From dc8352c80947536729ba49b81c5f8a0f254dad38 Mon Sep 17 00:00:00 2001
From: DaveyJonesBitPail <119518234+DaveyJonesBitPail@users.noreply.github.com>
Date: Wed, 6 Aug 2025 15:04:48 +0200
Subject: [PATCH 01/34] use vcpkg w/ auto-bootstrap

---
 CMakeLists.txt               | 23 +++++++++----
 CZICheck/CMakeLists.txt      |  2 +-
 modules/bootstrapVcpkg.cmake | 65 ++++++++++++++++++++++++++++++++++++
 vcpkg.json                   |  9 +++++
 4 files changed, 92 insertions(+), 7 deletions(-)
 create mode 100644 modules/bootstrapVcpkg.cmake
 create mode 100644 vcpkg.json

diff --git a/CMakeLists.txt b/CMakeLists.txt
index c505a62..2367f5a 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -4,11 +4,21 @@
 
 cmake_minimum_required(VERSION 3.15)
 
+option(CZICHECK_ENABLE_VCPKG_BOOTSTRAP
+       "Automatically fetch and bootstrap vcpkg if no toolchain is defined" ON)
+
+# Include the bootstrap script if the option is enabled
+if(CZICHECK_ENABLE_VCPKG_BOOTSTRAP)
+    include(modules/bootstrapVcpkg.cmake)
+endif()
+
 project(CZICheck 
       VERSION 0.6.3
       HOMEPAGE_URL "https://github.com/ZEISS/czicheck"
       DESCRIPTION "CZICheck is a validator for CZI-documents")
 
+
+
 if(WIN32)
   # use "static C-runtime" -> https://stackoverflow.com/questions/14172856/compile-with-mt-instead-of-md-using-cmake
   # Note: this requires CMAKE version 3.15+
@@ -21,12 +31,13 @@ set(CMAKE_CXX_STANDARD_REQUIRED ON)
 
 set (CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/modules" ${CMAKE_MODULE_PATH})
 
-include("${CMAKE_SOURCE_DIR}/modules/libCZI.cmake")
-include("${CMAKE_SOURCE_DIR}/modules/rapidJSON.cmake")
-include("${CMAKE_SOURCE_DIR}/modules/pugiXML.cmake")
-FetchContent_GetProperties(libCZI)
-set(LIBCZI_INCLUDE_DIR "${libczi_SOURCE_DIR}/Src/libCZI")
-
+if(NOT CZICHECK_ENABLE_VCPKG_BOOTSTRAP)
+  include("${CMAKE_SOURCE_DIR}/modules/libCZI.cmake")
+  include("${CMAKE_SOURCE_DIR}/modules/rapidJSON.cmake")
+  include("${CMAKE_SOURCE_DIR}/modules/pugiXML.cmake")
+  FetchContent_GetProperties(libCZI)
+  set(LIBCZI_INCLUDE_DIR "${libczi_SOURCE_DIR}/Src/libCZI")
+endif()
 # This option enables/disables the tests for the CZICheck-application. If enabled, the test
 #  runs with a ctest run (and test-data is being downloaded)
 option(CZICHECK_BUILD_TESTS "Run the tests-suite with CTest (requires external files)" OFF)
diff --git a/CZICheck/CMakeLists.txt b/CZICheck/CMakeLists.txt
index 434b560..e36a38f 100644
--- a/CZICheck/CMakeLists.txt
+++ b/CZICheck/CMakeLists.txt
@@ -14,7 +14,7 @@ function(embed_resource resource_file_name source_file_name variable_name)
     file(WRITE "${source_file_name}" "${source}")
 endfunction()
 
-find_package(XercesC  QUIET)
+find_package(XercesC CONFIG QUIET)
 if (XercesC_FOUND)
     set(CZICheck_XercesCAvailable 1)
     message("XercesC library available -> version: ${XercesC_VERSION}")
diff --git a/modules/bootstrapVcpkg.cmake b/modules/bootstrapVcpkg.cmake
new file mode 100644
index 0000000..bf88b74
--- /dev/null
+++ b/modules/bootstrapVcpkg.cmake
@@ -0,0 +1,65 @@
+if(NOT DEFINED CMAKE_TOOLCHAIN_FILE)
+
+    set(VCPKG_DIR "${CMAKE_SOURCE_DIR}/external/vcpkg")
+
+    if(WIN32)
+        set(VCPKG_EXECUTABLE "${VCPKG_DIR}/vcpkg.exe")
+    else()
+        set(VCPKG_EXECUTABLE "${VCPKG_DIR}/vcpkg")
+    endif()
+
+    if(EXISTS "${VCPKG_EXECUTABLE}")
+        message(STATUS "Found existing vcpkg executable at ${VCPKG_EXECUTABLE}")
+        set(VCPKG_IS_CLONED TRUE)
+        set(VCPKG_IS_BOOTSTRAPPED TRUE)
+    else()
+        set(VCPKG_IS_CLONED FALSE)
+        if(EXISTS "${VCPKG_DIR}/.git" OR EXISTS "${VCPKG_DIR}/README.md")
+            set(VCPKG_IS_CLONED TRUE)
+        endif()
+
+        if(VCPKG_IS_CLONED)
+            message(STATUS "Found vcpkg folder at ${VCPKG_DIR}")
+        else()
+            message(STATUS "vcpkg not found - cloning into ${VCPKG_DIR}...")
+            execute_process(
+                COMMAND git clone --depth 1 https://github.com/microsoft/vcpkg.git "${VCPKG_DIR}"
+                RESULT_VARIABLE GIT_CLONE_RESULT
+            )
+            if(NOT GIT_CLONE_RESULT EQUAL 0)
+                message(FATAL_ERROR "Failed to clone vcpkg from GitHub.")
+            endif()
+            set(VCPKG_IS_CLONED TRUE)
+        endif()
+
+        if(NOT EXISTS "${VCPKG_EXECUTABLE}")
+            message(STATUS "Bootstrapping vcpkg...")
+            if(WIN32)
+                execute_process(
+                    COMMAND ${CMAKE_COMMAND} -E chdir "${VCPKG_DIR}" cmd /c bootstrap-vcpkg.bat
+                    RESULT_VARIABLE BOOTSTRAP_RESULT
+                )
+            else()
+                execute_process(
+                    COMMAND ${CMAKE_COMMAND} -E chdir "${VCPKG_DIR}" ./bootstrap-vcpkg.sh
+                    RESULT_VARIABLE BOOTSTRAP_RESULT
+                )
+            endif()
+
+            if(NOT BOOTSTRAP_RESULT EQUAL 0)
+                message(FATAL_ERROR "Failed to bootstrap vcpkg.")
+            endif()
+            message(STATUS "vcpkg bootstrapped successfully.")
+        else()
+            message(STATUS "vcpkg already bootstrapped.")
+        endif()
+    endif()
+
+    set(CMAKE_TOOLCHAIN_FILE "${VCPKG_DIR}/scripts/buildsystems/vcpkg.cmake"
+        CACHE STRING "Vcpkg toolchain file")
+
+    set(VCPKG_FEATURE_FLAGS "manifests" CACHE STRING "")
+
+    message(STATUS "vcpkg is ready. Toolchain file: ${CMAKE_TOOLCHAIN_FILE}")
+
+endif()
diff --git a/vcpkg.json b/vcpkg.json
new file mode 100644
index 0000000..5c4cf17
--- /dev/null
+++ b/vcpkg.json
@@ -0,0 +1,9 @@
+{
+    "name": "czicheck",
+    "version-string": "1.0.0",
+    "dependencies": [
+        "libczi",
+        "pugixml",
+        "xerces-c"
+    ]
+}
\ No newline at end of file

From 4d2656a2cafd5a0fe6558a85a33724e0adc6f3c9 Mon Sep 17 00:00:00 2001
From: DaveyJonesBitPail <119518234+DaveyJonesBitPail@users.noreply.github.com>
Date: Wed, 6 Aug 2025 18:22:52 +0200
Subject: [PATCH 02/34] use pugixml header only and don't get xerces-c via
 vcpkg by default

---
 CMakeLists.txt               |   6 +-
 CZICheck/CMakeLists.txt      |  46 +++++++++++----
 CZICheck/inc_libCZI.h        |   2 +-
 CZICheck/pugiconfig.hpp      |  40 +++++++++++++
 CZICheck/resultgathererxml.h |   1 +
 modules/bootstrapVcpkg.cmake | 105 +++++++++++++++++++----------------
 modules/pugiXML.cmake        |   2 +-
 vcpkg.json                   |  17 +++---
 8 files changed, 148 insertions(+), 71 deletions(-)
 create mode 100644 CZICheck/pugiconfig.hpp

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 2367f5a..1d641db 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -23,7 +23,7 @@ if(WIN32)
   # use "static C-runtime" -> https://stackoverflow.com/questions/14172856/compile-with-mt-instead-of-md-using-cmake
   # Note: this requires CMAKE version 3.15+
   cmake_policy(SET CMP0091 NEW)
-  set(CMAKE_MSVC_RUNTIME_LIBRARY "MultiThreaded$<$<CONFIG:Debug>:Debug>")
+  #set(CMAKE_MSVC_RUNTIME_LIBRARY "MultiThreaded$<$<CONFIG:Debug>:Debug>")
 endif(WIN32)
 
 set(CMAKE_CXX_STANDARD 17)
@@ -34,10 +34,12 @@ set (CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/modules" ${CMAKE_MODULE_PATH})
 if(NOT CZICHECK_ENABLE_VCPKG_BOOTSTRAP)
   include("${CMAKE_SOURCE_DIR}/modules/libCZI.cmake")
   include("${CMAKE_SOURCE_DIR}/modules/rapidJSON.cmake")
-  include("${CMAKE_SOURCE_DIR}/modules/pugiXML.cmake")
   FetchContent_GetProperties(libCZI)
   set(LIBCZI_INCLUDE_DIR "${libczi_SOURCE_DIR}/Src/libCZI")
 endif()
+
+include("${CMAKE_SOURCE_DIR}/modules/pugiXML.cmake")
+
 # This option enables/disables the tests for the CZICheck-application. If enabled, the test
 #  runs with a ctest run (and test-data is being downloaded)
 option(CZICHECK_BUILD_TESTS "Run the tests-suite with CTest (requires external files)" OFF)
diff --git a/CZICheck/CMakeLists.txt b/CZICheck/CMakeLists.txt
index e36a38f..f96e9b8 100644
--- a/CZICheck/CMakeLists.txt
+++ b/CZICheck/CMakeLists.txt
@@ -14,7 +14,9 @@ function(embed_resource resource_file_name source_file_name variable_name)
     file(WRITE "${source_file_name}" "${source}")
 endfunction()
 
-find_package(XercesC CONFIG QUIET)
+
+find_package(XercesC QUIET)
+
 if (XercesC_FOUND)
     set(CZICheck_XercesCAvailable 1)
     message("XercesC library available -> version: ${XercesC_VERSION}")
@@ -29,15 +31,21 @@ else()
     message("XercesC library not found, the checker 'xmlmetadataschema' will **not** be available")
 endif()
 
-include(FetchContent)
-FetchContent_Declare(
-  cli11
-  GIT_REPOSITORY https://github.com/CLIUtils/CLI11
-  GIT_TAG        v2.3.2
-)
+if(NOT CZICHECK_ENABLE_VCPKG_BOOTSTRAP)
+  include(FetchContent)
+  FetchContent_Declare(
+    cli11
+    GIT_REPOSITORY https://github.com/CLIUtils/CLI11
+    GIT_TAG        v2.3.2
+  )
 
-FetchContent_MakeAvailable(cli11)
+  FetchContent_MakeAvailable(cli11)
+endif()
 
+if(CZICHECK_ENABLE_VCPKG_BOOTSTRAP)
+  find_package(libczi CONFIG REQUIRED)
+  find_package(CLI11 CONFIG REQUIRED)
+endif()
 
 set(CZICHECKSRCFILES 
 "checkers/checkerbase.h"
@@ -97,6 +105,7 @@ runchecks.cpp
 runchecks.h
 utils.h
 utils.cpp
+pugiconfig.hpp
 )
 
 add_executable(CZICheck ${CZICHECKSRCFILES} )
@@ -104,7 +113,24 @@ add_executable(CZICheck ${CZICHECKSRCFILES} )
 set_target_properties(CZICheck PROPERTIES CXX_STANDARD 17)
 target_compile_definitions(CZICheck PRIVATE _LIBCZISTATICLIB)
 
-target_link_libraries(CZICheck  PRIVATE libCZIStatic CLI11::CLI11 pugixml)
+target_link_libraries(CZICheck PRIVATE CLI11::CLI11)
+
+if(CZICHECK_ENABLE_VCPKG_BOOTSTRAP)
+  if(TARGET libczi::libCZI)
+      add_library(libczi::libCZI_selected ALIAS libczi::libCZI)
+  elseif(TARGET libczi::libCZIStatic)
+      add_library(libczi::libCZI_selected ALIAS libczi::libCZIStatic)
+  else()
+      message(FATAL_ERROR "No suitable libCZI target found (neither shared nor static).")
+  endif()
+
+    target_link_libraries(CZICheck PRIVATE libczi::libCZI_selected)
+else()
+  target_link_libraries(CZICheck PRIVATE libCZIStatic)
+endif()
+
+target_link_libraries(CZICheck PRIVATE pugixml)
+
 target_include_directories(CZICheck
   PRIVATE ${LIBCZI_INCLUDE_DIR}
   PRIVATE ${RAPIDJSON_INCLUDE_DIRS})
@@ -118,7 +144,7 @@ endif()
 
 IF(UNIX)
   # seems to be problem with glibc I'd reckon -> https://stackoverflow.com/questions/51584960/stdcall-once-throws-stdsystem-error-unknown-error-1
-  target_link_libraries(CZICheck  PUBLIC pthread)
+  target_link_libraries(CZICheck PUBLIC pthread)
 ENDIF(UNIX)
 
 IF(WIN32)
diff --git a/CZICheck/inc_libCZI.h b/CZICheck/inc_libCZI.h
index fc95f11..a0d4103 100644
--- a/CZICheck/inc_libCZI.h
+++ b/CZICheck/inc_libCZI.h
@@ -4,4 +4,4 @@
 
