CMake: vendor Eigen (5.0.1) and libjpeg-turbo so the build is self-contained

Two deps the Linux build picked up from the system were absent on Windows.
Bundle both, unconditionally (matching how libtiff/FFTW are vendored), so the
tree builds without system Eigen/JPEG:

- Eigen 5.0.1 via FetchContent with OVERRIDE_FIND_PACKAGE, so every
  find_package(Eigen3) -- ours, Ceres', and ffbidx' -- resolves to this copy and
  the requested 3.4 version is satisfied by the newer major. ffbidx's bundled
  eigen submodule is disabled (GIT_SUBMODULES "" on fast-indexer) so it no longer
  creates a duplicate Eigen3::Eigen target. Verified on a CUDA build: Ceres 2.3.0,
  the analysis libs, and ffbidx's CUDA code all compile against 5.0.1.

- libjpeg-turbo 3.0.4 via ExternalProject (upstream discourages add_subdirectory);
  built+installed static and imported as JPEG::JPEG, replacing find_package(JPEG)
  in preview/. SIMD is lazy: WITH_SIMD=ON + REQUIRE_SIMD=OFF means NASM-accelerated
  when nasm is present, otherwise a warning and a scalar build (no hard failure).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

CMakeLists.txt

@@ -213,6 +213,21 @@ FetchContent_MakeAvailable(fftw)
 TARGET_INCLUDE_DIRECTORIES(fftw3f INTERFACE $<BUILD_INTERFACE:${fftw_SOURCE_DIR}/api>)
 ADD_COMPILE_DEFINITIONS(JFJOCH_USE_FFTW)
 
+# Eigen (header-only): consumed by Ceres and by the analysis libs directly, and by ffbidx under
+# CUDA. Not auto-provided by FetchContent and absent on Windows, so vendor it here. OVERRIDE_FIND_PACKAGE
+# routes every find_package(Eigen3) -- ours, Ceres', ffbidx' -- to this copy and bypasses the version
+# request (they ask for 3.4; this is a newer major). ffbidx's own bundled eigen is disabled below
+# (GIT_SUBMODULES "" on fast-indexer) so it does not create a duplicate Eigen3::Eigen target.
+SET(EIGEN_BUILD_DOC OFF CACHE BOOL "" FORCE)
+SET(EIGEN_BUILD_TESTING OFF CACHE BOOL "" FORCE)
+SET(EIGEN_BUILD_PKGCONFIG OFF CACHE BOOL "" FORCE)
+FetchContent_Declare(Eigen3
+        GIT_REPOSITORY https://gitlab.com/libeigen/eigen.git
+        GIT_TAG 5.0.1
+        GIT_SHALLOW TRUE
+        EXCLUDE_FROM_ALL
+        OVERRIDE_FIND_PACKAGE)
+
 IF (JFJOCH_VIEWER_ONLY)
     # Minimal subtree: jfjoch_viewer and only the libraries it transitively links.
     # (broker here provides JFJochAPI only; its service targets are gated out.)

image_analysis/indexing/CMakeLists.txt

@@ -19,10 +19,14 @@ ADD_LIBRARY(JFJochIndexing STATIC
 TARGET_LINK_LIBRARIES(JFJochIndexing JFJochCommon JFJochLatticeSearch)
 
 IF (JFJOCH_CUDA_AVAILABLE)
+    # GIT_SUBMODULES "" -> do not fetch ffbidx's bundled eigen submodule; it would add_subdirectory
+    # a second Eigen3::Eigen target. ffbidx instead resolves Eigen via the project-level Eigen3
+    # (OVERRIDE_FIND_PACKAGE in the top-level CMakeLists).
     FetchContent_Declare(
             fast-indexer
             GIT_REPOSITORY https://github.com/paulscherrerinstitute/fast-feedback-indexer/
             GIT_TAG ca9e17486a1eb96319a738acef33cc24c9cd8845
+            GIT_SUBMODULES ""
     )
 
