Merge remote-tracking branch 'origin/hdf5_1_12_1' into 1.12/master forhdf5-1_12_1

HDF5 1.12.1 release.

26 files changed, 467 insertions, 213 deletions

diff --git a/hl/tools/COPYING b/hl/tools/COPYING
deleted file mode 100644
index 6497ace..0000000
--- a/hl/tools/COPYING
+++ /dev/null
@@ -1,13 +0,0 @@
-
-  Copyright by  The HDF Group and 
-                The Board of Trustees of the University of Illinois. 
-  All rights reserved. 
-
-  The files and subdirectories in this directory are part of HDF5.  
-  The full HDF5 copyright notice, including terms governing use, 
-  modification, and redistribution, is contained in the COPYING file
-  which can be found at the root of the source code distribution tree
-  or in https://support.hdfgroup.org/ftp/HDF5/releases.  If you do
-  not have access to either file, you may request a copy from 
-  help@hdfgroup.org. 
-
diff --git a/hl/tools/Makefile.am b/hl/tools/Makefile.am
index 5d814df..4b179f5 100644
--- a/hl/tools/Makefile.am
+++ b/hl/tools/Makefile.am
@@ -6,7 +6,7 @@
 # This file is part of HDF5.  The full HDF5 copyright notice, including
 # terms governing use, modification, and redistribution, is contained in
 # the COPYING file, which can be found at the root of the source code
-# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.
+# distribution tree, or in https://www.hdfgroup.org/licenses.
 # If you do not have access to either file, you may request a copy from
 # help@hdfgroup.org.
 ##
diff --git a/hl/tools/Makefile.in b/hl/tools/Makefile.in
index 230b78a..81c9cab 100644
--- a/hl/tools/Makefile.in
+++ b/hl/tools/Makefile.in
@@ -22,7 +22,7 @@
 # This file is part of HDF5.  The full HDF5 copyright notice, including
 # terms governing use, modification, and redistribution, is contained in
 # the COPYING file, which can be found at the root of the source code
-# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.
+# distribution tree, or in https://www.hdfgroup.org/licenses.
 # If you do not have access to either file, you may request a copy from
 # help@hdfgroup.org.
 #
@@ -113,6 +113,7 @@ am__aclocal_m4_deps = $(top_srcdir)/m4/aclocal_cxx.m4 \
 	$(top_srcdir)/m4/ax_check_junit.m4 \
 	$(top_srcdir)/m4/ax_java_options.m4 \
 	$(top_srcdir)/m4/ax_jni_include_dir.m4 \
+	$(top_srcdir)/m4/ax_prog_doxygen.m4 \
 	$(top_srcdir)/m4/ax_prog_jar.m4 \
 	$(top_srcdir)/m4/ax_prog_java.m4 \
 	$(top_srcdir)/m4/ax_prog_java_works.m4 \
@@ -387,7 +388,7 @@ am__set_b = \
 DIST_SUBDIRS = $(SUBDIRS)
 am__DIST_COMMON = $(srcdir)/Makefile.in $(top_srcdir)/bin/test-driver \
 	$(top_srcdir)/config/commence.am \
-	$(top_srcdir)/config/conclude.am COPYING
+	$(top_srcdir)/config/conclude.am
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 am__relativize = \
   dir0=`pwd`; \
@@ -420,7 +421,7 @@ AMTAR = @AMTAR@
 
