
rename from src/gui/shview/icons.h
rename to cpp/lib/gui/shview/icons.h
diff --git a/src/gui/shview/render_window.cpp b/cpp/lib/gui/shview/render_window.cpp
similarity index 100%
rename from src/gui/shview/render_window.cpp
rename to cpp/lib/gui/shview/render_window.cpp
diff --git a/src/gui/shview/render_window.h b/cpp/lib/gui/shview/render_window.h
similarity index 100%
rename from src/gui/shview/render_window.h
rename to cpp/lib/gui/shview/render_window.h
diff --git a/src/min_mem_array.h b/cpp/lib/min_mem_array.h
similarity index 100%
rename from src/min_mem_array.h
rename to cpp/lib/min_mem_array.h
diff --git a/core/version.cpp.in b/cpp/lib/mrtrix_version.cpp.in
similarity index 83%
rename from core/version.cpp.in
rename to cpp/lib/mrtrix_version.cpp.in
index 2143df497a..c8b70e8eaa 100644
--- a/core/version.cpp.in
+++ b/cpp/lib/mrtrix_version.cpp.in
@@ -1,4 +1,4 @@
-#include "version.h"
+#include "mrtrix_version.h"
 
 namespace MR {
     namespace App {
diff --git a/core/version.h b/cpp/lib/mrtrix_version.h
similarity index 100%
rename from core/version.h
rename to cpp/lib/mrtrix_version.h
diff --git a/src/registration/linear.cpp b/cpp/lib/registration/linear.cpp
similarity index 100%
rename from src/registration/linear.cpp
rename to cpp/lib/registration/linear.cpp
diff --git a/src/registration/linear.h b/cpp/lib/registration/linear.h
similarity index 100%
rename from src/registration/linear.h
rename to cpp/lib/registration/linear.h
diff --git a/src/registration/metric/cc_helper.h b/cpp/lib/registration/metric/cc_helper.h
similarity index 100%
rename from src/registration/metric/cc_helper.h
rename to cpp/lib/registration/metric/cc_helper.h
diff --git a/src/registration/metric/cross_correlation.h b/cpp/lib/registration/metric/cross_correlation.h
similarity index 100%
rename from src/registration/metric/cross_correlation.h
rename to cpp/lib/registration/metric/cross_correlation.h
diff --git a/src/registration/metric/demons.h b/cpp/lib/registration/metric/demons.h
similarity index 100%
rename from src/registration/metric/demons.h
rename to cpp/lib/registration/metric/demons.h
diff --git a/src/registration/metric/demons4D.h b/cpp/lib/registration/metric/demons4D.h
similarity index 100%
rename from src/registration/metric/demons4D.h
rename to cpp/lib/registration/metric/demons4D.h
diff --git a/src/registration/metric/demons_cc.h b/cpp/lib/registration/metric/demons_cc.h
similarity index 100%
rename from src/registration/metric/demons_cc.h
rename to cpp/lib/registration/metric/demons_cc.h
diff --git a/src/registration/metric/difference_robust.h b/cpp/lib/registration/metric/difference_robust.h
similarity index 100%
rename from src/registration/metric/difference_robust.h
rename to cpp/lib/registration/metric/difference_robust.h
diff --git a/src/registration/metric/evaluate.h b/cpp/lib/registration/metric/evaluate.h
similarity index 100%
rename from src/registration/metric/evaluate.h
rename to cpp/lib/registration/metric/evaluate.h
diff --git a/src/registration/metric/linear_base.h b/cpp/lib/registration/metric/linear_base.h
similarity index 100%
rename from src/registration/metric/linear_base.h
rename to cpp/lib/registration/metric/linear_base.h
diff --git a/src/registration/metric/local_cross_correlation.h b/cpp/lib/registration/metric/local_cross_correlation.h
similarity index 100%
rename from src/registration/metric/local_cross_correlation.h
rename to cpp/lib/registration/metric/local_cross_correlation.h
diff --git a/src/registration/metric/mean_squared.h b/cpp/lib/registration/metric/mean_squared.h
similarity index 100%
rename from src/registration/metric/mean_squared.h
rename to cpp/lib/registration/metric/mean_squared.h
diff --git a/src/registration/metric/params.h b/cpp/lib/registration/metric/params.h
similarity index 100%
rename from src/registration/metric/params.h
rename to cpp/lib/registration/metric/params.h
diff --git a/src/registration/metric/robust_estimators.h b/cpp/lib/registration/metric/robust_estimators.h