 #pragma once
 
-#include <libCZI.h>
+#include <libczi/libCZI.h>
diff --git a/CZICheck/pugiconfig.hpp b/CZICheck/pugiconfig.hpp
new file mode 100644
index 0000000..528ce14
--- /dev/null
+++ b/CZICheck/pugiconfig.hpp
@@ -0,0 +1,40 @@
+
+#ifndef HEADER_PUGICONFIG_HPP
+#define HEADER_PUGICONFIG_HPP
+
+// Uncomment this to enable wchar_t mode
+#define PUGIXML_WCHAR_MODE
+
+// Uncomment this to enable compact mode
+// #define PUGIXML_COMPACT
+
+// Uncomment this to disable XPath
+// #define PUGIXML_NO_XPATH
+
+// Uncomment this to disable STL
+// #define PUGIXML_NO_STL
+
+// Uncomment this to disable exceptions
+// #define PUGIXML_NO_EXCEPTIONS
+
+// Set this to control attributes for public classes/functions, i.e.:
+// #define PUGIXML_API __declspec(dllexport) // to export all public symbols from DLL
+// #define PUGIXML_CLASS __declspec(dllimport) // to import all classes from DLL
+// #define PUGIXML_FUNCTION __fastcall // to set calling conventions to all public functions to fastcall
+// In absence of PUGIXML_CLASS/PUGIXML_FUNCTION definitions PUGIXML_API is used instead
+
+// Tune these constants to adjust memory-related behavior
+// #define PUGIXML_MEMORY_PAGE_SIZE 32768
+// #define PUGIXML_MEMORY_OUTPUT_STACK 10240
+// #define PUGIXML_MEMORY_XPATH_PAGE_SIZE 4096
+
+// Tune this constant to adjust max nesting for XPath queries
+// #define PUGIXML_XPATH_DEPTH_LIMIT 1024
+
+// Uncomment this to switch to header-only version
+// #define PUGIXML_HEADER_ONLY
+
+// Uncomment this to enable long long support
+#define PUGIXML_HAS_LONG_LONG
+
+#endif
\ No newline at end of file
diff --git a/CZICheck/resultgathererxml.h b/CZICheck/resultgathererxml.h
index 4b458a7..9ce4786 100644
--- a/CZICheck/resultgathererxml.h
+++ b/CZICheck/resultgathererxml.h
@@ -12,6 +12,7 @@
 #include "pugiconfig.hpp"
 #include <string>
 
+
 class CResultGathererXml : public IResultGatherer
 {
 private:
diff --git a/modules/bootstrapVcpkg.cmake b/modules/bootstrapVcpkg.cmake
index bf88b74..b300f84 100644
--- a/modules/bootstrapVcpkg.cmake
+++ b/modules/bootstrapVcpkg.cmake
@@ -1,65 +1,72 @@
-if(NOT DEFINED CMAKE_TOOLCHAIN_FILE)
+if(DEFINED CMAKE_TOOLCHAIN_FILE)
+    message(STATUS "CMAKE_TOOLCHAIN_FILE already set to '${CMAKE_TOOLCHAIN_FILE}', skipping vcpkg bootstrap.")
+    return()
+endif()
 
-    set(VCPKG_DIR "${CMAKE_SOURCE_DIR}/external/vcpkg")
+set(BUILDING_IN_VISUAL_STUDIO OFF)
+if(DEFINED CMAKE_GENERATOR_INSTANCE OR DEFINED CMAKE_VS_INSTANCE)
+    set(BUILDING_IN_VISUAL_STUDIO ON)
+endif()
 
+set(VCPKG_DIR "${CMAKE_SOURCE_DIR}/external/vcpkg")
+if(WIN32)
+    set(VCPKG_EXECUTABLE "${VCPKG_DIR}/vcpkg.exe")
+else()
+    set(VCPKG_EXECUTABLE "${VCPKG_DIR}/vcpkg")
+endif()
+
+if(DEFINED ENV{VCPKG_ROOT} AND EXISTS "$ENV{VCPKG_ROOT}/vcpkg")
+    set(VCPKG_DIR "$ENV{VCPKG_ROOT}")
     if(WIN32)
         set(VCPKG_EXECUTABLE "${VCPKG_DIR}/vcpkg.exe")
     else()
         set(VCPKG_EXECUTABLE "${VCPKG_DIR}/vcpkg")
     endif()
+    message(STATUS "Using pre-existing vcpkg at ${VCPKG_DIR}")
+endif()
 
-    if(EXISTS "${VCPKG_EXECUTABLE}")
-        message(STATUS "Found existing vcpkg executable at ${VCPKG_EXECUTABLE}")
-        set(VCPKG_IS_CLONED TRUE)
-        set(VCPKG_IS_BOOTSTRAPPED TRUE)
-    else()
-        set(VCPKG_IS_CLONED FALSE)
-        if(EXISTS "${VCPKG_DIR}/.git" OR EXISTS "${VCPKG_DIR}/README.md")
-            set(VCPKG_IS_CLONED TRUE)
-        endif()
+if(NOT EXISTS "${VCPKG_EXECUTABLE}")
+    if(BUILDING_IN_VISUAL_STUDIO AND DEFINED ENV{VCPKG_ROOT})
+        message(STATUS "Visual Studio detected with VCPKG_ROOT, skipping local bootstrap.")
+        return()
+    endif()
 
-        if(VCPKG_IS_CLONED)
-            message(STATUS "Found vcpkg folder at ${VCPKG_DIR}")
-        else()
-            message(STATUS "vcpkg not found - cloning into ${VCPKG_DIR}...")
-            execute_process(
-                COMMAND git clone --depth 1 https://github.com/microsoft/vcpkg.git "${VCPKG_DIR}"
-                RESULT_VARIABLE GIT_CLONE_RESULT
-            )
-            if(NOT GIT_CLONE_RESULT EQUAL 0)
-                message(FATAL_ERROR "Failed to clone vcpkg from GitHub.")
-            endif()
-            set(VCPKG_IS_CLONED TRUE)
+    if(NOT EXISTS "${VCPKG_DIR}/.git")
+        message(STATUS "vcpkg not found - cloning into ${VCPKG_DIR}...")
+        execute_process(
+            COMMAND git clone --depth 1 https://github.com/microsoft/vcpkg.git "${VCPKG_DIR}"
+            RESULT_VARIABLE GIT_CLONE_RESULT
+        )
+        if(NOT GIT_CLONE_RESULT EQUAL 0)
+            message(FATAL_ERROR "Failed to clone vcpkg from GitHub.")
         endif()
+    else()
+        message(STATUS "Found vcpkg folder at ${VCPKG_DIR}, skipping clone.")
+    endif()
 
-        if(NOT EXISTS "${VCPKG_EXECUTABLE}")
-            message(STATUS "Bootstrapping vcpkg...")
-            if(WIN32)
-                execute_process(
-                    COMMAND ${CMAKE_COMMAND} -E chdir "${VCPKG_DIR}" cmd /c bootstrap-vcpkg.bat
-                    RESULT_VARIABLE BOOTSTRAP_RESULT
-                )
-            else()
-                execute_process(
-                    COMMAND ${CMAKE_COMMAND} -E chdir "${VCPKG_DIR}" ./bootstrap-vcpkg.sh
-                    RESULT_VARIABLE BOOTSTRAP_RESULT
-                )
-            endif()
-
-            if(NOT BOOTSTRAP_RESULT EQUAL 0)
-                message(FATAL_ERROR "Failed to bootstrap vcpkg.")
-            endif()
-            message(STATUS "vcpkg bootstrapped successfully.")
-        else()
-            message(STATUS "vcpkg already bootstrapped.")
-        endif()
+    message(STATUS "Bootstrapping vcpkg...")
+    if(WIN32)
+        execute_process(
+            COMMAND ${CMAKE_COMMAND} -E chdir "${VCPKG_DIR}" cmd /c bootstrap-vcpkg.bat
+            RESULT_VARIABLE BOOTSTRAP_RESULT
+        )
+    else()
+        execute_process(
+            COMMAND ${CMAKE_COMMAND} -E chdir "${VCPKG_DIR}" ./bootstrap-vcpkg.sh
+            RESULT_VARIABLE BOOTSTRAP_RESULT
+        )
     endif()
 
-    set(CMAKE_TOOLCHAIN_FILE "${VCPKG_DIR}/scripts/buildsystems/vcpkg.cmake"
-        CACHE STRING "Vcpkg toolchain file")
+    if(NOT BOOTSTRAP_RESULT EQUAL 0)
+        message(FATAL_ERROR "Failed to bootstrap vcpkg.")
+    endif()
+else()
+    message(STATUS "Found vcpkg executable at ${VCPKG_EXECUTABLE}, skipping bootstrap.")
+endif()
 
-    set(VCPKG_FEATURE_FLAGS "manifests" CACHE STRING "")
+set(CMAKE_TOOLCHAIN_FILE "${VCPKG_DIR}/scripts/buildsystems/vcpkg.cmake"
+    CACHE STRING "Vcpkg toolchain file")
 
-    message(STATUS "vcpkg is ready. Toolchain file: ${CMAKE_TOOLCHAIN_FILE}")
+set(VCPKG_FEATURE_FLAGS "manifests" CACHE STRING "")
 
-endif()
+message(STATUS "vcpkg is ready. Toolchain file: ${CMAKE_TOOLCHAIN_FILE}")
diff --git a/modules/pugiXML.cmake b/modules/pugiXML.cmake
index e99e31e..72ed5a9 100644
--- a/modules/pugiXML.cmake
+++ b/modules/pugiXML.cmake
@@ -16,8 +16,8 @@ if (NOT pugixml_POPULATED)
   set(pugixml_BUILD_TESTS OFF CACHE BOOL "" FORCE)
 
   FetchContent_MakeAvailable(pugixml)
-
   set(PUGIXML_INCLUDE_DIRS ${pugixml_SOURCE_DIR}/include)
+  target_compile_definitions(pugixml INTERFACE PUGIXML_WCHAR_MODE PUGIXML_HEADER_ONLY)
 endif()
 
 message(STATUS "PugiXML include dir at " ${PUGIXML_INCLUDE_DIRS})
diff --git a/vcpkg.json b/vcpkg.json
index 5c4cf17..5892527 100644
--- a/vcpkg.json
+++ b/vcpkg.json
@@ -1,9 +1,10 @@
 {
-    "name": "czicheck",
-    "version-string": "1.0.0",
-    "dependencies": [
-        "libczi",
-        "pugixml",
-        "xerces-c"
-    ]
-}
\ No newline at end of file
+  "name": "czicheck",
+  "version-string": "1.0.0",
+  "dependencies": [
+    "libczi",
+    "cli11",
+    "rapidjson"
+  ],
+  "builtin-baseline": "b0190b451303865b89ced9767caaab140c39f980"
+}

From f404722782b6f00a636b39e84d65a579a634b6e8 Mon Sep 17 00:00:00 2001
From: DaveyJonesBitPail <119518234+DaveyJonesBitPail@users.noreply.github.com>
Date: Wed, 6 Aug 2025 18:58:02 +0200
Subject: [PATCH 03/34] bump version

---
 CMakeLists.txt | 2 +-
 vcpkg.json     | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 1d641db..8ec7fd6 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -13,7 +13,7 @@ if(CZICHECK_ENABLE_VCPKG_BOOTSTRAP)
 endif()
 
 project(CZICheck 
-      VERSION 0.6.3
+      VERSION 0.6.4
       HOMEPAGE_URL "https://github.com/ZEISS/czicheck"
       DESCRIPTION "CZICheck is a validator for CZI-documents")
 
diff --git a/vcpkg.json b/vcpkg.json
index 5892527..fdf474f 100644
--- a/vcpkg.json
+++ b/vcpkg.json
@@ -1,6 +1,6 @@
 {
   "name": "czicheck",
-  "version-string": "1.0.0",
+  "version-string": "0.6.4",
   "dependencies": [
     "libczi",
     "cli11",

From 3f61f1c13b21c00d09d8998a9231761ea62dda6e Mon Sep 17 00:00:00 2001
From: DaveyJonesBitPail <119518234+DaveyJonesBitPail@users.noreply.github.com>
Date: Wed, 6 Aug 2025 18:58:29 +0200
Subject: [PATCH 04/34] conditionally use static msvc

---
 CMakeLists.txt | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 8ec7fd6..890f4c1 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -23,7 +23,10 @@ if(WIN32)
   # use "static C-runtime" -> https://stackoverflow.com/questions/14172856/compile-with-mt-instead-of-md-using-cmake
   # Note: this requires CMAKE version 3.15+
   cmake_policy(SET CMP0091 NEW)
-  #set(CMAKE_MSVC_RUNTIME_LIBRARY "MultiThreaded$<$<CONFIG:Debug>:Debug>")
+  if(NOT CZICHECK_ENABLE_VCPKG_BOOTSTRAP OR VCPKG_TARGET_TRIPLET MATCHES "-static$")
+    set(CMAKE_MSVC_RUNTIME_LIBRARY "MultiThreaded$<$<CONFIG:Debug>:Debug>")
+endif()
+
 endif(WIN32)
 
 set(CMAKE_CXX_STANDARD 17)

From f284769abd4d379643ed3eb55400c2207dc5e1e5 Mon Sep 17 00:00:00 2001
From: DaveyJonesBitPail <119518234+DaveyJonesBitPail@users.noreply.github.com>
Date: Wed, 6 Aug 2025 18:59:01 +0200
Subject: [PATCH 05/34] consume xerces-c via vcpkg when bootstrapped

---
 CZICheck/CMakeLists.txt | 14 +++++++++++---
 vcpkg.json              |  3 ++-
 2 files changed, 13 insertions(+), 4 deletions(-)

diff --git a/CZICheck/CMakeLists.txt b/CZICheck/CMakeLists.txt
index f96e9b8..e1da77a 100644
--- a/CZICheck/CMakeLists.txt
+++ b/CZICheck/CMakeLists.txt
@@ -14,8 +14,11 @@ function(embed_resource resource_file_name source_file_name variable_name)
     file(WRITE "${source_file_name}" "${source}")
 endfunction()
 
-
-find_package(XercesC QUIET)
+if(CZICHECK_ENABLE_VCPKG_BOOTSTRAP)
+  find_package(XercesC CONFIG REQUIRED)
+else()
+  find_package(XercesC QUIET)
+endif()
 
 if (XercesC_FOUND)
     set(CZICheck_XercesCAvailable 1)
@@ -134,11 +137,16 @@ target_link_libraries(CZICheck PRIVATE pugixml)
 target_include_directories(CZICheck
   PRIVATE ${LIBCZI_INCLUDE_DIR}
   PRIVATE ${RAPIDJSON_INCLUDE_DIRS})
+
 if (XercesC_FOUND)
+  if(CZICHECK_ENABLE_VCPKG_BOOTSTRAP)
+    target_link_libraries(CZICheck PRIVATE XercesC::XercesC)
+  else()
     target_link_libraries(CZICheck PRIVATE ${XercesC_LIBRARY})
+  endif()
 endif()
 target_include_directories(CZICheck PRIVATE ${CMAKE_CURRENT_BINARY_DIR})
-if (XercesC_FOUND)
+if (XercesC_FOUND AND NOT CZICHECK_ENABLE_VCPKG_BOOTSTRAP)
     target_include_directories(CZICheck PRIVATE ${XercesC_INCLUDE_DIR})
 endif()
 
diff --git a/vcpkg.json b/vcpkg.json
index fdf474f..65baeda 100644
--- a/vcpkg.json
+++ b/vcpkg.json
@@ -4,7 +4,8 @@
   "dependencies": [
     "libczi",
     "cli11",
-    "rapidjson"
+    "rapidjson",
+    "xerces-c"
   ],
   "builtin-baseline": "b0190b451303865b89ced9767caaab140c39f980"
 }