 # H5_CFLAGS holds flags that should be used when building hdf5,
 # but which should not be exported to h5cc for building other programs.
-# AM_CFLAGS is an automake construct which should be used by Makefiles 
+# AM_CFLAGS is an automake construct which should be used by Makefiles
 # instead of CFLAGS, as CFLAGS is reserved solely for the user to define.
 # This applies to FCFLAGS, CXXFLAGS, CPPFLAGS, and LDFLAGS as well.
 AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@
@@ -445,6 +446,7 @@ CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
 CFLAGS = @CFLAGS@
+CLANG_SANITIZE_CHECKS = @CLANG_SANITIZE_CHECKS@
 CODESTACK = @CODESTACK@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
@@ -461,11 +463,54 @@ DEFAULT_API_VERSION = @DEFAULT_API_VERSION@
 DEFS = @DEFS@
 DEPDIR = @DEPDIR@
 DEPRECATED_SYMBOLS = @DEPRECATED_SYMBOLS@
-DEV_WARNINGS = @DEV_WARNINGS@
+DESIRED_FILE_LOCKING = @DESIRED_FILE_LOCKING@
+DIAGS = @DIAGS@
 DIRECT_VFD = @DIRECT_VFD@
 DLLTOOL = @DLLTOOL@
+DOXYGEN_EXAMPLES_DIRECTORY = @DOXYGEN_EXAMPLES_DIRECTORY@
+DOXYGEN_EXTERNAL_SEARCH = @DOXYGEN_EXTERNAL_SEARCH@
+DOXYGEN_HTML_EXTRA_FILES = @DOXYGEN_HTML_EXTRA_FILES@
+DOXYGEN_HTML_EXTRA_STYLESHEET = @DOXYGEN_HTML_EXTRA_STYLESHEET@
+DOXYGEN_HTML_FOOTER = @DOXYGEN_HTML_FOOTER@
+DOXYGEN_HTML_HEADER = @DOXYGEN_HTML_HEADER@
+DOXYGEN_INCLUDE_ALIASES = @DOXYGEN_INCLUDE_ALIASES@
+DOXYGEN_INPUT_DIRECTORY = @DOXYGEN_INPUT_DIRECTORY@
+DOXYGEN_LAYOUT_FILE = @DOXYGEN_LAYOUT_FILE@
+DOXYGEN_MACRO_EXPANSION = @DOXYGEN_MACRO_EXPANSION@
+DOXYGEN_OPTIMIZE_OUTPUT_FOR_C = @DOXYGEN_OPTIMIZE_OUTPUT_FOR_C@
+DOXYGEN_OUTPUT_DIRECTORY = @DOXYGEN_OUTPUT_DIRECTORY@
+DOXYGEN_PACKAGE = @DOXYGEN_PACKAGE@
+DOXYGEN_PAPER_SIZE = @DOXYGEN_PAPER_SIZE@
+DOXYGEN_PROJECT_BRIEF = @DOXYGEN_PROJECT_BRIEF@
+DOXYGEN_PROJECT_LOGO = @DOXYGEN_PROJECT_LOGO@
+DOXYGEN_SEARCHENGINE_URL = @DOXYGEN_SEARCHENGINE_URL@
+DOXYGEN_SERVER_BASED_SEARCH = @DOXYGEN_SERVER_BASED_SEARCH@
+DOXYGEN_VERSION_STRING = @DOXYGEN_VERSION_STRING@
 DSYMUTIL = @DSYMUTIL@
 DUMPBIN = @DUMPBIN@
+DX_CONFIG = @DX_CONFIG@
+DX_DOCDIR = @DX_DOCDIR@
+DX_DOT = @DX_DOT@
+DX_DOXYGEN = @DX_DOXYGEN@
+DX_DVIPS = @DX_DVIPS@
+DX_EGREP = @DX_EGREP@
+DX_ENV = @DX_ENV@
+DX_FLAG_chi = @DX_FLAG_chi@
+DX_FLAG_chm = @DX_FLAG_chm@
+DX_FLAG_doc = @DX_FLAG_doc@
+DX_FLAG_dot = @DX_FLAG_dot@
+DX_FLAG_html = @DX_FLAG_html@
+DX_FLAG_man = @DX_FLAG_man@
+DX_FLAG_pdf = @DX_FLAG_pdf@
+DX_FLAG_ps = @DX_FLAG_ps@
+DX_FLAG_rtf = @DX_FLAG_rtf@
+DX_FLAG_xml = @DX_FLAG_xml@
+DX_HHC = @DX_HHC@
+DX_LATEX = @DX_LATEX@
+DX_MAKEINDEX = @DX_MAKEINDEX@
+DX_PDFLATEX = @DX_PDFLATEX@
+DX_PERL = @DX_PERL@
+DX_PROJECT = @DX_PROJECT@
 ECHO_C = @ECHO_C@
 ECHO_N = @ECHO_N@
 ECHO_T = @ECHO_T@
@@ -499,6 +544,7 @@ H5_CPPFLAGS = @H5_CPPFLAGS@
 H5_CXXFLAGS = @H5_CXXFLAGS@
 H5_FCFLAGS = @H5_FCFLAGS@
 H5_FORTRAN_SHARED = @H5_FORTRAN_SHARED@
+H5_IS_DARWIN = @H5_IS_DARWIN@
 H5_JAVACFLAGS = @H5_JAVACFLAGS@
 H5_JAVAFLAGS = @H5_JAVAFLAGS@
 H5_JNIFLAGS = @H5_JNIFLAGS@
@@ -509,6 +555,7 @@ HAVE_DMALLOC = @HAVE_DMALLOC@
 HAVE_Fortran_INTEGER_SIZEOF_16 = @HAVE_Fortran_INTEGER_SIZEOF_16@
 HAVE_LIBHDFS = @HAVE_LIBHDFS@
 HAVE_PTHREAD = @HAVE_PTHREAD@
+HDF5_DOXYGEN = @HDF5_DOXYGEN@
 HDF5_HL = @HDF5_HL@
 HDF5_INTERFACES = @HDF5_INTERFACES@
 HDF5_TESTS = @HDF5_TESTS@
@@ -521,6 +568,7 @@ HL = @HL@
 HL_FOR = @HL_FOR@
 HSIZE_T = @HSIZE_T@
 HSSIZE_T = @HSSIZE_T@
+IGNORE_DISABLED_FILE_LOCKS = @IGNORE_DISABLED_FILE_LOCKS@
 INSTALL = @INSTALL@
 INSTALL_DATA = @INSTALL_DATA@
 INSTALL_PROGRAM = @INSTALL_PROGRAM@
@@ -558,6 +606,7 @@ MAKEINFO = @MAKEINFO@
 MANIFEST_TOOL = @MANIFEST_TOOL@
 MAP_API = @MAP_API@
 MEMORYALLOCSANITYCHECK = @MEMORYALLOCSANITYCHECK@
+MIRROR_VFD = @MIRROR_VFD@
 MKDIR_P = @MKDIR_P@
 MPE = @MPE@
 NM = @NM@
@@ -594,6 +643,7 @@ PATH_SEPARATOR = @PATH_SEPARATOR@
 PREADWRITE = @PREADWRITE@
 PROFILING = @PROFILING@
 RANLIB = @RANLIB@
+RECURSIVE_RW_LOCKS = @RECURSIVE_RW_LOCKS@
 ROOT = @ROOT@
 ROS3_VFD = @ROS3_VFD@
 RUNPARALLEL = @RUNPARALLEL@
@@ -617,6 +667,7 @@ TIME = @TIME@
 TR = @TR@
 TRACE_API = @TRACE_API@
 UNAME_INFO = @UNAME_INFO@
+USE_FILE_LOCKING = @USE_FILE_LOCKING@
 USE_FILTER_DEFLATE = @USE_FILTER_DEFLATE@
 USE_FILTER_SZIP = @USE_FILTER_SZIP@
 USINGMEMCHECKER = @USINGMEMCHECKER@
@@ -709,15 +760,15 @@ LIBH5_HL = $(top_builddir)/hl/src/libhdf5_hl.la
 LIBH5F_HL = $(top_builddir)/hl/fortran/src/libhdf5hl_fortran.la
 LIBH5CPP_HL = $(top_builddir)/hl/c++/src/libhdf5_hl_cpp.la
 