similarity index 100%
rename from src/registration/metric/robust_estimators.h
rename to cpp/lib/registration/metric/robust_estimators.h
diff --git a/src/registration/metric/thread_kernel.h b/cpp/lib/registration/metric/thread_kernel.h
similarity index 100%
rename from src/registration/metric/thread_kernel.h
rename to cpp/lib/registration/metric/thread_kernel.h
diff --git a/src/registration/multi_contrast.cpp b/cpp/lib/registration/multi_contrast.cpp
similarity index 100%
rename from src/registration/multi_contrast.cpp
rename to cpp/lib/registration/multi_contrast.cpp
diff --git a/src/registration/multi_contrast.h b/cpp/lib/registration/multi_contrast.h
similarity index 100%
rename from src/registration/multi_contrast.h
rename to cpp/lib/registration/multi_contrast.h
diff --git a/src/registration/multi_resolution_lmax.h b/cpp/lib/registration/multi_resolution_lmax.h
similarity index 100%
rename from src/registration/multi_resolution_lmax.h
rename to cpp/lib/registration/multi_resolution_lmax.h
diff --git a/src/registration/nonlinear.cpp b/cpp/lib/registration/nonlinear.cpp
similarity index 100%
rename from src/registration/nonlinear.cpp
rename to cpp/lib/registration/nonlinear.cpp
diff --git a/src/registration/nonlinear.h b/cpp/lib/registration/nonlinear.h
similarity index 100%
rename from src/registration/nonlinear.h
rename to cpp/lib/registration/nonlinear.h
diff --git a/src/registration/shared.h b/cpp/lib/registration/shared.h
similarity index 100%
rename from src/registration/shared.h
rename to cpp/lib/registration/shared.h
diff --git a/src/registration/transform/affine.cpp b/cpp/lib/registration/transform/affine.cpp
similarity index 100%
rename from src/registration/transform/affine.cpp
rename to cpp/lib/registration/transform/affine.cpp
diff --git a/src/registration/transform/affine.h b/cpp/lib/registration/transform/affine.h
similarity index 100%
rename from src/registration/transform/affine.h
rename to cpp/lib/registration/transform/affine.h
diff --git a/src/registration/transform/base.cpp b/cpp/lib/registration/transform/base.cpp
similarity index 100%
rename from src/registration/transform/base.cpp
rename to cpp/lib/registration/transform/base.cpp
diff --git a/src/registration/transform/base.h b/cpp/lib/registration/transform/base.h
similarity index 100%
rename from src/registration/transform/base.h
rename to cpp/lib/registration/transform/base.h
diff --git a/src/registration/transform/convergence_check.cpp b/cpp/lib/registration/transform/convergence_check.cpp
similarity index 100%
rename from src/registration/transform/convergence_check.cpp
rename to cpp/lib/registration/transform/convergence_check.cpp
diff --git a/src/registration/transform/convergence_check.h b/cpp/lib/registration/transform/convergence_check.h
similarity index 100%
rename from src/registration/transform/convergence_check.h
rename to cpp/lib/registration/transform/convergence_check.h
diff --git a/src/registration/transform/initialiser.cpp b/cpp/lib/registration/transform/initialiser.cpp
similarity index 100%
rename from src/registration/transform/initialiser.cpp
rename to cpp/lib/registration/transform/initialiser.cpp
diff --git a/src/registration/transform/initialiser.h b/cpp/lib/registration/transform/initialiser.h
similarity index 100%
rename from src/registration/transform/initialiser.h
rename to cpp/lib/registration/transform/initialiser.h
diff --git a/src/registration/transform/initialiser_helpers.cpp b/cpp/lib/registration/transform/initialiser_helpers.cpp
similarity index 100%
rename from src/registration/transform/initialiser_helpers.cpp
rename to cpp/lib/registration/transform/initialiser_helpers.cpp
diff --git a/src/registration/transform/initialiser_helpers.h b/cpp/lib/registration/transform/initialiser_helpers.h
similarity index 100%
rename from src/registration/transform/initialiser_helpers.h
rename to cpp/lib/registration/transform/initialiser_helpers.h