From cad2fb769210b21d846b615ed3c3d35e98b049eb Mon Sep 17 00:00:00 2001
From: DaveyJonesBitPail <119518234+DaveyJonesBitPail@users.noreply.github.com>
Date: Wed, 6 Aug 2025 18:59:45 +0200
Subject: [PATCH 06/34] remove unecessary pugiconfig

---
 CZICheck/CMakeLists.txt |  1 -
 CZICheck/pugiconfig.hpp | 40 ----------------------------------------
 2 files changed, 41 deletions(-)
 delete mode 100644 CZICheck/pugiconfig.hpp

diff --git a/CZICheck/CMakeLists.txt b/CZICheck/CMakeLists.txt
index e1da77a..ae8e5ea 100644
--- a/CZICheck/CMakeLists.txt
+++ b/CZICheck/CMakeLists.txt
@@ -108,7 +108,6 @@ runchecks.cpp
 runchecks.h
 utils.h
 utils.cpp
-pugiconfig.hpp
 )
 
 add_executable(CZICheck ${CZICHECKSRCFILES} )
diff --git a/CZICheck/pugiconfig.hpp b/CZICheck/pugiconfig.hpp
deleted file mode 100644
index 528ce14..0000000
--- a/CZICheck/pugiconfig.hpp
+++ /dev/null
@@ -1,40 +0,0 @@
-
-#ifndef HEADER_PUGICONFIG_HPP
-#define HEADER_PUGICONFIG_HPP
-
-// Uncomment this to enable wchar_t mode
-#define PUGIXML_WCHAR_MODE
-
-// Uncomment this to enable compact mode
-// #define PUGIXML_COMPACT
-
-// Uncomment this to disable XPath
-// #define PUGIXML_NO_XPATH
-
-// Uncomment this to disable STL
-// #define PUGIXML_NO_STL
-
-// Uncomment this to disable exceptions
-// #define PUGIXML_NO_EXCEPTIONS
-
-// Set this to control attributes for public classes/functions, i.e.:
-// #define PUGIXML_API __declspec(dllexport) // to export all public symbols from DLL
-// #define PUGIXML_CLASS __declspec(dllimport) // to import all classes from DLL
-// #define PUGIXML_FUNCTION __fastcall // to set calling conventions to all public functions to fastcall
-// In absence of PUGIXML_CLASS/PUGIXML_FUNCTION definitions PUGIXML_API is used instead
-
-// Tune these constants to adjust memory-related behavior
-// #define PUGIXML_MEMORY_PAGE_SIZE 32768
-// #define PUGIXML_MEMORY_OUTPUT_STACK 10240
-// #define PUGIXML_MEMORY_XPATH_PAGE_SIZE 4096
-
-// Tune this constant to adjust max nesting for XPath queries
-// #define PUGIXML_XPATH_DEPTH_LIMIT 1024
-
-// Uncomment this to switch to header-only version
-// #define PUGIXML_HEADER_ONLY
-
-// Uncomment this to enable long long support
-#define PUGIXML_HAS_LONG_LONG
-
-#endif
\ No newline at end of file

From bc3f72f1525abc2490dea92b08833d358d3cb03d Mon Sep 17 00:00:00 2001
From: DaveyJonesBitPail <119518234+DaveyJonesBitPail@users.noreply.github.com>
Date: Wed, 6 Aug 2025 19:01:36 +0200
Subject: [PATCH 07/34] remove explicit vcpkg installs

---
 .github/workflows/cmake.yml | 14 --------------
 1 file changed, 14 deletions(-)

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
index 766d238..a247a4b 100644
--- a/.github/workflows/cmake.yml
+++ b/.github/workflows/cmake.yml
@@ -27,20 +27,6 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v3
 
-      - name: Install dependencies (Windows)
-        if: ${{ (matrix.os == 'windows-latest') }}
-        # on Windows, we rely on vcpkg to pull in dependencies
-        shell: bash
-        run: |
-          vcpkg install xerces-c --triplet x64-windows-static
-
-      - name: Install dependencies (Linux)
-        if: ${{ (matrix.os == 'ubuntu-latest') }}
-        # on Linux, we use apt to get our dependencies
-        shell: bash
-        run: |
-          sudo apt-get install libxerces-c-dev -y
-
       - name: Configure CMake (Windows)
         if: ${{ (matrix.os == 'windows-latest') }}
         shell: bash

From 59cf2ed47ab0eeab36fd3b47170b539b35c5c96c Mon Sep 17 00:00:00 2001
From: DaveyJonesBitPail <119518234+DaveyJonesBitPail@users.noreply.github.com>
Date: Wed, 6 Aug 2025 19:03:34 +0200
Subject: [PATCH 08/34] add vcpkg.json to dep5

---
 .reuse/dep5 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.reuse/dep5 b/.reuse/dep5
index ff697e9..35f266c 100644
--- a/.reuse/dep5
+++ b/.reuse/dep5
@@ -3,7 +3,7 @@ Upstream-Name: CZICheck
 Upstream-Contact: Carl Zeiss Microscopy GmbH <github.microscopy@zeiss.com>
 Source: https://github.com/ZEISS/czicheck
 
-Files: .github/* .gitignore README.md LICENSE CODE_OF_CONDUCT.md CONTRIBUTING.md README.md SECURITY.md cla_corporate.txt cla_individual.txt THIRD_PARTY_LICENSES.txt
+Files: .github/* .gitignore README.md LICENSE CODE_OF_CONDUCT.md CONTRIBUTING.md README.md SECURITY.md cla_corporate.txt cla_individual.txt THIRD_PARTY_LICENSES.txt vcpkg.json
 Copyright: 2023 Carl Zeiss Microscopy GmbH
 License: MIT
 

From 05345f035d0e59102043dbe9eaf8c7149d50b9bc Mon Sep 17 00:00:00 2001
From: DaveyJonesBitPail <119518234+DaveyJonesBitPail@users.noreply.github.com>
Date: Wed, 6 Aug 2025 19:21:57 +0200
Subject: [PATCH 09/34] get vcpkg at appropriate baseline commit

---
 modules/bootstrapVcpkg.cmake | 32 +++++++++++++++++++++++++++++++-
 1 file changed, 31 insertions(+), 1 deletion(-)

diff --git a/modules/bootstrapVcpkg.cmake b/modules/bootstrapVcpkg.cmake
index b300f84..59e5de8 100644
--- a/modules/bootstrapVcpkg.cmake
+++ b/modules/bootstrapVcpkg.cmake
@@ -32,7 +32,23 @@ if(NOT EXISTS "${VCPKG_EXECUTABLE}")
     endif()
 
     if(NOT EXISTS "${VCPKG_DIR}/.git")
-        message(STATUS "vcpkg not found - cloning into ${VCPKG_DIR}...")
+        message(STATUS "vcpkg not found")
+        message(STATUS "Attempting to find baseline from vcpkg.json...")
+        file(READ "${CMAKE_SOURCE_DIR}/vcpkg.json" _vcpkg_manifest)
+        string(REGEX MATCH "\"builtin-baseline\"[ \t]*:[ \t]*\"([0-9a-f]+)\"" _ ${_vcpkg_manifest})
+        set(VCPKG_BASELINE_COMMIT "${CMAKE_MATCH_1}")
+
+        if(NOT VCPKG_BASELINE_COMMIT OR NOT VCPKG_BASELINE_COMMIT MATCHES "^[0-9a-f]+$")
+            message(WARNING
+                "Failed to extract builtin-baseline from vcpkg.json. "
+                "Ensure that your manifest defines a valid baseline like:\n"
+                "  \"builtin-baseline\": \"<commit sha>\""
+            )
+        else()
+            message(STATUS "Determined baseline commit: ${VCPKG_BASELINE_COMMIT}")
+        endif()
+
+        message(STATUS "Cloning vcpkg...")
         execute_process(
             COMMAND git clone --depth 1 https://github.com/microsoft/vcpkg.git "${VCPKG_DIR}"
             RESULT_VARIABLE GIT_CLONE_RESULT
@@ -40,6 +56,20 @@ if(NOT EXISTS "${VCPKG_EXECUTABLE}")
         if(NOT GIT_CLONE_RESULT EQUAL 0)
             message(FATAL_ERROR "Failed to clone vcpkg from GitHub.")
         endif()
+        
+        if(DEFINED VCPKG_BASELINE_COMMIT)
+          message(STATUS "Fetching vcpkg baseline commit: ${VCPKG_BASELINE_COMMIT}"
+          execute_process(
+            COMMAND ${CMAKE_COMMAND} -E chdir "${VCPKG_DIR}" git fetch --depth 1 origin ${VCPKG_BASELINE_COMMIT}
+            RESULT_VARIABLE GIT_FETCH_RESULT
+            )
+          if(NOT GIT_FETCH_RESULT EQUAL 0)
+            message(FATAL_ERROR
+              "Failed to fetch vcpkg baseline commit ${VCPKG_BASELINE_COMMIT}. "
+              "Check that your builtin-baseline is correct and exists in the vcpkg repo."
+            )
+          endif()
+        endif()
     else()
         message(STATUS "Found vcpkg folder at ${VCPKG_DIR}, skipping clone.")
     endif()

From 186514e75eda38ba814b77815fb1a4ddead543bd Mon Sep 17 00:00:00 2001
From: DaveyJonesBitPail <119518234+DaveyJonesBitPail@users.noreply.github.com>
Date: Wed, 6 Aug 2025 19:25:01 +0200
Subject: [PATCH 10/34] add missing parentheses

---
 modules/bootstrapVcpkg.cmake | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/bootstrapVcpkg.cmake b/modules/bootstrapVcpkg.cmake
index 59e5de8..9f9bbf6 100644
--- a/modules/bootstrapVcpkg.cmake
+++ b/modules/bootstrapVcpkg.cmake
@@ -58,7 +58,7 @@ if(NOT EXISTS "${VCPKG_EXECUTABLE}")
         endif()
         
         if(DEFINED VCPKG_BASELINE_COMMIT)
-          message(STATUS "Fetching vcpkg baseline commit: ${VCPKG_BASELINE_COMMIT}"
+          message(STATUS "Fetching vcpkg baseline commit: ${VCPKG_BASELINE_COMMIT}")
           execute_process(
             COMMAND ${CMAKE_COMMAND} -E chdir "${VCPKG_DIR}" git fetch --depth 1 origin ${VCPKG_BASELINE_COMMIT}
             RESULT_VARIABLE GIT_FETCH_RESULT

From f1211a3d082afb72e2ba82fabe40d56a9d3b9b01 Mon Sep 17 00:00:00 2001
From: DaveyJonesBitPail <119518234+DaveyJonesBitPail@users.noreply.github.com>
Date: Wed, 6 Aug 2025 19:30:13 +0200
Subject: [PATCH 11/34] add update vcpkg install step

---
 .github/workflows/cmake.yml | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
index a247a4b..5325868 100644
--- a/.github/workflows/cmake.yml
+++ b/.github/workflows/cmake.yml
@@ -27,6 +27,25 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v3
 
+      - name: Prep existing vcpkg installation
+        shell: bash
+        run: |
+          set -e
+          BASELINE=$(grep -Po '"builtin-baseline"\s*:\s*"\K[0-9a-f]+' vcpkg.json)
+          echo "Detected vcpkg baseline: $BASELINE"
+          if [ -d "$VCPKG_ROOT/.git" ]; then
+              echo "Using preinstalled vcpkg at $VCPKG_ROOT"
+              cd "$VCPKG_ROOT"
+          if ! git cat-file -e "$BASELINE"^{commit} 2>/dev/null; then
+              echo "Fetching vcpkg baseline commit $BASELINE..."
+              git fetch --depth 1 origin "$BASELINE"
+          fi
+          git checkout "$BASELINE"
+          if [ ! -f ./vcpkg ]; then
+              ./bootstrap-vcpkg.sh
+          fi
+          echo "vcpkg is now at commit: $(git rev-parse HEAD)"
+
       - name: Configure CMake (Windows)
         if: ${{ (matrix.os == 'windows-latest') }}
         shell: bash

From 6e842b8e670f36d29d2847e8db97cf457b6de975 Mon Sep 17 00:00:00 2001
From: DaveyJonesBitPail <119518234+DaveyJonesBitPail@users.noreply.github.com>
Date: Wed, 6 Aug 2025 19:33:53 +0200
Subject: [PATCH 12/34] try to fix linespacing

---
 .github/workflows/cmake.yml | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
index 5325868..b372436 100644
--- a/.github/workflows/cmake.yml
+++ b/.github/workflows/cmake.yml
@@ -30,20 +30,25 @@ jobs:
       - name: Prep existing vcpkg installation
         shell: bash
         run: |
-          set -e
           BASELINE=$(grep -Po '"builtin-baseline"\s*:\s*"\K[0-9a-f]+' vcpkg.json)
           echo "Detected vcpkg baseline: $BASELINE"
+
           if [ -d "$VCPKG_ROOT/.git" ]; then
               echo "Using preinstalled vcpkg at $VCPKG_ROOT"
               cd "$VCPKG_ROOT"
+          fi
+
           if ! git cat-file -e "$BASELINE"^{commit} 2>/dev/null; then
               echo "Fetching vcpkg baseline commit $BASELINE..."
               git fetch --depth 1 origin "$BASELINE"
           fi
+
           git checkout "$BASELINE"
+
           if [ ! -f ./vcpkg ]; then
               ./bootstrap-vcpkg.sh
           fi
+
           echo "vcpkg is now at commit: $(git rev-parse HEAD)"
 
       - name: Configure CMake (Windows)

From bad674e0350da1d81ac31fcfeff2312021ba3575 Mon Sep 17 00:00:00 2001
From: DaveyJonesBitPail <119518234+DaveyJonesBitPail@users.noreply.github.com>
Date: Wed, 6 Aug 2025 19:36:43 +0200
Subject: [PATCH 13/34] stop trying to be clever and do a normal fetch...