-# Note that in svn revision 19400 the '/' after DESTDIR in H5* variables below  
-# has been removed. According to the official description of DESTDIR by Gnu at 
-# http://www.gnu.org/prep/standards/html_node/DESTDIR.html, DESTDIR is 
-# prepended to the normal and complete install path that it precedes for the 
-# purpose of installing in a temporary directory which is useful for building 
-# rpms and other packages.  The '/' after ${DESTDIR} will be followed by another 
-# '/' at the beginning of the normal install path.  When DESTDIR is empty the  
-# path then begins with '//', which is incorrect and causes problems at least for 
-# Cygwin.   
+# Note that in svn revision 19400 the '/' after DESTDIR in H5* variables below
+# has been removed. According to the official description of DESTDIR by Gnu at
+# http://www.gnu.org/prep/standards/html_node/DESTDIR.html, DESTDIR is
+# prepended to the normal and complete install path that it precedes for the
+# purpose of installing in a temporary directory which is useful for building
+# rpms and other packages.  The '/' after ${DESTDIR} will be followed by another
+# '/' at the beginning of the normal install path.  When DESTDIR is empty the
+# path then begins with '//', which is incorrect and causes problems at least for
+# Cygwin.
 
 # Scripts used to build examples
 # If only shared libraries have been installed, have h5cc build examples with
@@ -752,7 +803,7 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
-chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST)
 TEST_EXTENSIONS = .sh
 SH_LOG_COMPILER = $(SHELL)
 AM_SH_LOG_FLAGS = 
@@ -1231,9 +1282,9 @@ uninstall-am:
 # commands that should be executed even if a file with the same name already
 # exists.
 .PHONY: build-check-clean build-check-p build-check-s build-lib build-progs \
-        build-tests check-clean check-install check-p check-s check-vfd \
-        check-passthrough-vol install-doc lib progs tests uninstall-doc \
-        _exec_check-s _test help
+	build-tests check-clean check-install check-p check-s check-vfd \
+	check-passthrough-vol install-doc lib progs tests uninstall-doc \
+	_exec_check-s _test help trace doxygen
 
 help:
 	@$(top_srcdir)/bin/makehelp
diff --git a/hl/tools/gif2h5/CMakeLists.txt b/hl/tools/gif2h5/CMakeLists.txt
index cc2ba68..372fb60 100644
--- a/hl/tools/gif2h5/CMakeLists.txt
+++ b/hl/tools/gif2h5/CMakeLists.txt
@@ -16,7 +16,8 @@ set (GIF2H5_SOURCES
 #-- Add gif2hdf5 program
 if (NOT ONLY_SHARED_LIBS)
   add_executable (gif2h5 ${GIF2H5_SOURCES})
-  target_include_directories (gif2h5 PRIVATE "${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_compile_options(gif2h5 PRIVATE "${HDF5_CMAKE_C_FLAGS}")
+  target_include_directories (gif2h5 PRIVATE "${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   TARGET_C_PROPERTIES (gif2h5 STATIC)
   target_link_libraries (gif2h5 PRIVATE ${HDF5_HL_LIB_TARGET} ${HDF5_LIB_TARGET} ${HDF5_TOOLS_LIB_TARGET})
   set_target_properties (gif2h5 PROPERTIES FOLDER tools/hl)
@@ -28,7 +29,8 @@ endif ()
 
 if (BUILD_SHARED_LIBS)
   add_executable (gif2h5-shared ${GIF2H5_SOURCES})
-  target_include_directories (gif2h5-shared PRIVATE "${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_compile_options(gif2h5-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}")
+  target_include_directories (gif2h5-shared PRIVATE "${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   TARGET_C_PROPERTIES (gif2h5-shared SHARED)
   target_link_libraries (gif2h5-shared PRIVATE ${HDF5_HL_LIBSH_TARGET} ${HDF5_LIBSH_TARGET} ${HDF5_TOOLS_LIBSH_TARGET})
   set_target_properties (gif2h5-shared PROPERTIES FOLDER tools/hl)
@@ -38,6 +40,17 @@ if (BUILD_SHARED_LIBS)
   )
 endif ()
 