     FetchContent_MakeAvailable(fast-indexer)

preview/CMakeLists.txt

@@ -1,7 +1,48 @@
 include(ExternalProject)
 
 find_package(ZLIB REQUIRED)
-find_package(JPEG REQUIRED)
+
+# libjpeg-turbo: upstream does NOT support add_subdirectory/FetchContent inclusion, so build and
+# install it out-of-line and import the static lib. (Adapted from aseprite's FindJpegTurbo.cmake.)
+# The static lib is `jpeg-static.lib` on MSVC and `libjpeg.a` elsewhere.
+IF (MSVC)
+    SET(LIBJPEG_TURBO_STATIC_SUFFIX "-static")
+ELSE()
+    SET(LIBJPEG_TURBO_STATIC_SUFFIX "")
+ENDIF()
+SET(LIBJPEG_TURBO_DIR "${CMAKE_CURRENT_BINARY_DIR}/libjpeg-turbo")
+SET(LIBJPEG_TURBO_LIBRARY "${LIBJPEG_TURBO_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}jpeg${LIBJPEG_TURBO_STATIC_SUFFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}")
+SET(LIBJPEG_TURBO_INCLUDE_DIRS "${LIBJPEG_TURBO_DIR}/include")
+
+ExternalProject_Add(libjpeg-turbo-project
+        GIT_REPOSITORY https://github.com/libjpeg-turbo/libjpeg-turbo
+        GIT_TAG 3.0.4
+        PREFIX "${LIBJPEG_TURBO_DIR}"
+        INSTALL_DIR "${LIBJPEG_TURBO_DIR}"
+        BUILD_BYPRODUCTS "${LIBJPEG_TURBO_LIBRARY}"
+        CMAKE_CACHE_ARGS
+        -DENABLE_SHARED:BOOL=OFF
+        -DENABLE_STATIC:BOOL=ON
+        -DWITH_ARITH_DEC:BOOL=ON
+        -DWITH_ARITH_ENC:BOOL=ON
+        -DWITH_JPEG8:BOOL=OFF
+        -DWITH_JPEG7:BOOL=OFF
+        -DWITH_TURBOJPEG:BOOL=OFF
+        # Lazy SIMD: use NASM-accelerated SIMD when nasm is present, otherwise warn and build a
+        # scalar libjpeg (REQUIRE_SIMD=OFF is libjpeg-turbo's default; pinned here to be explicit).
+        -DWITH_SIMD:BOOL=ON
+        -DREQUIRE_SIMD:BOOL=OFF
+        -DCMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE}
+        -DCMAKE_INSTALL_PREFIX:PATH=<INSTALL_DIR>
+        -DCMAKE_INSTALL_LIBDIR:PATH=<INSTALL_DIR>/lib)
+
+# Create the include dir up front so setting INTERFACE_INCLUDE_DIRECTORIES below does not fail.
+FILE(MAKE_DIRECTORY ${LIBJPEG_TURBO_INCLUDE_DIRS})
+
+ADD_LIBRARY(JPEG::JPEG STATIC IMPORTED GLOBAL)
+SET_TARGET_PROPERTIES(JPEG::JPEG PROPERTIES
+        IMPORTED_LOCATION "${LIBJPEG_TURBO_LIBRARY}"
+        INTERFACE_INCLUDE_DIRECTORIES "${LIBJPEG_TURBO_INCLUDE_DIRS}")
 
 ADD_LIBRARY(JFJochPreview STATIC
         JFJochTIFF.cpp JFJochTIFF.h
@@ -14,6 +55,10 @@ ADD_LIBRARY(JFJochPreview STATIC
         ZMQMetadataSocket.h
 )
 
+# JPEG::JPEG is an IMPORTED target, so the build-order dependency on the ExternalProject must be
+# attached to the consuming target instead.
+ADD_DEPENDENCIES(JFJochPreview libjpeg-turbo-project)
+
 TARGET_LINK_LIBRARIES(JFJochPreview PUBLIC JFJochZMQ JFJochCommon CBORStream2FrameSerialize)
 TARGET_LINK_LIBRARIES(JFJochPreview PUBLIC JPEG::JPEG tiff tiffxx ZLIB::ZLIB)