---
 .github/workflows/cmake.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
index b372436..a0dab6f 100644
--- a/.github/workflows/cmake.yml
+++ b/.github/workflows/cmake.yml
@@ -40,7 +40,7 @@ jobs:
 
           if ! git cat-file -e "$BASELINE"^{commit} 2>/dev/null; then
               echo "Fetching vcpkg baseline commit $BASELINE..."
-              git fetch --depth 1 origin "$BASELINE"
+              git fetch
           fi
 
           git checkout "$BASELINE"

From e0b471a379222752b20b2cdb8dfd2574c60d8ecf Mon Sep 17 00:00:00 2001
From: DaveyJonesBitPail <119518234+DaveyJonesBitPail@users.noreply.github.com>
Date: Wed, 6 Aug 2025 19:41:40 +0200
Subject: [PATCH 14/34] bump checkout action

---
 .github/workflows/cmake.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
index a0dab6f..95dcdfa 100644
--- a/.github/workflows/cmake.yml
+++ b/.github/workflows/cmake.yml
@@ -25,7 +25,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Prep existing vcpkg installation
         shell: bash

From c5e92e922857c24f88780c7eff34089622e862c7 Mon Sep 17 00:00:00 2001
From: DaveyJonesBitPail <119518234+DaveyJonesBitPail@users.noreply.github.com>
Date: Wed, 6 Aug 2025 19:47:52 +0200
Subject: [PATCH 15/34] try being clever again and overriding vcpkg_dir

---
 .github/workflows/cmake.yml | 43 +++++++++++++++++++++++++++++++------
 1 file changed, 37 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
index 95dcdfa..008d49e 100644
--- a/.github/workflows/cmake.yml
+++ b/.github/workflows/cmake.yml
@@ -27,30 +27,61 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
+      - name: Cache vcpkg and packages
+        uses: actions/cache@v4
+        with:
+          path: |
+            external/vcpkg
+            build/vcpkg_installed
+          key: vcpkg-${{ runner.os }}-${{ hashFiles('vcpkg.json') }}
+
       - name: Prep existing vcpkg installation
-        shell: bash
+                shell: bash
         run: |
+          set -euo pipefail
           BASELINE=$(grep -Po '"builtin-baseline"\s*:\s*"\K[0-9a-f]+' vcpkg.json)
           echo "Detected vcpkg baseline: $BASELINE"
 
-          if [ -d "$VCPKG_ROOT/.git" ]; then
+          if [ -d "$GITHUB_WORKSPACE/external/vcpkg/.git" ]; then
+              echo "Using cached vcpkg at external/vcpkg"
+              cd "$GITHUB_WORKSPACE/external/vcpkg"
+          elif [ -d "$VCPKG_ROOT/.git" ]; then
               echo "Using preinstalled vcpkg at $VCPKG_ROOT"
               cd "$VCPKG_ROOT"
+          else
+              echo "Performing minimal clone of vcpkg..."
+              git clone --filter=blob:none --no-checkout https://github.com/microsoft/vcpkg.git external/vcpkg
+              cd external/vcpkg
           fi
 
           if ! git cat-file -e "$BASELINE"^{commit} 2>/dev/null; then
-              echo "Fetching vcpkg baseline commit $BASELINE..."
-              git fetch
+              echo "Baseline commit not present; fetching..."
+              git fetch origin "$BASELINE" --depth=1 || git fetch --unshallow
           fi
 
           git checkout "$BASELINE"
 
           if [ ! -f ./vcpkg ]; then
-              ./bootstrap-vcpkg.sh
+              if [[ "$RUNNER_OS" == "Windows" ]]; then
+                  ./bootstrap-vcpkg.bat
+              else
+                  ./bootstrap-vcpkg.sh
+              fi
           fi
 
           echo "vcpkg is now at commit: $(git rev-parse HEAD)"
 
+          if [ -d "$GITHUB_WORKSPACE/external/vcpkg/.git" ]; then
+              VCPKG_DIR="$GITHUB_WORKSPACE/external/vcpkg"
+          elif [ -d "$VCPKG_ROOT/.git" ]; then
+              VCPKG_DIR="$VCPKG_ROOT"
+          else
+              VCPKG_DIR="$GITHUB_WORKSPACE/external/vcpkg"
+          fi
+
+          echo "VCPKG_DIR=$VCPKG_DIR" >> $GITHUB_ENV
+
+
       - name: Configure CMake (Windows)
         if: ${{ (matrix.os == 'windows-latest') }}
         shell: bash
@@ -59,7 +90,7 @@ jobs:
           # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
           # on Windows, we need to point CMake to the vcpkg-toolchain-file
           cmake -B "${{github.workspace}}/build" -DCMAKE_BUILD_TYPE=${{matrix.build}} \
-                -DCMAKE_TOOLCHAIN_FILE="${VCPKG_INSTALLATION_ROOT}/scripts/buildsystems/vcpkg.cmake" \
+                -DCMAKE_TOOLCHAIN_FILE="${VCPKG_DIR}/scripts/buildsystems/vcpkg.cmake" \
                 -DVCPKG_TARGET_TRIPLET=x64-windows-static \
                 -DCZICHECK_BUILD_TESTS=ON
 

From 75ec2440075d11c0ef119d175972ab603a2841b1 Mon Sep 17 00:00:00 2001
From: DaveyJonesBitPail <119518234+DaveyJonesBitPail@users.noreply.github.com>
Date: Wed, 6 Aug 2025 19:49:58 +0200
Subject: [PATCH 16/34] Add SPDX header

---
 modules/bootstrapVcpkg.cmake | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/modules/bootstrapVcpkg.cmake b/modules/bootstrapVcpkg.cmake
index 9f9bbf6..7447669 100644
--- a/modules/bootstrapVcpkg.cmake
+++ b/modules/bootstrapVcpkg.cmake
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2024 Carl Zeiss Microscopy GmbH
+#
+# SPDX-License-Identifier: MIT
+
 if(DEFINED CMAKE_TOOLCHAIN_FILE)
     message(STATUS "CMAKE_TOOLCHAIN_FILE already set to '${CMAKE_TOOLCHAIN_FILE}', skipping vcpkg bootstrap.")
     return()

From 22df7fdf55a105debaf49eff815b8981fbd7ed31 Mon Sep 17 00:00:00 2001
From: DaveyJonesBitPail <119518234+DaveyJonesBitPail@users.noreply.github.com>
Date: Wed, 6 Aug 2025 19:51:51 +0200
Subject: [PATCH 17/34] fix indent....

---
 .github/workflows/cmake.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
index 008d49e..2dff785 100644
--- a/.github/workflows/cmake.yml
+++ b/.github/workflows/cmake.yml
@@ -36,7 +36,7 @@ jobs:
           key: vcpkg-${{ runner.os }}-${{ hashFiles('vcpkg.json') }}
 
       - name: Prep existing vcpkg installation
-                shell: bash
+        shell: bash
         run: |
           set -euo pipefail
           BASELINE=$(grep -Po '"builtin-baseline"\s*:\s*"\K[0-9a-f]+' vcpkg.json)

From 02af2a446d4dbfe605e461c7ac57b1b7ff482372 Mon Sep 17 00:00:00 2001
From: DaveyJonesBitPail <119518234+DaveyJonesBitPail@users.noreply.github.com>
Date: Wed, 6 Aug 2025 19:56:40 +0200
Subject: [PATCH 18/34] handle if runner doesn't define vcpkgroot

---
 .github/workflows/cmake.yml | 27 ++++++++++-----------------
 1 file changed, 10 insertions(+), 17 deletions(-)

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
index 2dff785..5f47551 100644
--- a/.github/workflows/cmake.yml
+++ b/.github/workflows/cmake.yml
@@ -44,24 +44,26 @@ jobs:
 
           if [ -d "$GITHUB_WORKSPACE/external/vcpkg/.git" ]; then
               echo "Using cached vcpkg at external/vcpkg"
-              cd "$GITHUB_WORKSPACE/external/vcpkg"
-          elif [ -d "$VCPKG_ROOT/.git" ]; then
+              VCPKG_DIR="$GITHUB_WORKSPACE/external/vcpkg"
+          elif [ -n "${VCPKG_ROOT:-}" ] && [ -d "$VCPKG_ROOT/.git" ]; then
               echo "Using preinstalled vcpkg at $VCPKG_ROOT"
-              cd "$VCPKG_ROOT"
+              VCPKG_DIR="$VCPKG_ROOT"
           else
-              echo "Performing minimal clone of vcpkg..."
+              echo "Performing minimal vcpkg clone..."
               git clone --filter=blob:none --no-checkout https://github.com/microsoft/vcpkg.git external/vcpkg
-              cd external/vcpkg
+              VCPKG_DIR="$GITHUB_WORKSPACE/external/vcpkg"
           fi
 
+          cd "$VCPKG_DIR"
+
           if ! git cat-file -e "$BASELINE"^{commit} 2>/dev/null; then
-              echo "Baseline commit not present; fetching..."
+              echo "Fetching baseline commit $BASELINE..."
               git fetch origin "$BASELINE" --depth=1 || git fetch --unshallow
           fi
 
           git checkout "$BASELINE"
 
-          if [ ! -f ./vcpkg ]; then
+          if [ ! -f ./vcpkg ] && [ ! -f ./vcpkg.exe ]; then
               if [[ "$RUNNER_OS" == "Windows" ]]; then
                   ./bootstrap-vcpkg.bat
               else
@@ -70,16 +72,7 @@ jobs:
           fi
 
           echo "vcpkg is now at commit: $(git rev-parse HEAD)"
-
-          if [ -d "$GITHUB_WORKSPACE/external/vcpkg/.git" ]; then
-              VCPKG_DIR="$GITHUB_WORKSPACE/external/vcpkg"
-          elif [ -d "$VCPKG_ROOT/.git" ]; then
-              VCPKG_DIR="$VCPKG_ROOT"
-          else
-              VCPKG_DIR="$GITHUB_WORKSPACE/external/vcpkg"
-          fi
-
-          echo "VCPKG_DIR=$VCPKG_DIR" >> $GITHUB_ENV
+          echo "VCPKG_DIR=$VCPKG_DIR" >> "$GITHUB_ENV"
 
 
       - name: Configure CMake (Windows)

From ee61aecf5bccf4afa40c752b9abb9f772abcdd82 Mon Sep 17 00:00:00 2001
From: DaveyJonesBitPail <119518234+DaveyJonesBitPail@users.noreply.github.com>
Date: Wed, 6 Aug 2025 19:58:46 +0200
Subject: [PATCH 19/34] Let's try jq instead of grep and pray

---
 .github/workflows/cmake.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
index 5f47551..3e02049 100644
--- a/.github/workflows/cmake.yml
+++ b/.github/workflows/cmake.yml
@@ -39,7 +39,7 @@ jobs:
         shell: bash
         run: |
           set -euo pipefail
-          BASELINE=$(grep -Po '"builtin-baseline"\s*:\s*"\K[0-9a-f]+' vcpkg.json)
+          BASELINE=$(jq -r '.["builtin-baseline"]' vcpkg.json)
           echo "Detected vcpkg baseline: $BASELINE"
 
           if [ -d "$GITHUB_WORKSPACE/external/vcpkg/.git" ]; then

From 406ac779f2be7440771a51267993818ea36b60c4 Mon Sep 17 00:00:00 2001
From: DaveyJonesBitPail <119518234+DaveyJonesBitPail@users.noreply.github.com>
Date: Wed, 6 Aug 2025 20:11:19 +0200
Subject: [PATCH 20/34] make linux build also use vcpkg

---
 .github/workflows/cmake.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
index 3e02049..c42c346 100644
--- a/.github/workflows/cmake.yml
+++ b/.github/workflows/cmake.yml
@@ -92,6 +92,7 @@ jobs:
         shell: bash
         run: |
           cmake -B "${{github.workspace}}/build" -DCMAKE_BUILD_TYPE=${{matrix.build}} \
+                -DCMAKE_TOOLCHAIN_FILE="${VCPKG_DIR}/scripts/buildsystems/vcpkg.cmake" \
                 -DCZICHECK_BUILD_TESTS=ON
 
       - name: Build

From abd8b7d7c41ede0bc176a452f1997ddbd9213234 Mon Sep 17 00:00:00 2001
From: DaveyJonesBitPail <119518234+DaveyJonesBitPail@users.noreply.github.com>
Date: Wed, 6 Aug 2025 20:15:48 +0200
Subject: [PATCH 21/34] =?UTF-8?q?properly=20capitalize=20libczi....=20?=
 =?UTF-8?q?=F0=9F=A4=A6?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 CZICheck/CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CZICheck/CMakeLists.txt b/CZICheck/CMakeLists.txt
index ae8e5ea..e803c0f 100644
--- a/CZICheck/CMakeLists.txt
+++ b/CZICheck/CMakeLists.txt
@@ -46,7 +46,7 @@ if(NOT CZICHECK_ENABLE_VCPKG_BOOTSTRAP)
 endif()
 
 if(CZICHECK_ENABLE_VCPKG_BOOTSTRAP)
-  find_package(libczi CONFIG REQUIRED)
+  find_package(libCZI CONFIG REQUIRED)
   find_package(CLI11 CONFIG REQUIRED)
 endif()
 

From c1916d28c88ad553372657242e931671954e8066 Mon Sep 17 00:00:00 2001
From: DaveyJonesBitPail <119518234+DaveyJonesBitPail@users.noreply.github.com>
Date: Wed, 6 Aug 2025 20:24:12 +0200
Subject: [PATCH 22/34] properly capitalize part 2

---
 CZICheck/inc_libCZI.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CZICheck/inc_libCZI.h b/CZICheck/inc_libCZI.h
index a0d4103..803a70f 100644
--- a/CZICheck/inc_libCZI.h
+++ b/CZICheck/inc_libCZI.h
@@ -4,4 +4,4 @@
 
 #pragma once
 
-#include <libczi/libCZI.h>
+#include <libCZI/libCZI.h>

From 767110f846d2e9dd385d08968a59325de250f3ad Mon Sep 17 00:00:00 2001
From: DaveyJonesBitPail <119518234+DaveyJonesBitPail@users.noreply.github.com>
Date: Wed, 6 Aug 2025 20:26:28 +0200
Subject: [PATCH 23/34] bump version in tests