+#-----------------------------------------------------------------------------
+# Add Target to clang-format
+#-----------------------------------------------------------------------------
+if (HDF5_ENABLE_FORMATTERS)
+  if (NOT ONLY_SHARED_LIBS)
+    clang_format (HDF5_HL_TOOLS_GIF2H5_FORMAT gif2h5)
+  else ()
+    clang_format (HDF5_HL_TOOLS_GIF2H5_FORMAT gif2h5-shared)
+  endif ()
+endif ()
+
 #-- Add h52gif program
 set (hdf2gif_SOURCES
     ${HDF5_HL_TOOLS_GIF2H5_SOURCE_DIR}/hdf2gif.c
@@ -45,7 +58,8 @@ set (hdf2gif_SOURCES
 )
 if (NOT ONLY_SHARED_LIBS)
   add_executable (h52gif ${hdf2gif_SOURCES})
-  target_include_directories (h52gif PRIVATE "${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_compile_options(h52gif PRIVATE "${HDF5_CMAKE_C_FLAGS}")
+  target_include_directories (h52gif PRIVATE "${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   TARGET_C_PROPERTIES (h52gif STATIC)
   target_link_libraries (h52gif PRIVATE ${HDF5_HL_LIB_TARGET} ${HDF5_LIB_TARGET} ${HDF5_TOOLS_LIB_TARGET})
   set_target_properties (h52gif PROPERTIES FOLDER tools/hl)
@@ -57,7 +71,8 @@ endif ()
 
 if (BUILD_SHARED_LIBS)
   add_executable (h52gif-shared ${hdf2gif_SOURCES})
-  target_include_directories (h52gif-shared PRIVATE "${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_compile_options(h52gif-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}")
+  target_include_directories (h52gif-shared PRIVATE "${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   TARGET_C_PROPERTIES (h52gif-shared SHARED)
   target_link_libraries (h52gif-shared PRIVATE ${HDF5_HL_LIBSH_TARGET} PRIVATE ${HDF5_LIBSH_TARGET} ${HDF5_TOOLS_LIBSH_TARGET})
   set_target_properties (h52gif-shared PROPERTIES FOLDER tools/hl)
@@ -67,6 +82,17 @@ if (BUILD_SHARED_LIBS)
   )
 endif ()
 
+#-----------------------------------------------------------------------------
+# Add Target to clang-format
+#-----------------------------------------------------------------------------
+if (HDF5_ENABLE_FORMATTERS)
+  if (NOT ONLY_SHARED_LIBS)
+    clang_format (HDF5_HL_TOOLS_H52GIF_FORMAT h52gif)
+  else ()
+    clang_format (HDF5_HL_TOOLS_H52GIF_FORMAT h52gif-shared)
+  endif ()
+endif ()
+
 if (BUILD_TESTING AND HDF5_TEST_SERIAL)
   # --------------------------------------------------------------------
   # This executable can generate the actual test files - Currently not
@@ -75,11 +101,18 @@ if (BUILD_TESTING AND HDF5_TEST_SERIAL)
   # --------------------------------------------------------------------
   if (HDF5_BUILD_GENERATORS AND NOT ONLY_SHARED_LIBS)
       add_executable (hl_h52gifgentest ${HDF5_HL_TOOLS_GIF2H5_SOURCE_DIR}/h52gifgentst.c)
-      target_include_directories (hl_h52gifgentest PRIVATE "${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+      target_include_directories (hl_h52gifgentest PRIVATE "${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
       TARGET_C_PROPERTIES (hl_h52gifgentest STATIC)
       target_link_libraries (hl_h52gifgentest PRIVATE ${HDF5_HL_LIB_TARGET} ${HDF5_LIB_TARGET})
       set_target_properties (hl_h52gifgentest PROPERTIES FOLDER generator/tools/hl)
 
+      #-----------------------------------------------------------------------------
+      # Add Target to clang-format
+      #-----------------------------------------------------------------------------
+      if (HDF5_ENABLE_FORMATTERS)
+        clang_format (HDF5_HL_TOOLS_hl_h52gifgentest_FORMAT hl_h52gifgentest)
+      endif ()
+
 #      add_test (NAME hl_h52gifgentest COMMAND ${CMAKE_CROSSCOMPILING_EMULATOR} $<TARGET_FILE:hl_h52gifgentest>)
   endif ()
 
diff --git a/hl/tools/gif2h5/CMakeTests.cmake b/hl/tools/gif2h5/CMakeTests.cmake
index 094a7b5..36ea5f9 100644
--- a/hl/tools/gif2h5/CMakeTests.cmake
+++ b/hl/tools/gif2h5/CMakeTests.cmake
@@ -5,7 +5,7 @@
 # This file is part of HDF5.  The full HDF5 copyright notice, including
 # terms governing use, modification, and redistribution, is contained in
 # the COPYING file, which can be found at the root of the source code
-# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.
+# distribution tree, or in https://www.hdfgroup.org/licenses.
 # If you do not have access to either file, you may request a copy from
 # help@hdfgroup.org.
 #
diff --git a/hl/tools/gif2h5/Makefile.am b/hl/tools/gif2h5/Makefile.am
index 9ffde58..f1d45dc 100644
--- a/hl/tools/gif2h5/Makefile.am
+++ b/hl/tools/gif2h5/Makefile.am
@@ -6,7 +6,7 @@
 # This file is part of HDF5.  The full HDF5 copyright notice, including
 # terms governing use, modification, and redistribution, is contained in
 # the COPYING file, which can be found at the root of the source code
-# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.
+# distribution tree, or in https://www.hdfgroup.org/licenses.
 # If you do not have access to either file, you may request a copy from
 # help@hdfgroup.org.
 ##
@@ -29,9 +29,9 @@ bin_PROGRAMS=gif2h5 h52gif
 h52gif_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
 gif2h5_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
 
-gif2h5_SOURCES=gif2hdf.c gif2mem.c decompress.c gifread.c writehdf.c 
+gif2h5_SOURCES=gif2hdf.c gif2mem.c decompress.c gifread.c writehdf.c
 
