[CMake] Init git before patches to ensure correct paths of patched files

This fixes issue where the build directory is somewhere underneath a git
repository, which affects `git apply` behaviour.

This is commit 836cf1a from master, partially applied.

Author: will-cern

builtins/cfitsio/CMakeLists.txt

@@ -27,7 +27,7 @@ if(WIN32)
 endif()
 
 if(NOT EXISTS "${CFITSIO_PREFIX}/src/BUILTIN_CFITSIO/._patched")
-  set(CFITSIO_PATCH_COMMAND PATCH_COMMAND git apply ${patch_args}
+  set(CFITSIO_PATCH_COMMAND PATCH_COMMAND git init COMMAND git apply ${patch_args}
                 ${CMAKE_CURRENT_SOURCE_DIR}/cfitsio-no-find-zlib.diff
                 ${CMAKE_CURRENT_SOURCE_DIR}/no-fortran-wrapper.diff
                 ${CMAKE_CURRENT_SOURCE_DIR}/cfitsio-marker.diff)

builtins/gl2ps/CMakeLists.txt

@@ -31,7 +31,7 @@ endif()
 
 # check if the patch has already been applied
 if(NOT EXISTS "${ROOT_GL2PS_PREFIX}/src/BUILTIN_GL2PS/._patched")
-  set(GL2PS_PATCH_COMMAND PATCH_COMMAND git apply ${patch_args} ${ROOT_GL2PS_PATCH_FILES})
+  set(GL2PS_PATCH_COMMAND PATCH_COMMAND git init COMMAND git apply ${patch_args} ${ROOT_GL2PS_PATCH_FILES})
 endif()
 
 ExternalProject_Add(

builtins/libgif/CMakeLists.txt

@@ -30,7 +30,7 @@ endif()
 
 # check if the patch has already been applied
 if(NOT EXISTS "${ROOT_LIBGIF_PREFIX}/src/BUILTIN_LIBGIF/CMakeLists.txt")
-  set(LIBGIF_PATCH_COMMAND PATCH_COMMAND git apply ${patch_args} ${ROOT_LIBGIF_PATCH_FILE})
+  set(LIBGIF_PATCH_COMMAND PATCH_COMMAND git init COMMAND git apply ${patch_args} ${ROOT_LIBGIF_PATCH_FILE})
 endif()
 
 ExternalProject_Add(