diff --git a/src/registration/transform/reorient.cpp b/cpp/lib/registration/transform/reorient.cpp
similarity index 100%
rename from src/registration/transform/reorient.cpp
rename to cpp/lib/registration/transform/reorient.cpp
diff --git a/src/registration/transform/reorient.h b/cpp/lib/registration/transform/reorient.h
similarity index 100%
rename from src/registration/transform/reorient.h
rename to cpp/lib/registration/transform/reorient.h
diff --git a/src/registration/transform/rigid.cpp b/cpp/lib/registration/transform/rigid.cpp
similarity index 100%
rename from src/registration/transform/rigid.cpp
rename to cpp/lib/registration/transform/rigid.cpp
diff --git a/src/registration/transform/rigid.h b/cpp/lib/registration/transform/rigid.h
similarity index 100%
rename from src/registration/transform/rigid.h
rename to cpp/lib/registration/transform/rigid.h
diff --git a/src/registration/transform/search.h b/cpp/lib/registration/transform/search.h
similarity index 100%
rename from src/registration/transform/search.h
rename to cpp/lib/registration/transform/search.h
diff --git a/src/registration/warp/compose.h b/cpp/lib/registration/warp/compose.h
similarity index 100%
rename from src/registration/warp/compose.h
rename to cpp/lib/registration/warp/compose.h
diff --git a/src/registration/warp/convert.h b/cpp/lib/registration/warp/convert.h
similarity index 100%
rename from src/registration/warp/convert.h
rename to cpp/lib/registration/warp/convert.h
diff --git a/src/registration/warp/helpers.h b/cpp/lib/registration/warp/helpers.h
similarity index 100%
rename from src/registration/warp/helpers.h
rename to cpp/lib/registration/warp/helpers.h
diff --git a/src/registration/warp/invert.h b/cpp/lib/registration/warp/invert.h
similarity index 100%
rename from src/registration/warp/invert.h
rename to cpp/lib/registration/warp/invert.h
diff --git a/src/stats/cfe.cpp b/cpp/lib/stats/cfe.cpp
similarity index 100%
rename from src/stats/cfe.cpp
rename to cpp/lib/stats/cfe.cpp
diff --git a/src/stats/cfe.h b/cpp/lib/stats/cfe.h
similarity index 100%
rename from src/stats/cfe.h
rename to cpp/lib/stats/cfe.h
diff --git a/src/stats/cluster.cpp b/cpp/lib/stats/cluster.cpp
similarity index 100%
rename from src/stats/cluster.cpp
rename to cpp/lib/stats/cluster.cpp
diff --git a/src/stats/cluster.h b/cpp/lib/stats/cluster.h
similarity index 100%
rename from src/stats/cluster.h
rename to cpp/lib/stats/cluster.h
diff --git a/src/stats/enhance.h b/cpp/lib/stats/enhance.h
similarity index 100%
rename from src/stats/enhance.h
rename to cpp/lib/stats/enhance.h
diff --git a/src/stats/permtest.cpp b/cpp/lib/stats/permtest.cpp
similarity index 100%
rename from src/stats/permtest.cpp
rename to cpp/lib/stats/permtest.cpp
diff --git a/src/stats/permtest.h b/cpp/lib/stats/permtest.h
similarity index 100%
rename from src/stats/permtest.h
rename to cpp/lib/stats/permtest.h
diff --git a/src/stats/tfce.cpp b/cpp/lib/stats/tfce.cpp
similarity index 100%
rename from src/stats/tfce.cpp
rename to cpp/lib/stats/tfce.cpp
diff --git a/src/stats/tfce.h b/cpp/lib/stats/tfce.h
similarity index 100%
rename from src/stats/tfce.h
rename to cpp/lib/stats/tfce.h
diff --git a/src/surface/algo/image2mesh.h b/cpp/lib/surface/algo/image2mesh.h
similarity index 100%
rename from src/surface/algo/image2mesh.h
rename to cpp/lib/surface/algo/image2mesh.h
diff --git a/src/surface/algo/mesh2image.cpp b/cpp/lib/surface/algo/mesh2image.cpp
similarity index 100%
rename from src/surface/algo/mesh2image.cpp
rename to cpp/lib/surface/algo/mesh2image.cpp
diff --git a/src/surface/algo/mesh2image.h b/cpp/lib/surface/algo/mesh2image.h
similarity index 100%
rename from src/surface/algo/mesh2image.h
rename to cpp/lib/surface/algo/mesh2image.h
diff --git a/src/surface/filter/base.cpp b/cpp/lib/surface/filter/base.cpp
similarity index 100%
rename from src/surface/filter/base.cpp
rename to cpp/lib/surface/filter/base.cpp
diff --git a/src/surface/filter/base.h b/cpp/lib/surface/filter/base.h