-h52gif_SOURCES=hdf2gif.c hdfgifwr.c 
+h52gif_SOURCES=hdf2gif.c hdfgifwr.c
 
 
 # Programs all depend on the hdf5 library, the tools library, and the HL
@@ -42,7 +42,7 @@ if BUILD_TESTS_CONDITIONAL
   TEST_SCRIPT=h52giftest.sh
   check_SCRIPTS=$(TEST_SCRIPT)
   noinst_PROGRAMS=h52gifgentst
-  h52gifgentst_SOURCES=h52gifgentst.c 
+  h52gifgentst_SOURCES=h52gifgentst.c
 endif
 
 CHECK_CLEANFILES+=*.h5
diff --git a/hl/tools/gif2h5/Makefile.in b/hl/tools/gif2h5/Makefile.in
index 1fe2819..e69aec7 100644
--- a/hl/tools/gif2h5/Makefile.in
+++ b/hl/tools/gif2h5/Makefile.in
@@ -22,7 +22,7 @@
 # This file is part of HDF5.  The full HDF5 copyright notice, including
 # terms governing use, modification, and redistribution, is contained in
 # the COPYING file, which can be found at the root of the source code
-# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.
+# distribution tree, or in https://www.hdfgroup.org/licenses.
 # If you do not have access to either file, you may request a copy from
 # help@hdfgroup.org.
 #
@@ -116,6 +116,7 @@ am__aclocal_m4_deps = $(top_srcdir)/m4/aclocal_cxx.m4 \
 	$(top_srcdir)/m4/ax_check_junit.m4 \
 	$(top_srcdir)/m4/ax_java_options.m4 \
 	$(top_srcdir)/m4/ax_jni_include_dir.m4 \
+	$(top_srcdir)/m4/ax_prog_doxygen.m4 \
 	$(top_srcdir)/m4/ax_prog_jar.m4 \
 	$(top_srcdir)/m4/ax_prog_java.m4 \
 	$(top_srcdir)/m4/ax_prog_java_works.m4 \
@@ -433,7 +434,7 @@ AMTAR = @AMTAR@
 