---
 Test/CZICheckSamples/differentpixeltypeinchannel.txt.xml        | 2 +-
 Test/CZICheckSamples/duplicate_coordinates.txt.xml              | 2 +-
 Test/CZICheckSamples/edf-missing-texture.txt.xml                | 2 +-
 .../edf-superfluous-missing-channel-subblock.txt.xml            | 2 +-
 Test/CZICheckSamples/edf-superfluous.txt.xml                    | 2 +-
 Test/CZICheckSamples/inconsistent_coordinates.txt.xml           | 2 +-
 Test/CZICheckSamples/invalid_componentbitcount.txt.xml          | 2 +-
 .../jpgxrcompressed_inconsistent_pixeltype.txt.xml              | 2 +-
 Test/CZICheckSamples/jpgxrcompressed_inconsistent_size.txt.xml  | 2 +-
 Test/CZICheckSamples/layer_0_subblocks_with_no_m_index.txt.xml  | 2 +-
 Test/CZICheckSamples/negative_plane_start_index.txt.xml         | 2 +-
 Test/CZICheckSamples/overlapping_scenes.txt.xml                 | 2 +-
 .../pixeltype_mismatch_between_metadata_and_subblocks.txt.xml   | 2 +-
 Test/CZICheckSamples/positive_plane_start_index.txt.xml         | 2 +-
 Test/CZICheckSamples/sparse_planes.txt.xml                      | 2 +-
 15 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/Test/CZICheckSamples/differentpixeltypeinchannel.txt.xml b/Test/CZICheckSamples/differentpixeltypeinchannel.txt.xml
index c9304be..8786fd8 100644
--- a/Test/CZICheckSamples/differentpixeltypeinchannel.txt.xml
+++ b/Test/CZICheckSamples/differentpixeltypeinchannel.txt.xml
@@ -99,6 +99,6 @@
   <AggregatedResult>WARN</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.3</Version>
+    <Version>0.6.4</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/duplicate_coordinates.txt.xml b/Test/CZICheckSamples/duplicate_coordinates.txt.xml
index ee81f94..75987a3 100644
--- a/Test/CZICheckSamples/duplicate_coordinates.txt.xml
+++ b/Test/CZICheckSamples/duplicate_coordinates.txt.xml
@@ -99,6 +99,6 @@
   <AggregatedResult>FAIL</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.3</Version>
+    <Version>0.6.4</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/edf-missing-texture.txt.xml b/Test/CZICheckSamples/edf-missing-texture.txt.xml
index ed8fc3a..5fefa33 100644
--- a/Test/CZICheckSamples/edf-missing-texture.txt.xml
+++ b/Test/CZICheckSamples/edf-missing-texture.txt.xml
@@ -92,6 +92,6 @@
   <AggregatedResult>FAIL</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.3</Version>
+    <Version>0.6.4</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/edf-superfluous-missing-channel-subblock.txt.xml b/Test/CZICheckSamples/edf-superfluous-missing-channel-subblock.txt.xml
index 9af42ad..fbe5ba8 100644
--- a/Test/CZICheckSamples/edf-superfluous-missing-channel-subblock.txt.xml
+++ b/Test/CZICheckSamples/edf-superfluous-missing-channel-subblock.txt.xml
@@ -113,6 +113,6 @@
   <AggregatedResult>FAIL</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.3</Version>
+    <Version>0.6.4</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/edf-superfluous.txt.xml b/Test/CZICheckSamples/edf-superfluous.txt.xml
index f63ff10..7c3095b 100644
--- a/Test/CZICheckSamples/edf-superfluous.txt.xml
+++ b/Test/CZICheckSamples/edf-superfluous.txt.xml
@@ -92,6 +92,6 @@
   <AggregatedResult>FAIL</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.3</Version>
+    <Version>0.6.4</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/inconsistent_coordinates.txt.xml b/Test/CZICheckSamples/inconsistent_coordinates.txt.xml
index 574383a..a5df585 100644
--- a/Test/CZICheckSamples/inconsistent_coordinates.txt.xml
+++ b/Test/CZICheckSamples/inconsistent_coordinates.txt.xml
@@ -99,6 +99,6 @@
   <AggregatedResult>FAIL</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.3</Version>
+    <Version>0.6.4</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/invalid_componentbitcount.txt.xml b/Test/CZICheckSamples/invalid_componentbitcount.txt.xml
index f1d706f..55481ba 100644
--- a/Test/CZICheckSamples/invalid_componentbitcount.txt.xml
+++ b/Test/CZICheckSamples/invalid_componentbitcount.txt.xml
@@ -81,6 +81,6 @@
   <AggregatedResult>WARN</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.3</Version>
+    <Version>0.6.4</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/jpgxrcompressed_inconsistent_pixeltype.txt.xml b/Test/CZICheckSamples/jpgxrcompressed_inconsistent_pixeltype.txt.xml
index a915c37..6732271 100644
--- a/Test/CZICheckSamples/jpgxrcompressed_inconsistent_pixeltype.txt.xml
+++ b/Test/CZICheckSamples/jpgxrcompressed_inconsistent_pixeltype.txt.xml
@@ -81,6 +81,6 @@
   <AggregatedResult>WARN</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.3</Version>
+    <Version>0.6.4</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/jpgxrcompressed_inconsistent_size.txt.xml b/Test/CZICheckSamples/jpgxrcompressed_inconsistent_size.txt.xml
index a915c37..6732271 100644
--- a/Test/CZICheckSamples/jpgxrcompressed_inconsistent_size.txt.xml
+++ b/Test/CZICheckSamples/jpgxrcompressed_inconsistent_size.txt.xml
@@ -81,6 +81,6 @@
   <AggregatedResult>WARN</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.3</Version>
+    <Version>0.6.4</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/layer_0_subblocks_with_no_m_index.txt.xml b/Test/CZICheckSamples/layer_0_subblocks_with_no_m_index.txt.xml
index 4a32b6e..5ec6f00 100644
--- a/Test/CZICheckSamples/layer_0_subblocks_with_no_m_index.txt.xml
+++ b/Test/CZICheckSamples/layer_0_subblocks_with_no_m_index.txt.xml
@@ -87,6 +87,6 @@
   <AggregatedResult>WARN</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.3</Version>
+    <Version>0.6.4</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/negative_plane_start_index.txt.xml b/Test/CZICheckSamples/negative_plane_start_index.txt.xml
index 911cde6..66584fb 100644
--- a/Test/CZICheckSamples/negative_plane_start_index.txt.xml
+++ b/Test/CZICheckSamples/negative_plane_start_index.txt.xml
@@ -92,6 +92,6 @@
   <AggregatedResult>WARN</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.3</Version>
+    <Version>0.6.4</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/overlapping_scenes.txt.xml b/Test/CZICheckSamples/overlapping_scenes.txt.xml
index 1bfdc77..3101890 100644
--- a/Test/CZICheckSamples/overlapping_scenes.txt.xml
+++ b/Test/CZICheckSamples/overlapping_scenes.txt.xml
@@ -123,6 +123,6 @@
   <AggregatedResult>FAIL</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.3</Version>
+    <Version>0.6.4</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/pixeltype_mismatch_between_metadata_and_subblocks.txt.xml b/Test/CZICheckSamples/pixeltype_mismatch_between_metadata_and_subblocks.txt.xml
index 9be72d5..d7313b1 100644
--- a/Test/CZICheckSamples/pixeltype_mismatch_between_metadata_and_subblocks.txt.xml
+++ b/Test/CZICheckSamples/pixeltype_mismatch_between_metadata_and_subblocks.txt.xml
@@ -168,6 +168,6 @@
   <AggregatedResult>FAIL</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.3</Version>
+    <Version>0.6.4</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/positive_plane_start_index.txt.xml b/Test/CZICheckSamples/positive_plane_start_index.txt.xml
index 3f003de..35e04ad 100644
--- a/Test/CZICheckSamples/positive_plane_start_index.txt.xml
+++ b/Test/CZICheckSamples/positive_plane_start_index.txt.xml
@@ -92,6 +92,6 @@
   <AggregatedResult>WARN</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.3</Version>
+    <Version>0.6.4</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/sparse_planes.txt.xml b/Test/CZICheckSamples/sparse_planes.txt.xml
index d1d415c..77b328c 100644
--- a/Test/CZICheckSamples/sparse_planes.txt.xml
+++ b/Test/CZICheckSamples/sparse_planes.txt.xml
@@ -92,6 +92,6 @@
   <AggregatedResult>WARN</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.3</Version>
+    <Version>0.6.4</Version>
   </OutputVersion>
 </TestResults>

From 601cfb86a5b04a292d3a3771092b0d30efe3960a Mon Sep 17 00:00:00 2001
From: DaveyJonesBitPail <119518234+DaveyJonesBitPail@users.noreply.github.com>
Date: Wed, 6 Aug 2025 20:34:15 +0200
Subject: [PATCH 24/34] try to make megalinter happy

---
 .github/workflows/cmake.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
index c42c346..3070f07 100644
--- a/.github/workflows/cmake.yml
+++ b/.github/workflows/cmake.yml
@@ -56,7 +56,7 @@ jobs:
 
           cd "$VCPKG_DIR"
 
-          if ! git cat-file -e "$BASELINE"^{commit} 2>/dev/null; then
+          if ! git cat-file -e "${BASELINE}^{commit}" 2>/dev/null; then
               echo "Fetching baseline commit $BASELINE..."
               git fetch origin "$BASELINE" --depth=1 || git fetch --unshallow
           fi

From eb48638a7d12973c58c513bb959855185c6f452d Mon Sep 17 00:00:00 2001
From: DaveyJonesBitPail <119518234+DaveyJonesBitPail@users.noreply.github.com>
Date: Wed, 6 Aug 2025 20:37:33 +0200
Subject: [PATCH 25/34] bump version in test json files

---
 Test/CZICheckSamples/differentpixeltypeinchannel.txt.json       | 2 +-
 Test/CZICheckSamples/duplicate_coordinates.txt.json             | 2 +-
 Test/CZICheckSamples/edf-missing-texture.txt.json               | 2 +-
 .../edf-superfluous-missing-channel-subblock.txt.json           | 2 +-
 Test/CZICheckSamples/edf-superfluous.txt.json                   | 2 +-
 Test/CZICheckSamples/inconsistent_coordinates.txt.json          | 2 +-
 Test/CZICheckSamples/invalid_componentbitcount.txt.json         | 2 +-
 .../jpgxrcompressed_inconsistent_pixeltype.txt.json             | 2 +-
 Test/CZICheckSamples/jpgxrcompressed_inconsistent_size.txt.json | 2 +-
 Test/CZICheckSamples/layer_0_subblocks_with_no_m_index.txt.json | 2 +-
 Test/CZICheckSamples/negative_plane_start_index.txt.json        | 2 +-
 Test/CZICheckSamples/overlapping_scenes.txt.json                | 2 +-
 .../pixeltype_mismatch_between_metadata_and_subblocks.txt.json  | 2 +-
 Test/CZICheckSamples/positive_plane_start_index.txt.json        | 2 +-
 Test/CZICheckSamples/sparse_planes.txt.json                     | 2 +-
 15 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/Test/CZICheckSamples/differentpixeltypeinchannel.txt.json b/Test/CZICheckSamples/differentpixeltypeinchannel.txt.json
index f43ec29..74ea8fd 100644
--- a/Test/CZICheckSamples/differentpixeltypeinchannel.txt.json
+++ b/Test/CZICheckSamples/differentpixeltypeinchannel.txt.json
@@ -112,6 +112,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.3"
+        "version": "0.6.4"
     }
 }
\ No newline at end of file
diff --git a/Test/CZICheckSamples/duplicate_coordinates.txt.json b/Test/CZICheckSamples/duplicate_coordinates.txt.json
index 181f41d..f49dff0 100644
--- a/Test/CZICheckSamples/duplicate_coordinates.txt.json
+++ b/Test/CZICheckSamples/duplicate_coordinates.txt.json
@@ -112,6 +112,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.3"
+        "version": "0.6.4"
     }
 }
\ No newline at end of file
diff --git a/Test/CZICheckSamples/edf-missing-texture.txt.json b/Test/CZICheckSamples/edf-missing-texture.txt.json
index c8e9bc0..2205402 100644
--- a/Test/CZICheckSamples/edf-missing-texture.txt.json
+++ b/Test/CZICheckSamples/edf-missing-texture.txt.json
@@ -105,6 +105,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.3"
+        "version": "0.6.4"
     }
 }
\ No newline at end of file
diff --git a/Test/CZICheckSamples/edf-superfluous-missing-channel-subblock.txt.json b/Test/CZICheckSamples/edf-superfluous-missing-channel-subblock.txt.json
index c19844e..4c3913c 100644
--- a/Test/CZICheckSamples/edf-superfluous-missing-channel-subblock.txt.json
+++ b/Test/CZICheckSamples/edf-superfluous-missing-channel-subblock.txt.json
@@ -126,6 +126,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.3"
+        "version": "0.6.4"
     }
 }
\ No newline at end of file
diff --git a/Test/CZICheckSamples/edf-superfluous.txt.json b/Test/CZICheckSamples/edf-superfluous.txt.json
index 3a5a643..b855e12 100644
--- a/Test/CZICheckSamples/edf-superfluous.txt.json
+++ b/Test/CZICheckSamples/edf-superfluous.txt.json
@@ -105,6 +105,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.3"
+        "version": "0.6.4"
     }
 }
\ No newline at end of file
diff --git a/Test/CZICheckSamples/inconsistent_coordinates.txt.json b/Test/CZICheckSamples/inconsistent_coordinates.txt.json
index d9e780f..3f0c9a9 100644
--- a/Test/CZICheckSamples/inconsistent_coordinates.txt.json
+++ b/Test/CZICheckSamples/inconsistent_coordinates.txt.json
@@ -112,6 +112,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.3"
+        "version": "0.6.4"
     }
 }
\ No newline at end of file
diff --git a/Test/CZICheckSamples/invalid_componentbitcount.txt.json b/Test/CZICheckSamples/invalid_componentbitcount.txt.json
index 0bff9bb..e3caf81 100644
--- a/Test/CZICheckSamples/invalid_componentbitcount.txt.json
+++ b/Test/CZICheckSamples/invalid_componentbitcount.txt.json
@@ -94,6 +94,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.3"
+        "version": "0.6.4"
     }
 }
\ No newline at end of file
diff --git a/Test/CZICheckSamples/jpgxrcompressed_inconsistent_pixeltype.txt.json b/Test/CZICheckSamples/jpgxrcompressed_inconsistent_pixeltype.txt.json
index 5d972a9..3b6c4f9 100644
--- a/Test/CZICheckSamples/jpgxrcompressed_inconsistent_pixeltype.txt.json
+++ b/Test/CZICheckSamples/jpgxrcompressed_inconsistent_pixeltype.txt.json
@@ -94,6 +94,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.3"
+        "version": "0.6.4"
     }
 }
\ No newline at end of file
diff --git a/Test/CZICheckSamples/jpgxrcompressed_inconsistent_size.txt.json b/Test/CZICheckSamples/jpgxrcompressed_inconsistent_size.txt.json
index 5d972a9..3b6c4f9 100644
--- a/Test/CZICheckSamples/jpgxrcompressed_inconsistent_size.txt.json
+++ b/Test/CZICheckSamples/jpgxrcompressed_inconsistent_size.txt.json
@@ -94,6 +94,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.3"
+        "version": "0.6.4"
     }
 }
\ No newline at end of file
diff --git a/Test/CZICheckSamples/layer_0_subblocks_with_no_m_index.txt.json b/Test/CZICheckSamples/layer_0_subblocks_with_no_m_index.txt.json
index 1ff7067..76613cc 100644
--- a/Test/CZICheckSamples/layer_0_subblocks_with_no_m_index.txt.json
+++ b/Test/CZICheckSamples/layer_0_subblocks_with_no_m_index.txt.json
@@ -100,6 +100,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.3"
+        "version": "0.6.4"
     }
 }
\ No newline at end of file
diff --git a/Test/CZICheckSamples/negative_plane_start_index.txt.json b/Test/CZICheckSamples/negative_plane_start_index.txt.json
index 12bb7af..e211eb8 100644
--- a/Test/CZICheckSamples/negative_plane_start_index.txt.json
+++ b/Test/CZICheckSamples/negative_plane_start_index.txt.json
@@ -105,6 +105,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.3"
+        "version": "0.6.4"
     }
 }
\ No newline at end of file
diff --git a/Test/CZICheckSamples/overlapping_scenes.txt.json b/Test/CZICheckSamples/overlapping_scenes.txt.json
index fc7f26c..73a1344 100644
--- a/Test/CZICheckSamples/overlapping_scenes.txt.json
+++ b/Test/CZICheckSamples/overlapping_scenes.txt.json
@@ -136,6 +136,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.3"
+        "version": "0.6.4"
     }
 }
\ No newline at end of file
diff --git a/Test/CZICheckSamples/pixeltype_mismatch_between_metadata_and_subblocks.txt.json b/Test/CZICheckSamples/pixeltype_mismatch_between_metadata_and_subblocks.txt.json
index 2de4c11..3cd08b2 100644
--- a/Test/CZICheckSamples/pixeltype_mismatch_between_metadata_and_subblocks.txt.json
+++ b/Test/CZICheckSamples/pixeltype_mismatch_between_metadata_and_subblocks.txt.json
@@ -181,6 +181,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.3"
+        "version": "0.6.4"
     }
 }
\ No newline at end of file
diff --git a/Test/CZICheckSamples/positive_plane_start_index.txt.json b/Test/CZICheckSamples/positive_plane_start_index.txt.json
index 010850b..c6e97cd 100644
--- a/Test/CZICheckSamples/positive_plane_start_index.txt.json
+++ b/Test/CZICheckSamples/positive_plane_start_index.txt.json
@@ -105,6 +105,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.3"
+        "version": "0.6.4"
     }
 }
\ No newline at end of file
diff --git a/Test/CZICheckSamples/sparse_planes.txt.json b/Test/CZICheckSamples/sparse_planes.txt.json
index cc67fda..5cf88f0 100644
--- a/Test/CZICheckSamples/sparse_planes.txt.json
+++ b/Test/CZICheckSamples/sparse_planes.txt.json
@@ -105,6 +105,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.3"
+        "version": "0.6.4"
     }
 }
\ No newline at end of file