similarity index 100%
rename from src/surface/filter/base.h
rename to cpp/lib/surface/filter/base.h
diff --git a/src/surface/filter/smooth.cpp b/cpp/lib/surface/filter/smooth.cpp
similarity index 100%
rename from src/surface/filter/smooth.cpp
rename to cpp/lib/surface/filter/smooth.cpp
diff --git a/src/surface/filter/smooth.h b/cpp/lib/surface/filter/smooth.h
similarity index 100%
rename from src/surface/filter/smooth.h
rename to cpp/lib/surface/filter/smooth.h
diff --git a/src/surface/filter/vertex_transform.cpp b/cpp/lib/surface/filter/vertex_transform.cpp
similarity index 100%
rename from src/surface/filter/vertex_transform.cpp
rename to cpp/lib/surface/filter/vertex_transform.cpp
diff --git a/src/surface/filter/vertex_transform.h b/cpp/lib/surface/filter/vertex_transform.h
similarity index 100%
rename from src/surface/filter/vertex_transform.h
rename to cpp/lib/surface/filter/vertex_transform.h
diff --git a/src/surface/freesurfer.cpp b/cpp/lib/surface/freesurfer.cpp
similarity index 100%
rename from src/surface/freesurfer.cpp
rename to cpp/lib/surface/freesurfer.cpp
diff --git a/src/surface/freesurfer.h b/cpp/lib/surface/freesurfer.h
similarity index 100%
rename from src/surface/freesurfer.h
rename to cpp/lib/surface/freesurfer.h
diff --git a/src/surface/mesh.cpp b/cpp/lib/surface/mesh.cpp
similarity index 100%
rename from src/surface/mesh.cpp
rename to cpp/lib/surface/mesh.cpp
diff --git a/src/surface/mesh.h b/cpp/lib/surface/mesh.h
similarity index 100%
rename from src/surface/mesh.h
rename to cpp/lib/surface/mesh.h
diff --git a/src/surface/mesh_multi.cpp b/cpp/lib/surface/mesh_multi.cpp
similarity index 100%
rename from src/surface/mesh_multi.cpp
rename to cpp/lib/surface/mesh_multi.cpp
diff --git a/src/surface/mesh_multi.h b/cpp/lib/surface/mesh_multi.h
similarity index 100%
rename from src/surface/mesh_multi.h
rename to cpp/lib/surface/mesh_multi.h
diff --git a/src/surface/polygon.cpp b/cpp/lib/surface/polygon.cpp
similarity index 100%
rename from src/surface/polygon.cpp
rename to cpp/lib/surface/polygon.cpp
diff --git a/src/surface/polygon.h b/cpp/lib/surface/polygon.h
similarity index 100%
rename from src/surface/polygon.h
rename to cpp/lib/surface/polygon.h
diff --git a/src/surface/scalar.cpp b/cpp/lib/surface/scalar.cpp
similarity index 100%
rename from src/surface/scalar.cpp
rename to cpp/lib/surface/scalar.cpp
diff --git a/src/surface/scalar.h b/cpp/lib/surface/scalar.h
similarity index 100%
rename from src/surface/scalar.h
rename to cpp/lib/surface/scalar.h
diff --git a/src/surface/types.h b/cpp/lib/surface/types.h
similarity index 100%
rename from src/surface/types.h
rename to cpp/lib/surface/types.h
diff --git a/src/surface/utils.h b/cpp/lib/surface/utils.h
similarity index 100%
rename from src/surface/utils.h
rename to cpp/lib/surface/utils.h
diff --git a/src/wrap_r.h b/cpp/lib/wrap_r.h
similarity index 100%
rename from src/wrap_r.h
rename to cpp/lib/wrap_r.h
diff --git a/testing/tools/CMakeLists.txt b/testing/tools/CMakeLists.txt
index 946b5f7370..dc6ef4abbb 100644
--- a/testing/tools/CMakeLists.txt
+++ b/testing/tools/CMakeLists.txt
@@ -32,7 +32,7 @@ function(add_cpp_tool TOOL_SRC)
     add_executable(${TOOL_NAME} ${TOOL_SRC})
     target_link_libraries(${TOOL_NAME} PRIVATE
         mrtrix::headless
-        mrtrix::exec-version-lib
+        mrtrix::cmd-version-lib
         mrtrix::tests-lib
     )
     set_target_properties(${TOOL_NAME} PROPERTIES LINK_DEPENDS_NO_SHARED true)
diff --git a/testing/unit_tests/CMakeLists.txt b/testing/unit_tests/CMakeLists.txt
index c161343f54..d362794b9d 100644
--- a/testing/unit_tests/CMakeLists.txt
+++ b/testing/unit_tests/CMakeLists.txt
@@ -50,7 +50,7 @@ function(add_cpp_unit_test FILE_SRC)
     add_executable(${NAME} ${FILE_SRC})
     target_link_libraries(${NAME} PRIVATE
         mrtrix::headless
-        mrtrix::exec-version-lib
+        mrtrix::cmd-version-lib
         mrtrix::tests-lib
     )
     set_target_properties(${NAME} PROPERTIES