 # H5_CFLAGS holds flags that should be used when building hdf5,
 # but which should not be exported to h5cc for building other programs.
-# AM_CFLAGS is an automake construct which should be used by Makefiles 
+# AM_CFLAGS is an automake construct which should be used by Makefiles
 # instead of CFLAGS, as CFLAGS is reserved solely for the user to define.
 # This applies to FCFLAGS, CXXFLAGS, CPPFLAGS, and LDFLAGS as well.
 AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@
@@ -461,6 +462,7 @@ CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
 CFLAGS = @CFLAGS@
+CLANG_SANITIZE_CHECKS = @CLANG_SANITIZE_CHECKS@
 CODESTACK = @CODESTACK@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
@@ -477,11 +479,54 @@ DEFAULT_API_VERSION = @DEFAULT_API_VERSION@
 DEFS = @DEFS@
 DEPDIR = @DEPDIR@
 DEPRECATED_SYMBOLS = @DEPRECATED_SYMBOLS@
-DEV_WARNINGS = @DEV_WARNINGS@
+DESIRED_FILE_LOCKING = @DESIRED_FILE_LOCKING@
+DIAGS = @DIAGS@
 DIRECT_VFD = @DIRECT_VFD@
 DLLTOOL = @DLLTOOL@
+DOXYGEN_EXAMPLES_DIRECTORY = @DOXYGEN_EXAMPLES_DIRECTORY@
+DOXYGEN_EXTERNAL_SEARCH = @DOXYGEN_EXTERNAL_SEARCH@
+DOXYGEN_HTML_EXTRA_FILES = @DOXYGEN_HTML_EXTRA_FILES@
+DOXYGEN_HTML_EXTRA_STYLESHEET = @DOXYGEN_HTML_EXTRA_STYLESHEET@
+DOXYGEN_HTML_FOOTER = @DOXYGEN_HTML_FOOTER@
+DOXYGEN_HTML_HEADER = @DOXYGEN_HTML_HEADER@
+DOXYGEN_INCLUDE_ALIASES = @DOXYGEN_INCLUDE_ALIASES@
+DOXYGEN_INPUT_DIRECTORY = @DOXYGEN_INPUT_DIRECTORY@
+DOXYGEN_LAYOUT_FILE = @DOXYGEN_LAYOUT_FILE@
+DOXYGEN_MACRO_EXPANSION = @DOXYGEN_MACRO_EXPANSION@
+DOXYGEN_OPTIMIZE_OUTPUT_FOR_C = @DOXYGEN_OPTIMIZE_OUTPUT_FOR_C@
+DOXYGEN_OUTPUT_DIRECTORY = @DOXYGEN_OUTPUT_DIRECTORY@
+DOXYGEN_PACKAGE = @DOXYGEN_PACKAGE@
+DOXYGEN_PAPER_SIZE = @DOXYGEN_PAPER_SIZE@
+DOXYGEN_PROJECT_BRIEF = @DOXYGEN_PROJECT_BRIEF@
+DOXYGEN_PROJECT_LOGO = @DOXYGEN_PROJECT_LOGO@
+DOXYGEN_SEARCHENGINE_URL = @DOXYGEN_SEARCHENGINE_URL@
+DOXYGEN_SERVER_BASED_SEARCH = @DOXYGEN_SERVER_BASED_SEARCH@
+DOXYGEN_VERSION_STRING = @DOXYGEN_VERSION_STRING@
 DSYMUTIL = @DSYMUTIL@
 DUMPBIN = @DUMPBIN@
+DX_CONFIG = @DX_CONFIG@
+DX_DOCDIR = @DX_DOCDIR@
+DX_DOT = @DX_DOT@
+DX_DOXYGEN = @DX_DOXYGEN@
+DX_DVIPS = @DX_DVIPS@
+DX_EGREP = @DX_EGREP@
+DX_ENV = @DX_ENV@
+DX_FLAG_chi = @DX_FLAG_chi@
+DX_FLAG_chm = @DX_FLAG_chm@
+DX_FLAG_doc = @DX_FLAG_doc@
+DX_FLAG_dot = @DX_FLAG_dot@
+DX_FLAG_html = @DX_FLAG_html@
+DX_FLAG_man = @DX_FLAG_man@
+DX_FLAG_pdf = @DX_FLAG_pdf@
+DX_FLAG_ps = @DX_FLAG_ps@
+DX_FLAG_rtf = @DX_FLAG_rtf@
+DX_FLAG_xml = @DX_FLAG_xml@
+DX_HHC = @DX_HHC@
+DX_LATEX = @DX_LATEX@
+DX_MAKEINDEX = @DX_MAKEINDEX@
+DX_PDFLATEX = @DX_PDFLATEX@
+DX_PERL = @DX_PERL@
+DX_PROJECT = @DX_PROJECT@
 ECHO_C = @ECHO_C@
 ECHO_N = @ECHO_N@
 ECHO_T = @ECHO_T@
@@ -515,6 +560,7 @@ H5_CPPFLAGS = @H5_CPPFLAGS@
 H5_CXXFLAGS = @H5_CXXFLAGS@
 H5_FCFLAGS = @H5_FCFLAGS@
 H5_FORTRAN_SHARED = @H5_FORTRAN_SHARED@
+H5_IS_DARWIN = @H5_IS_DARWIN@
 H5_JAVACFLAGS = @H5_JAVACFLAGS@
 H5_JAVAFLAGS = @H5_JAVAFLAGS@
 H5_JNIFLAGS = @H5_JNIFLAGS@
@@ -525,6 +571,7 @@ HAVE_DMALLOC = @HAVE_DMALLOC@
 HAVE_Fortran_INTEGER_SIZEOF_16 = @HAVE_Fortran_INTEGER_SIZEOF_16@
 HAVE_LIBHDFS = @HAVE_LIBHDFS@
 HAVE_PTHREAD = @HAVE_PTHREAD@
+HDF5_DOXYGEN = @HDF5_DOXYGEN@
 HDF5_HL = @HDF5_HL@
 HDF5_INTERFACES = @HDF5_INTERFACES@
 HDF5_TESTS = @HDF5_TESTS@
@@ -537,6 +584,7 @@ HL = @HL@
 HL_FOR = @HL_FOR@
 HSIZE_T = @HSIZE_T@
 HSSIZE_T = @HSSIZE_T@
+IGNORE_DISABLED_FILE_LOCKS = @IGNORE_DISABLED_FILE_LOCKS@
 INSTALL = @INSTALL@
 INSTALL_DATA = @INSTALL_DATA@
 INSTALL_PROGRAM = @INSTALL_PROGRAM@
@@ -574,6 +622,7 @@ MAKEINFO = @MAKEINFO@
 MANIFEST_TOOL = @MANIFEST_TOOL@
 MAP_API = @MAP_API@
 MEMORYALLOCSANITYCHECK = @MEMORYALLOCSANITYCHECK@
+MIRROR_VFD = @MIRROR_VFD@
 MKDIR_P = @MKDIR_P@
 MPE = @MPE@
 NM = @NM@
@@ -610,6 +659,7 @@ PATH_SEPARATOR = @PATH_SEPARATOR@
 PREADWRITE = @PREADWRITE@
 PROFILING = @PROFILING@
 RANLIB = @RANLIB@
+RECURSIVE_RW_LOCKS = @RECURSIVE_RW_LOCKS@
 ROOT = @ROOT@
 ROS3_VFD = @ROS3_VFD@
 RUNPARALLEL = @RUNPARALLEL@
@@ -633,6 +683,7 @@ TIME = @TIME@
 TR = @TR@
 TRACE_API = @TRACE_API@
 UNAME_INFO = @UNAME_INFO@
+USE_FILE_LOCKING = @USE_FILE_LOCKING@
 USE_FILTER_DEFLATE = @USE_FILTER_DEFLATE@
 USE_FILTER_SZIP = @USE_FILTER_SZIP@
 USINGMEMCHECKER = @USINGMEMCHECKER@
@@ -725,15 +776,15 @@ LIBH5_HL = $(top_builddir)/hl/src/libhdf5_hl.la
 LIBH5F_HL = $(top_builddir)/hl/fortran/src/libhdf5hl_fortran.la
 LIBH5CPP_HL = $(top_builddir)/hl/c++/src/libhdf5_hl_cpp.la
 
-# Note that in svn revision 19400 the '/' after DESTDIR in H5* variables below  
-# has been removed. According to the official description of DESTDIR by Gnu at 
-# http://www.gnu.org/prep/standards/html_node/DESTDIR.html, DESTDIR is 
-# prepended to the normal and complete install path that it precedes for the 
-# purpose of installing in a temporary directory which is useful for building 
-# rpms and other packages.  The '/' after ${DESTDIR} will be followed by another 
-# '/' at the beginning of the normal install path.  When DESTDIR is empty the  
-# path then begins with '//', which is incorrect and causes problems at least for 
-# Cygwin.   
+# Note that in svn revision 19400 the '/' after DESTDIR in H5* variables below
+# has been removed. According to the official description of DESTDIR by Gnu at
+# http://www.gnu.org/prep/standards/html_node/DESTDIR.html, DESTDIR is
+# prepended to the normal and complete install path that it precedes for the
+# purpose of installing in a temporary directory which is useful for building
+# rpms and other packages.  The '/' after ${DESTDIR} will be followed by another
+# '/' at the beginning of the normal install path.  When DESTDIR is empty the
+# path then begins with '//', which is incorrect and causes problems at least for
+# Cygwin.
 