From ab58e8c19df7dc72b635443b0c552b5350164eb7 Mon Sep 17 00:00:00 2001
From: DaveyJonesBitPail <119518234+DaveyJonesBitPail@users.noreply.github.com>
Date: Wed, 6 Aug 2025 20:49:28 +0200
Subject: [PATCH 26/34] generate appropriate inc_libCZI

---
 CZICheck/CMakeLists.txt                    | 11 ++++++++++-
 CZICheck/checkers/checkerbase.h            |  2 +-
 CZICheck/{inc_libCZI.h => inc_libCZI.h.in} |  2 +-
 3 files changed, 12 insertions(+), 3 deletions(-)
 rename CZICheck/{inc_libCZI.h => inc_libCZI.h.in} (77%)

diff --git a/CZICheck/CMakeLists.txt b/CZICheck/CMakeLists.txt
index e803c0f..9002674 100644
--- a/CZICheck/CMakeLists.txt
+++ b/CZICheck/CMakeLists.txt
@@ -50,6 +50,16 @@ if(CZICHECK_ENABLE_VCPKG_BOOTSTRAP)
   find_package(CLI11 CONFIG REQUIRED)
 endif()
 
+if(CZICHECK_ENABLE_VCPKG_BOOTSTRAP)
+  set(LIBCZI_HEADER_PATH "libCZI/libCZI.h")
+else()
+  set(LIBCZI_HEADER_PATH "libCZI.h")
+endif()
+
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/inc_libCZI.h.in
+               ${CMAKE_CURRENT_BINARY_DIR}/inc_libCZI.h
+               @ONLY)
+
 set(CZICHECKSRCFILES 
 "checkers/checkerbase.h"
 "checkers/checkerbase.cpp"
@@ -95,7 +105,6 @@ consoleio.h
 CZICheck.cpp
 IChecker.h
 IResultGatherer.h
-inc_libCZI.h
 resultgatherer.cpp
 resultgatherer.h
 resultgathererjson.h
diff --git a/CZICheck/checkers/checkerbase.h b/CZICheck/checkers/checkerbase.h
index 562c6c7..162b20a 100644
--- a/CZICheck/checkers/checkerbase.h
+++ b/CZICheck/checkers/checkerbase.h
@@ -4,7 +4,7 @@
 
 #pragma once
 
-#include "../inc_libCZI.h"
+#include "inc_libCZI.h"
 #include "../checkerfactory.h"
 #include <memory>
 #include <utility>
diff --git a/CZICheck/inc_libCZI.h b/CZICheck/inc_libCZI.h.in
similarity index 77%
rename from CZICheck/inc_libCZI.h
rename to CZICheck/inc_libCZI.h.in
index 803a70f..8b20203 100644
--- a/CZICheck/inc_libCZI.h
+++ b/CZICheck/inc_libCZI.h.in
@@ -4,4 +4,4 @@
 
 #pragma once
 
-#include <libCZI/libCZI.h>
+#include <@LIBCZI_HEADER_PATH@>

From 5de3d423e4bcf2de4a5aac8b17491b593f9dd368 Mon Sep 17 00:00:00 2001
From: DaveyJonesBitPail <119518234+DaveyJonesBitPail@users.noreply.github.com>
Date: Wed, 6 Aug 2025 21:05:48 +0200
Subject: [PATCH 27/34] guard comp defs behind bootstrap flag

---
 modules/pugiXML.cmake | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/modules/pugiXML.cmake b/modules/pugiXML.cmake
index 72ed5a9..c524421 100644
--- a/modules/pugiXML.cmake
+++ b/modules/pugiXML.cmake
@@ -17,7 +17,9 @@ if (NOT pugixml_POPULATED)
 
   FetchContent_MakeAvailable(pugixml)
   set(PUGIXML_INCLUDE_DIRS ${pugixml_SOURCE_DIR}/include)
-  target_compile_definitions(pugixml INTERFACE PUGIXML_WCHAR_MODE PUGIXML_HEADER_ONLY)
+  if(CZICHECK_ENABLE_VCPKG_BOOTSTRAP)
+    target_compile_definitions(pugixml INTERFACE PUGIXML_WCHAR_MODE PUGIXML_HEADER_ONLY)
+  endif()
 endif()
 
 message(STATUS "PugiXML include dir at " ${PUGIXML_INCLUDE_DIRS})

From f905bdb2f4f3f62818ea1a8f4c8d020ca3dc3390 Mon Sep 17 00:00:00 2001
From: DaveyJonesBitPail <119518234+DaveyJonesBitPail@users.noreply.github.com>
Date: Wed, 6 Aug 2025 21:16:00 +0200
Subject: [PATCH 28/34] use czicheck specific var

---
 CZICheck/CMakeLists.txt | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/CZICheck/CMakeLists.txt b/CZICheck/CMakeLists.txt
index 9002674..ecebc06 100644
--- a/CZICheck/CMakeLists.txt
+++ b/CZICheck/CMakeLists.txt
@@ -51,9 +51,9 @@ if(CZICHECK_ENABLE_VCPKG_BOOTSTRAP)
 endif()
 
 if(CZICHECK_ENABLE_VCPKG_BOOTSTRAP)
-  set(LIBCZI_HEADER_PATH "libCZI/libCZI.h")
+  set(CZICHECK_LIBCZI_HEADER_PATH "libCZI/libCZI.h")
 else()
-  set(LIBCZI_HEADER_PATH "libCZI.h")
+  set(CZICHECK_LIBCZI_HEADER_PATH "libCZI.h")
 endif()
 
 configure_file(${CMAKE_CURRENT_SOURCE_DIR}/inc_libCZI.h.in

From 8d11da5a8f96f0a7e4bb5ecfef5c9196ffd2e7dc Mon Sep 17 00:00:00 2001
From: DaveyJonesBitPail <119518234+DaveyJonesBitPail@users.noreply.github.com>
Date: Wed, 6 Aug 2025 21:18:53 +0200
Subject: [PATCH 29/34] =?UTF-8?q?update=20the=20var=20in=20the=20in=20file?=
 =?UTF-8?q?=20too....=20=F0=9F=A4=A6?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 CZICheck/inc_libCZI.h.in | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CZICheck/inc_libCZI.h.in b/CZICheck/inc_libCZI.h.in
index 8b20203..5f6410f 100644
--- a/CZICheck/inc_libCZI.h.in
+++ b/CZICheck/inc_libCZI.h.in
@@ -4,4 +4,4 @@
 
 #pragma once
 
-#include <@LIBCZI_HEADER_PATH@>
+#include <@CZICHECK_LIBCZI_HEADER_PATH@>

From 2b64dc70ae4169ebabdd5d0ef9dd0eb34bef9a05 Mon Sep 17 00:00:00 2001
From: DaveyJonesBitPail <119518234+DaveyJonesBitPail@users.noreply.github.com>
Date: Wed, 6 Aug 2025 21:37:30 +0200
Subject: [PATCH 30/34] unpin libczi version

---
 CMakeLists.txt        | 1 -
 modules/libCZI.cmake  | 2 +-
 modules/pugiXML.cmake | 4 +---
 3 files changed, 2 insertions(+), 5 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 890f4c1..d6d9180 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -18,7 +18,6 @@ project(CZICheck
       DESCRIPTION "CZICheck is a validator for CZI-documents")
 
 
-
 if(WIN32)
   # use "static C-runtime" -> https://stackoverflow.com/questions/14172856/compile-with-mt-instead-of-md-using-cmake
   # Note: this requires CMAKE version 3.15+
diff --git a/modules/libCZI.cmake b/modules/libCZI.cmake
index 9430dcb..20ebaaf 100644
--- a/modules/libCZI.cmake
+++ b/modules/libCZI.cmake
@@ -7,7 +7,7 @@ include(FetchContent)
 FetchContent_Declare(
   libCZI
   GIT_REPOSITORY https://github.com/ZEISS/libczi.git
-  GIT_TAG        545098455ef50fdc7d4d8615bfa0c5bd78f52df7
+  GIT_TAG        origin/main
 )
 
 if(NOT libCZI_POPULATED)
diff --git a/modules/pugiXML.cmake b/modules/pugiXML.cmake
index c524421..72ed5a9 100644
--- a/modules/pugiXML.cmake
+++ b/modules/pugiXML.cmake
@@ -17,9 +17,7 @@ if (NOT pugixml_POPULATED)
 
   FetchContent_MakeAvailable(pugixml)
   set(PUGIXML_INCLUDE_DIRS ${pugixml_SOURCE_DIR}/include)
-  if(CZICHECK_ENABLE_VCPKG_BOOTSTRAP)
-    target_compile_definitions(pugixml INTERFACE PUGIXML_WCHAR_MODE PUGIXML_HEADER_ONLY)
-  endif()
+  target_compile_definitions(pugixml INTERFACE PUGIXML_WCHAR_MODE PUGIXML_HEADER_ONLY)
 endif()
 
 message(STATUS "PugiXML include dir at " ${PUGIXML_INCLUDE_DIRS})

From d254688bc2edcb2a98af56e0f1504cee16d56ac3 Mon Sep 17 00:00:00 2001
From: DaveyJonesBitPail <119518234+DaveyJonesBitPail@users.noreply.github.com>
Date: Wed, 6 Aug 2025 21:53:05 +0200
Subject: [PATCH 31/34] Revert "unpin libczi version"

This reverts commit 2b64dc70ae4169ebabdd5d0ef9dd0eb34bef9a05.
---
 CMakeLists.txt        | 1 +
 modules/libCZI.cmake  | 2 +-
 modules/pugiXML.cmake | 4 +++-
 3 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index d6d9180..890f4c1 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -18,6 +18,7 @@ project(CZICheck
       DESCRIPTION "CZICheck is a validator for CZI-documents")
 
 
+
 if(WIN32)
   # use "static C-runtime" -> https://stackoverflow.com/questions/14172856/compile-with-mt-instead-of-md-using-cmake
   # Note: this requires CMAKE version 3.15+
diff --git a/modules/libCZI.cmake b/modules/libCZI.cmake
index 20ebaaf..9430dcb 100644
--- a/modules/libCZI.cmake
+++ b/modules/libCZI.cmake
@@ -7,7 +7,7 @@ include(FetchContent)
 FetchContent_Declare(
   libCZI
   GIT_REPOSITORY https://github.com/ZEISS/libczi.git
-  GIT_TAG        origin/main
+  GIT_TAG        545098455ef50fdc7d4d8615bfa0c5bd78f52df7
 )
 
 if(NOT libCZI_POPULATED)
diff --git a/modules/pugiXML.cmake b/modules/pugiXML.cmake
index 72ed5a9..c524421 100644
--- a/modules/pugiXML.cmake
+++ b/modules/pugiXML.cmake
@@ -17,7 +17,9 @@ if (NOT pugixml_POPULATED)
 
   FetchContent_MakeAvailable(pugixml)
   set(PUGIXML_INCLUDE_DIRS ${pugixml_SOURCE_DIR}/include)
-  target_compile_definitions(pugixml INTERFACE PUGIXML_WCHAR_MODE PUGIXML_HEADER_ONLY)
+  if(CZICHECK_ENABLE_VCPKG_BOOTSTRAP)
+    target_compile_definitions(pugixml INTERFACE PUGIXML_WCHAR_MODE PUGIXML_HEADER_ONLY)
+  endif()
 endif()
 
 message(STATUS "PugiXML include dir at " ${PUGIXML_INCLUDE_DIRS})