 # Scripts used to build examples
 # If only shared libraries have been installed, have h5cc build examples with
@@ -757,15 +808,15 @@ CHECK_CLEANFILES = *.chkexe *.chklog *.clog *.clog2 *.h5 *.gif
 # Add h52gif and gif2h5 specific linker flags here
 h52gif_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
 gif2h5_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
-gif2h5_SOURCES = gif2hdf.c gif2mem.c decompress.c gifread.c writehdf.c 
-h52gif_SOURCES = hdf2gif.c hdfgifwr.c 
+gif2h5_SOURCES = gif2hdf.c gif2mem.c decompress.c gifread.c writehdf.c
+h52gif_SOURCES = hdf2gif.c hdfgifwr.c
 
 # Programs all depend on the hdf5 library, the tools library, and the HL
 # library.
 LDADD = $(LIBH5_HL) $(LIBH5TOOLS) $(LIBHDF5)
 @BUILD_TESTS_CONDITIONAL_TRUE@TEST_SCRIPT = h52giftest.sh
 @BUILD_TESTS_CONDITIONAL_TRUE@check_SCRIPTS = $(TEST_SCRIPT)
-@BUILD_TESTS_CONDITIONAL_TRUE@h52gifgentst_SOURCES = h52gifgentst.c 
+@BUILD_TESTS_CONDITIONAL_TRUE@h52gifgentst_SOURCES = h52gifgentst.c
 
 # Automake needs to be taught how to build lib, progs and tests targets.
 # These will be filled in automatically for the most part (e.g.,
@@ -778,7 +829,7 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
-chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST)
 TEST_EXTENSIONS = .sh
 SH_LOG_COMPILER = $(SHELL)
 AM_SH_LOG_FLAGS = 
@@ -1305,9 +1356,9 @@ uninstall-am: uninstall-binPROGRAMS
 # commands that should be executed even if a file with the same name already
 # exists.
 .PHONY: build-check-clean build-check-p build-check-s build-lib build-progs \
-        build-tests check-clean check-install check-p check-s check-vfd \
-        check-passthrough-vol install-doc lib progs tests uninstall-doc \
-        _exec_check-s _test help
+	build-tests check-clean check-install check-p check-s check-vfd \
+	check-passthrough-vol install-doc lib progs tests uninstall-doc \
+	_exec_check-s _test help trace doxygen
 
 help:
 	@$(top_srcdir)/bin/makehelp
diff --git a/hl/tools/gif2h5/decompress.c b/hl/tools/gif2h5/decompress.c
index 9df843a..64d9643 100644
--- a/hl/tools/gif2h5/decompress.c
+++ b/hl/tools/gif2h5/decompress.c
@@ -6,7 +6,7 @@
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
  * the COPYING file, which can be found at the root of the source code       *
- * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * distribution tree, or in https://www.hdfgroup.org/licenses.               *
  * If you do not have access to either file, you may request a copy from     *
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
@@ -55,12 +55,12 @@ GIFBYTE *Raster; /* The raster data stream, unblocked            */
 
 /* The hash table used by the decompressor */
 
-int Prefix[4096];
-int Suffix[4096];
+int *Prefix;
+int *Suffix;
 
 /* An output array used by the decompressor */
 
-int OutCode[1025];
+int *OutCode;
 
 /* The color map, read from the GIF header */
 
@@ -156,6 +156,19 @@ Decompress(GIFIMAGEDESC *GifImageDesc, GIFHEAD *GifHead)
 {
     int i;
 
+    if (!(Prefix = calloc(4096, sizeof(int)))) {
+        printf("Out of memory");
+        exit(EXIT_FAILURE);
+    }
+    if (!(Suffix = calloc(4096, sizeof(int)))) {
+        printf("Out of memory");
+        exit(EXIT_FAILURE);
+    }
+    if (!(OutCode = calloc(1024, sizeof(int)))) {
+        printf("Out of memory");
+        exit(EXIT_FAILURE);
+    }
+
     XC        = 0;
     YC        = 0;
     Pass      = 0;
@@ -307,5 +320,9 @@ Decompress(GIFIMAGEDESC *GifImageDesc, GIFHEAD *GifHead)
         Code = ReadCode();
     }
 
+    free(Prefix);
+    free(Suffix);
+    free(OutCode);
+
     return Image;
 }
diff --git a/hl/tools/gif2h5/gif.h b/hl/tools/gif2h5/gif.h
index cb54b9b..1a8cfe4 100644
--- a/hl/tools/gif2h5/gif.h
+++ b/hl/tools/gif2h5/gif.h
@@ -6,7 +6,7 @@
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
  * the COPYING file, which can be found at the root of the source code       *
- * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * distribution tree, or in https://www.hdfgroup.org/licenses.               *
  * If you do not have access to either file, you may request a copy from     *
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
@@ -157,8 +157,8 @@ int ReadGifApplication(GIFAPPLICATION *, GIFBYTE **);
 int ReadGifComment(GIFCOMMENT *, GIFBYTE **);
 