From 9540a557693c2378280a421bfea0de7e0440685b Mon Sep 17 00:00:00 2001
From: DaveyJonesBitPail <119518234+DaveyJonesBitPail@users.noreply.github.com>
Date: Wed, 24 Sep 2025 09:20:22 +0200
Subject: [PATCH 32/34] address pr comments

---
 CZICheck/CMakeLists.txt                    | 90 ++++++++++------------
 CZICheck/checkers/checkerbase.h            |  2 +-
 CZICheck/{inc_libCZI.h.in => inc_libCZI.h} |  2 +-
 CZICheck/resultgathererxml.h               |  1 -
 modules/bootstrapVcpkg.cmake               |  6 +-
 vcpkg.json                                 |  1 -
 6 files changed, 47 insertions(+), 55 deletions(-)
 rename CZICheck/{inc_libCZI.h.in => inc_libCZI.h} (72%)

diff --git a/CZICheck/CMakeLists.txt b/CZICheck/CMakeLists.txt
index ecebc06..5466a7e 100644
--- a/CZICheck/CMakeLists.txt
+++ b/CZICheck/CMakeLists.txt
@@ -34,32 +34,19 @@ else()
     message("XercesC library not found, the checker 'xmlmetadataschema' will **not** be available")
 endif()
 
-if(NOT CZICHECK_ENABLE_VCPKG_BOOTSTRAP)
-  include(FetchContent)
-  FetchContent_Declare(
-    cli11
-    GIT_REPOSITORY https://github.com/CLIUtils/CLI11
-    GIT_TAG        v2.3.2
-  )
+include(FetchContent)
+FetchContent_Declare(
+  cli11
+  GIT_REPOSITORY https://github.com/CLIUtils/CLI11
+  GIT_TAG        v2.3.2
+)
 
-  FetchContent_MakeAvailable(cli11)
-endif()
+FetchContent_MakeAvailable(cli11)
 
 if(CZICHECK_ENABLE_VCPKG_BOOTSTRAP)
   find_package(libCZI CONFIG REQUIRED)
-  find_package(CLI11 CONFIG REQUIRED)
-endif()
-
-if(CZICHECK_ENABLE_VCPKG_BOOTSTRAP)
-  set(CZICHECK_LIBCZI_HEADER_PATH "libCZI/libCZI.h")
-else()
-  set(CZICHECK_LIBCZI_HEADER_PATH "libCZI.h")
 endif()
 
-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/inc_libCZI.h.in
-               ${CMAKE_CURRENT_BINARY_DIR}/inc_libCZI.h
-               @ONLY)
-
 set(CZICHECKSRCFILES 
 "checkers/checkerbase.h"
 "checkers/checkerbase.cpp"
@@ -93,30 +80,31 @@ set(CZICHECKSRCFILES
 "checkers/checkerSubBlkBitmapValid.cpp"
 "checkers/checkerTopographyApplianceValidation.h"
 "checkers/checkerTopographyApplianceValidation.cpp"
-checkerfactory.cpp
-checkerfactory.h
-checks.h
-checks.cpp
-CMakeLists.txt
-cmdlineoptions.cpp
-cmdlineoptions.h
-consoleio.cpp
-consoleio.h
-CZICheck.cpp
-IChecker.h
-IResultGatherer.h
-resultgatherer.cpp
-resultgatherer.h
-resultgathererjson.h
-resultgathererjson.cpp
-resultgathererxml.h
-resultgathererxml.cpp
-resultgathererfactory.h
-resultgathererfactory.cpp
-runchecks.cpp
-runchecks.h
-utils.h
-utils.cpp
+"checkerfactory.cpp"
+"checkerfactory.h"
+"checks.h"
+"checks.cpp"
+"CMakeLists.txt"
+"cmdlineoptions.cpp"
+"cmdlineoptions.h"
+"consoleio.cpp"
+"consoleio.h"
+"CZICheck.cpp"
+"IChecker.h"
+"IResultGatherer.h"
+"resultgatherer.cpp"
+"resultgatherer.h"
+"resultgathererjson.h"
+"resultgathererjson.cpp"
+"resultgathererxml.h"
+"resultgathererxml.cpp"
+"resultgathererfactory.h"
+"resultgathererfactory.cpp"
+"runchecks.cpp"
+"runchecks.h"
+"utils.h"
+"utils.cpp"
+"inc_libCZI.h"
 )
 
 add_executable(CZICheck ${CZICHECKSRCFILES} )
@@ -126,6 +114,8 @@ target_compile_definitions(CZICheck PRIVATE _LIBCZISTATICLIB)
 
 target_link_libraries(CZICheck PRIVATE CLI11::CLI11)
 
+target_include_directories(CZICheck PRIVATE ${CMAKE_CURRENT_SOURCE_DIR})
+
 if(CZICHECK_ENABLE_VCPKG_BOOTSTRAP)
   if(TARGET libczi::libCZI)
       add_library(libczi::libCZI_selected ALIAS libczi::libCZI)
@@ -134,16 +124,20 @@ if(CZICHECK_ENABLE_VCPKG_BOOTSTRAP)
   else()
       message(FATAL_ERROR "No suitable libCZI target found (neither shared nor static).")
   endif()
-
-    target_link_libraries(CZICheck PRIVATE libczi::libCZI_selected)
+  target_link_libraries(CZICheck PRIVATE libczi::libCZI_selected)
 else()
   target_link_libraries(CZICheck PRIVATE libCZIStatic)
 endif()
-
+if(CZICHECK_ENABLE_VCPKG_BOOTSTRAP)
+  get_target_property(_libczi_includes libczi::libCZI_selected INTERFACE_INCLUDE_DIRECTORIES)
+  set(_libczi_include_with_subdir "${_libczi_includes}/libCZI")
+  target_include_directories(CZICheck PRIVATE ${_libczi_include_with_subdir})
+else()
+  target_include_directories(CZICheck PRIVATE ${LIBCZI_INCLUDE_DIR})
+endif()
 target_link_libraries(CZICheck PRIVATE pugixml)
 
 target_include_directories(CZICheck
-  PRIVATE ${LIBCZI_INCLUDE_DIR}
   PRIVATE ${RAPIDJSON_INCLUDE_DIRS})
 
 if (XercesC_FOUND)
diff --git a/CZICheck/checkers/checkerbase.h b/CZICheck/checkers/checkerbase.h
index 162b20a..cce41eb 100644
--- a/CZICheck/checkers/checkerbase.h
+++ b/CZICheck/checkers/checkerbase.h
@@ -4,7 +4,7 @@
 
 #pragma once
 
-#include "inc_libCZI.h"
+#include <inc_libCZI.h>
 #include "../checkerfactory.h"
 #include <memory>
 #include <utility>
diff --git a/CZICheck/inc_libCZI.h.in b/CZICheck/inc_libCZI.h
similarity index 72%
rename from CZICheck/inc_libCZI.h.in
rename to CZICheck/inc_libCZI.h
index 5f6410f..fc95f11 100644
--- a/CZICheck/inc_libCZI.h.in
+++ b/CZICheck/inc_libCZI.h
@@ -4,4 +4,4 @@
 
 #pragma once
 
-#include <@CZICHECK_LIBCZI_HEADER_PATH@>
+#include <libCZI.h>
diff --git a/CZICheck/resultgathererxml.h b/CZICheck/resultgathererxml.h
index 9ce4786..4b458a7 100644
--- a/CZICheck/resultgathererxml.h
+++ b/CZICheck/resultgathererxml.h
@@ -12,7 +12,6 @@
 #include "pugiconfig.hpp"
 #include <string>
 
-
 class CResultGathererXml : public IResultGatherer
 {
 private:
diff --git a/modules/bootstrapVcpkg.cmake b/modules/bootstrapVcpkg.cmake
index 7447669..a332fd2 100644
--- a/modules/bootstrapVcpkg.cmake
+++ b/modules/bootstrapVcpkg.cmake
@@ -19,7 +19,7 @@ else()
     set(VCPKG_EXECUTABLE "${VCPKG_DIR}/vcpkg")
 endif()
 
-if(DEFINED ENV{VCPKG_ROOT} AND EXISTS "$ENV{VCPKG_ROOT}/vcpkg")
+if(DEFINED ENV{VCPKG_ROOT} AND EXISTS "$ENV{VCPKG_ROOT}/vcpkg" AND NOT DEFINED VCPKG_EXECUTABLE)
     set(VCPKG_DIR "$ENV{VCPKG_ROOT}")
     if(WIN32)
         set(VCPKG_EXECUTABLE "${VCPKG_DIR}/vcpkg.exe")
@@ -75,7 +75,7 @@ if(NOT EXISTS "${VCPKG_EXECUTABLE}")
           endif()
         endif()
     else()
-        message(STATUS "Found vcpkg folder at ${VCPKG_DIR}, skipping clone.")
+        message(STATUS "Found vcpkg directory at ${VCPKG_DIR}, skipping clone.")
     endif()
 
     message(STATUS "Bootstrapping vcpkg...")
@@ -103,4 +103,4 @@ set(CMAKE_TOOLCHAIN_FILE "${VCPKG_DIR}/scripts/buildsystems/vcpkg.cmake"
 
 set(VCPKG_FEATURE_FLAGS "manifests" CACHE STRING "")
 
-message(STATUS "vcpkg is ready. Toolchain file: ${CMAKE_TOOLCHAIN_FILE}")
+message(STATUS "vcpkg is ready. Toolchain file: ${CMAKE_TOOLCHAIN_FILE}")
\ No newline at end of file
diff --git a/vcpkg.json b/vcpkg.json
index 65baeda..789044e 100644
--- a/vcpkg.json
+++ b/vcpkg.json
@@ -3,7 +3,6 @@
   "version-string": "0.6.4",
   "dependencies": [
     "libczi",
-    "cli11",
     "rapidjson",
     "xerces-c"
   ],

From 8dad9a877e275ddbeea78023107961a8ed5999d4 Mon Sep 17 00:00:00 2001
From: DaveyJonesBitPail <119518234+DaveyJonesBitPail@users.noreply.github.com>
Date: Wed, 24 Sep 2025 09:36:41 +0200
Subject: [PATCH 33/34] bump version

---
 CMakeLists.txt                   | 2 +-
 documentation/version-history.md | 1 +
 vcpkg.json                       | 2 +-
 3 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 890f4c1..1fbc490 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -13,7 +13,7 @@ if(CZICHECK_ENABLE_VCPKG_BOOTSTRAP)
 endif()
 
 project(CZICheck 
-      VERSION 0.6.4
+      VERSION 0.6.5
       HOMEPAGE_URL "https://github.com/ZEISS/czicheck"
       DESCRIPTION "CZICheck is a validator for CZI-documents")
 
diff --git a/documentation/version-history.md b/documentation/version-history.md
index 2d8af9b..d43574e 100644
--- a/documentation/version-history.md
+++ b/documentation/version-history.md
@@ -17,3 +17,4 @@ version history                 {#version_history}
  0.6.2          | [29](https://github.com/ZEISS/czicheck/pull/29)      | fix issue in metadata-schema (with "TopographyDataItem" and with AxioScan-documents)
  0.6.3          | [31](https://github.com/ZEISS/czicheck/pull/31)      | add option to ignore "size-m-field-for-pyramid-subblocks"
  0.6.4          | [34](https://github.com/ZEISS/czicheck/pull/34)      | align with libCZI 0.64.0 and pin version
+ 0.6.5          | [36](https://github.com/ZEISS/czicheck/pull/36)      | enable libCZI vpkg consumption and add optional bootstrap
diff --git a/vcpkg.json b/vcpkg.json
index 789044e..4fb8cb1 100644
--- a/vcpkg.json
+++ b/vcpkg.json
@@ -1,6 +1,6 @@
 {
   "name": "czicheck",
-  "version-string": "0.6.4",
+  "version-string": "0.6.5",
   "dependencies": [
     "libczi",
     "rapidjson",

From 8d0e4a53cf8c47b202e29527f38003908d56fae6 Mon Sep 17 00:00:00 2001
From: DaveyJonesBitPail <119518234+DaveyJonesBitPail@users.noreply.github.com>
Date: Wed, 24 Sep 2025 09:43:38 +0200
Subject: [PATCH 34/34] blindly update version in tests

---
 Test/CZICheckSamples/differentpixeltypeinchannel.txt.json       | 2 +-
 Test/CZICheckSamples/differentpixeltypeinchannel.txt.xml        | 2 +-
 Test/CZICheckSamples/duplicate_coordinates.txt.json             | 2 +-
 Test/CZICheckSamples/duplicate_coordinates.txt.xml              | 2 +-
 Test/CZICheckSamples/edf-missing-texture.txt.json               | 2 +-
 Test/CZICheckSamples/edf-missing-texture.txt.xml                | 2 +-
 .../edf-superfluous-missing-channel-subblock.txt.json           | 2 +-
 .../edf-superfluous-missing-channel-subblock.txt.xml            | 2 +-
 Test/CZICheckSamples/edf-superfluous.txt.json                   | 2 +-
 Test/CZICheckSamples/edf-superfluous.txt.xml                    | 2 +-
 Test/CZICheckSamples/inconsistent_coordinates.txt.json          | 2 +-
 Test/CZICheckSamples/inconsistent_coordinates.txt.xml           | 2 +-
 Test/CZICheckSamples/invalid_componentbitcount.txt.json         | 2 +-
 Test/CZICheckSamples/invalid_componentbitcount.txt.xml          | 2 +-
 .../jpgxrcompressed_inconsistent_pixeltype.txt.json             | 2 +-
 .../jpgxrcompressed_inconsistent_pixeltype.txt.xml              | 2 +-
 Test/CZICheckSamples/jpgxrcompressed_inconsistent_size.txt.json | 2 +-
 Test/CZICheckSamples/jpgxrcompressed_inconsistent_size.txt.xml  | 2 +-
 Test/CZICheckSamples/layer_0_subblocks_with_no_m_index.txt.json | 2 +-
 Test/CZICheckSamples/layer_0_subblocks_with_no_m_index.txt.xml  | 2 +-
 Test/CZICheckSamples/negative_plane_start_index.txt.json        | 2 +-
 Test/CZICheckSamples/negative_plane_start_index.txt.xml         | 2 +-
 Test/CZICheckSamples/overlapping_scenes.txt.json                | 2 +-
 Test/CZICheckSamples/overlapping_scenes.txt.xml                 | 2 +-
 .../pixeltype_mismatch_between_metadata_and_subblocks.txt.json  | 2 +-
 .../pixeltype_mismatch_between_metadata_and_subblocks.txt.xml   | 2 +-
 Test/CZICheckSamples/positive_plane_start_index.txt.json        | 2 +-
 Test/CZICheckSamples/positive_plane_start_index.txt.xml         | 2 +-
 Test/CZICheckSamples/sparse_planes.txt.json                     | 2 +-
 Test/CZICheckSamples/sparse_planes.txt.xml                      | 2 +-
 30 files changed, 30 insertions(+), 30 deletions(-)

diff --git a/Test/CZICheckSamples/differentpixeltypeinchannel.txt.json b/Test/CZICheckSamples/differentpixeltypeinchannel.txt.json
index 74ea8fd..8a50d76 100644
--- a/Test/CZICheckSamples/differentpixeltypeinchannel.txt.json
+++ b/Test/CZICheckSamples/differentpixeltypeinchannel.txt.json
@@ -112,6 +112,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.4"
+        "version": "0.6.5"
     }
 }
\ No newline at end of file
diff --git a/Test/CZICheckSamples/differentpixeltypeinchannel.txt.xml b/Test/CZICheckSamples/differentpixeltypeinchannel.txt.xml
index 8786fd8..f469313 100644
--- a/Test/CZICheckSamples/differentpixeltypeinchannel.txt.xml
+++ b/Test/CZICheckSamples/differentpixeltypeinchannel.txt.xml
@@ -99,6 +99,6 @@
   <AggregatedResult>WARN</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.4</Version>
+    <Version>0.6.5</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/duplicate_coordinates.txt.json b/Test/CZICheckSamples/duplicate_coordinates.txt.json
index f49dff0..402b1e7 100644
--- a/Test/CZICheckSamples/duplicate_coordinates.txt.json
+++ b/Test/CZICheckSamples/duplicate_coordinates.txt.json
@@ -112,6 +112,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.4"
+        "version": "0.6.5"
     }
 }
\ No newline at end of file
diff --git a/Test/CZICheckSamples/duplicate_coordinates.txt.xml b/Test/CZICheckSamples/duplicate_coordinates.txt.xml
index 75987a3..fdda618 100644
--- a/Test/CZICheckSamples/duplicate_coordinates.txt.xml
+++ b/Test/CZICheckSamples/duplicate_coordinates.txt.xml
@@ -99,6 +99,6 @@
   <AggregatedResult>FAIL</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.4</Version>
+    <Version>0.6.5</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/edf-missing-texture.txt.json b/Test/CZICheckSamples/edf-missing-texture.txt.json
index 2205402..2efe61d 100644
--- a/Test/CZICheckSamples/edf-missing-texture.txt.json
+++ b/Test/CZICheckSamples/edf-missing-texture.txt.json
@@ -105,6 +105,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.4"
+        "version": "0.6.5"
     }
 }
\ No newline at end of file
diff --git a/Test/CZICheckSamples/edf-missing-texture.txt.xml b/Test/CZICheckSamples/edf-missing-texture.txt.xml
index 5fefa33..236bfe6 100644
--- a/Test/CZICheckSamples/edf-missing-texture.txt.xml
+++ b/Test/CZICheckSamples/edf-missing-texture.txt.xml
@@ -92,6 +92,6 @@
   <AggregatedResult>FAIL</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.4</Version>
+    <Version>0.6.5</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/edf-superfluous-missing-channel-subblock.txt.json b/Test/CZICheckSamples/edf-superfluous-missing-channel-subblock.txt.json
index 4c3913c..7979331 100644
--- a/Test/CZICheckSamples/edf-superfluous-missing-channel-subblock.txt.json
+++ b/Test/CZICheckSamples/edf-superfluous-missing-channel-subblock.txt.json
@@ -126,6 +126,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.4"
+        "version": "0.6.5"
     }
 }
\ No newline at end of file
diff --git a/Test/CZICheckSamples/edf-superfluous-missing-channel-subblock.txt.xml b/Test/CZICheckSamples/edf-superfluous-missing-channel-subblock.txt.xml
index fbe5ba8..60477d7 100644
--- a/Test/CZICheckSamples/edf-superfluous-missing-channel-subblock.txt.xml
+++ b/Test/CZICheckSamples/edf-superfluous-missing-channel-subblock.txt.xml
@@ -113,6 +113,6 @@
   <AggregatedResult>FAIL</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.4</Version>
+    <Version>0.6.5</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/edf-superfluous.txt.json b/Test/CZICheckSamples/edf-superfluous.txt.json
index b855e12..8ec892a 100644
--- a/Test/CZICheckSamples/edf-superfluous.txt.json
+++ b/Test/CZICheckSamples/edf-superfluous.txt.json
@@ -105,6 +105,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.4"
+        "version": "0.6.5"
     }
 }
\ No newline at end of file
diff --git a/Test/CZICheckSamples/edf-superfluous.txt.xml b/Test/CZICheckSamples/edf-superfluous.txt.xml
index 7c3095b..ad38504 100644
--- a/Test/CZICheckSamples/edf-superfluous.txt.xml
+++ b/Test/CZICheckSamples/edf-superfluous.txt.xml
@@ -92,6 +92,6 @@
   <AggregatedResult>FAIL</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.4</Version>
+    <Version>0.6.5</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/inconsistent_coordinates.txt.json b/Test/CZICheckSamples/inconsistent_coordinates.txt.json
index 3f0c9a9..5f61086 100644
--- a/Test/CZICheckSamples/inconsistent_coordinates.txt.json
+++ b/Test/CZICheckSamples/inconsistent_coordinates.txt.json
@@ -112,6 +112,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.4"
+        "version": "0.6.5"
     }
 }
\ No newline at end of file
diff --git a/Test/CZICheckSamples/inconsistent_coordinates.txt.xml b/Test/CZICheckSamples/inconsistent_coordinates.txt.xml
index a5df585..1ca061b 100644
--- a/Test/CZICheckSamples/inconsistent_coordinates.txt.xml
+++ b/Test/CZICheckSamples/inconsistent_coordinates.txt.xml
@@ -99,6 +99,6 @@
   <AggregatedResult>FAIL</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.4</Version>
+    <Version>0.6.5</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/invalid_componentbitcount.txt.json b/Test/CZICheckSamples/invalid_componentbitcount.txt.json
index e3caf81..90e958a 100644
--- a/Test/CZICheckSamples/invalid_componentbitcount.txt.json
+++ b/Test/CZICheckSamples/invalid_componentbitcount.txt.json
@@ -94,6 +94,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.4"
+        "version": "0.6.5"
     }
 }
\ No newline at end of file
diff --git a/Test/CZICheckSamples/invalid_componentbitcount.txt.xml b/Test/CZICheckSamples/invalid_componentbitcount.txt.xml
index 55481ba..a8f83b5 100644
--- a/Test/CZICheckSamples/invalid_componentbitcount.txt.xml
+++ b/Test/CZICheckSamples/invalid_componentbitcount.txt.xml
@@ -81,6 +81,6 @@
   <AggregatedResult>WARN</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.4</Version>
+    <Version>0.6.5</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/jpgxrcompressed_inconsistent_pixeltype.txt.json b/Test/CZICheckSamples/jpgxrcompressed_inconsistent_pixeltype.txt.json
index 3b6c4f9..66027c4 100644
--- a/Test/CZICheckSamples/jpgxrcompressed_inconsistent_pixeltype.txt.json
+++ b/Test/CZICheckSamples/jpgxrcompressed_inconsistent_pixeltype.txt.json
@@ -94,6 +94,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.4"
+        "version": "0.6.5"
     }
 }
\ No newline at end of file
diff --git a/Test/CZICheckSamples/jpgxrcompressed_inconsistent_pixeltype.txt.xml b/Test/CZICheckSamples/jpgxrcompressed_inconsistent_pixeltype.txt.xml
index 6732271..e3b5814 100644
--- a/Test/CZICheckSamples/jpgxrcompressed_inconsistent_pixeltype.txt.xml
+++ b/Test/CZICheckSamples/jpgxrcompressed_inconsistent_pixeltype.txt.xml
@@ -81,6 +81,6 @@
   <AggregatedResult>WARN</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.4</Version>
+    <Version>0.6.5</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/jpgxrcompressed_inconsistent_size.txt.json b/Test/CZICheckSamples/jpgxrcompressed_inconsistent_size.txt.json
index 3b6c4f9..66027c4 100644
--- a/Test/CZICheckSamples/jpgxrcompressed_inconsistent_size.txt.json
+++ b/Test/CZICheckSamples/jpgxrcompressed_inconsistent_size.txt.json
@@ -94,6 +94,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.4"
+        "version": "0.6.5"
     }
 }
\ No newline at end of file
diff --git a/Test/CZICheckSamples/jpgxrcompressed_inconsistent_size.txt.xml b/Test/CZICheckSamples/jpgxrcompressed_inconsistent_size.txt.xml
index 6732271..e3b5814 100644
--- a/Test/CZICheckSamples/jpgxrcompressed_inconsistent_size.txt.xml
+++ b/Test/CZICheckSamples/jpgxrcompressed_inconsistent_size.txt.xml
@@ -81,6 +81,6 @@
   <AggregatedResult>WARN</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.4</Version>
+    <Version>0.6.5</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/layer_0_subblocks_with_no_m_index.txt.json b/Test/CZICheckSamples/layer_0_subblocks_with_no_m_index.txt.json
index 76613cc..3803c0c 100644
--- a/Test/CZICheckSamples/layer_0_subblocks_with_no_m_index.txt.json
+++ b/Test/CZICheckSamples/layer_0_subblocks_with_no_m_index.txt.json
@@ -100,6 +100,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.4"
+        "version": "0.6.5"
     }
 }
\ No newline at end of file
diff --git a/Test/CZICheckSamples/layer_0_subblocks_with_no_m_index.txt.xml b/Test/CZICheckSamples/layer_0_subblocks_with_no_m_index.txt.xml
index 5ec6f00..ea15682 100644
--- a/Test/CZICheckSamples/layer_0_subblocks_with_no_m_index.txt.xml
+++ b/Test/CZICheckSamples/layer_0_subblocks_with_no_m_index.txt.xml
@@ -87,6 +87,6 @@
   <AggregatedResult>WARN</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.4</Version>
+    <Version>0.6.5</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/negative_plane_start_index.txt.json b/Test/CZICheckSamples/negative_plane_start_index.txt.json
index e211eb8..7cfff63 100644
--- a/Test/CZICheckSamples/negative_plane_start_index.txt.json
+++ b/Test/CZICheckSamples/negative_plane_start_index.txt.json
@@ -105,6 +105,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.4"
+        "version": "0.6.5"
     }
 }
\ No newline at end of file
diff --git a/Test/CZICheckSamples/negative_plane_start_index.txt.xml b/Test/CZICheckSamples/negative_plane_start_index.txt.xml
index 66584fb..ee324a5 100644
--- a/Test/CZICheckSamples/negative_plane_start_index.txt.xml
+++ b/Test/CZICheckSamples/negative_plane_start_index.txt.xml
@@ -92,6 +92,6 @@
   <AggregatedResult>WARN</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.4</Version>
+    <Version>0.6.5</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/overlapping_scenes.txt.json b/Test/CZICheckSamples/overlapping_scenes.txt.json
index 73a1344..7e3f896 100644
--- a/Test/CZICheckSamples/overlapping_scenes.txt.json
+++ b/Test/CZICheckSamples/overlapping_scenes.txt.json
@@ -136,6 +136,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.4"
+        "version": "0.6.5"
     }
 }
\ No newline at end of file
diff --git a/Test/CZICheckSamples/overlapping_scenes.txt.xml b/Test/CZICheckSamples/overlapping_scenes.txt.xml
index 3101890..219aa04 100644
--- a/Test/CZICheckSamples/overlapping_scenes.txt.xml
+++ b/Test/CZICheckSamples/overlapping_scenes.txt.xml
@@ -123,6 +123,6 @@
   <AggregatedResult>FAIL</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.4</Version>
+    <Version>0.6.5</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/pixeltype_mismatch_between_metadata_and_subblocks.txt.json b/Test/CZICheckSamples/pixeltype_mismatch_between_metadata_and_subblocks.txt.json
index 3cd08b2..72ef0b8 100644
--- a/Test/CZICheckSamples/pixeltype_mismatch_between_metadata_and_subblocks.txt.json
+++ b/Test/CZICheckSamples/pixeltype_mismatch_between_metadata_and_subblocks.txt.json
@@ -181,6 +181,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.4"
+        "version": "0.6.5"
     }
 }
\ No newline at end of file
diff --git a/Test/CZICheckSamples/pixeltype_mismatch_between_metadata_and_subblocks.txt.xml b/Test/CZICheckSamples/pixeltype_mismatch_between_metadata_and_subblocks.txt.xml
index d7313b1..1d07722 100644
--- a/Test/CZICheckSamples/pixeltype_mismatch_between_metadata_and_subblocks.txt.xml
+++ b/Test/CZICheckSamples/pixeltype_mismatch_between_metadata_and_subblocks.txt.xml
@@ -168,6 +168,6 @@
   <AggregatedResult>FAIL</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.4</Version>
+    <Version>0.6.5</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/positive_plane_start_index.txt.json b/Test/CZICheckSamples/positive_plane_start_index.txt.json
index c6e97cd..a018613 100644
--- a/Test/CZICheckSamples/positive_plane_start_index.txt.json
+++ b/Test/CZICheckSamples/positive_plane_start_index.txt.json
@@ -105,6 +105,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.4"
+        "version": "0.6.5"
     }
 }
\ No newline at end of file
diff --git a/Test/CZICheckSamples/positive_plane_start_index.txt.xml b/Test/CZICheckSamples/positive_plane_start_index.txt.xml
index 35e04ad..684e945 100644
--- a/Test/CZICheckSamples/positive_plane_start_index.txt.xml
+++ b/Test/CZICheckSamples/positive_plane_start_index.txt.xml
@@ -92,6 +92,6 @@
   <AggregatedResult>WARN</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.4</Version>
+    <Version>0.6.5</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/sparse_planes.txt.json b/Test/CZICheckSamples/sparse_planes.txt.json
index 5cf88f0..f0040a9 100644
--- a/Test/CZICheckSamples/sparse_planes.txt.json
+++ b/Test/CZICheckSamples/sparse_planes.txt.json
@@ -105,6 +105,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.4"
+        "version": "0.6.5"
     }
 }
\ No newline at end of file
diff --git a/Test/CZICheckSamples/sparse_planes.txt.xml b/Test/CZICheckSamples/sparse_planes.txt.xml
index 77b328c..3caed41 100644
--- a/Test/CZICheckSamples/sparse_planes.txt.xml
+++ b/Test/CZICheckSamples/sparse_planes.txt.xml
@@ -92,6 +92,6 @@
   <AggregatedResult>WARN</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.4</Version>
+    <Version>0.6.5</Version>
   </OutputVersion>
 </TestResults>