 /* HDFGIFWR.C */
-int hdfWriteGIF(FILE *fp, GIFBYTE *pic, int ptype, int w, int h, GIFBYTE *rmap, GIFBYTE *gmap, GIFBYTE *bmap,
-                GIFBYTE *pc2ncmap, int numcols, int colorstyle, int BitsPerPixel);
+int hdfWriteGIF(FILE *fp, GIFBYTE *pic, int ptype, int w, int h, const GIFBYTE *rmap, const GIFBYTE *gmap,
+                const GIFBYTE *bmap, const GIFBYTE *pc2ncmap, int numcols, int colorstyle, int BitsPerPixel);
 
 /* WRITEHDF.C */
 int WriteHDF(GIFTOMEM, GIFCHAR *);
@@ -176,7 +176,7 @@ int ReadHDF(GIFBYTE **data, GIFBYTE palette[256][3], hsize_t *image_size, GIFCHA
             GIFCHAR *dset_name, GIFCHAR *pal_name);
 
 GIFBYTE *Decompress(GIFIMAGEDESC *, GIFHEAD *);
-GIFBYTE  GetByte(GIFBYTE *);
+GIFBYTE  GetByte(const GIFBYTE *);
 GIFWORD  GetWord(GIFBYTE *);
 
 void cleanup(GIFBYTE *);
diff --git a/hl/tools/gif2h5/gif2hdf.c b/hl/tools/gif2h5/gif2hdf.c
index 939844c..8de6d9a 100644
--- a/hl/tools/gif2h5/gif2hdf.c
+++ b/hl/tools/gif2h5/gif2hdf.c
@@ -6,7 +6,7 @@
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
  * the COPYING file, which can be found at the root of the source code       *
- * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * distribution tree, or in https://www.hdfgroup.org/licenses.               *
  * If you do not have access to either file, you may request a copy from     *
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
diff --git a/hl/tools/gif2h5/gif2mem.c b/hl/tools/gif2h5/gif2mem.c
index b1ea718..c66250b 100644
--- a/hl/tools/gif2h5/gif2mem.c
+++ b/hl/tools/gif2h5/gif2mem.c
@@ -6,7 +6,7 @@
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
  * the COPYING file, which can be found at the root of the source code       *
- * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * distribution tree, or in https://www.hdfgroup.org/licenses.               *
  * If you do not have access to either file, you may request a copy from     *
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
diff --git a/hl/tools/gif2h5/gifread.c b/hl/tools/gif2h5/gifread.c
index 2b267ef..dd9e5be 100644
--- a/hl/tools/gif2h5/gifread.c
+++ b/hl/tools/gif2h5/gifread.c
@@ -6,7 +6,7 @@
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
  * the COPYING file, which can be found at the root of the source code       *
- * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * distribution tree, or in https://www.hdfgroup.org/licenses.               *
  * If you do not have access to either file, you may request a copy from     *
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
@@ -38,7 +38,7 @@ GetWord(GIFBYTE *MemGif)
 }
 
 GIFBYTE
-GetByte(GIFBYTE *MemGif)
+GetByte(const GIFBYTE *MemGif)
 {
     return *MemGif;
 }
@@ -65,7 +65,7 @@ ReadGifHeader(GIFHEAD * GifHead, /* Pointer to GIF header structure  */
         GifHead->HeaderDump[i] = *(*MemGif2)++;
     }
 
-    if (strncmp((const char *)GifHead->HeaderDump, "GIF", (size_t)3)) {
+    if (strncmp((const char *)GifHead->HeaderDump, "GIF", (size_t)3) != 0) {
         printf("The file does not appear to be a valid GIF file.\n");
         exit(EXIT_FAILURE);
     }
diff --git a/hl/tools/gif2h5/h52gifgentst.c b/hl/tools/gif2h5/h52gifgentst.c
index 9bd7874..ba2e4f5 100644
--- a/hl/tools/gif2h5/h52gifgentst.c
+++ b/hl/tools/gif2h5/h52gifgentst.c
@@ -6,7 +6,7 @@
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
  * the COPYING file, which can be found at the root of the source code       *
- * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * distribution tree, or in https://www.hdfgroup.org/licenses.               *
  * If you do not have access to either file, you may request a copy from     *
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
@@ -22,7 +22,7 @@
  *
  * Purpose: generate files for h52gif testing
  *
- * Programmer: Pedro Vicente, pvn@hdfgroup.org
+ * Programmer: Pedro Vicente
  *
  * Date: March 15, 2007
  *
diff --git a/hl/tools/gif2h5/h52giftest.sh.in b/hl/tools/gif2h5/h52giftest.sh.in
index 5643e30..2f84ef6 100644
--- a/hl/tools/gif2h5/h52giftest.sh.in
+++ b/hl/tools/gif2h5/h52giftest.sh.in
@@ -7,7 +7,7 @@
 # This file is part of HDF5.  The full HDF5 copyright notice, including
 # terms governing use, modification, and redistribution, is contained in
 # the COPYING file, which can be found at the root of the source code
-# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.
+# distribution tree, or in https://www.hdfgroup.org/licenses.
 # If you do not have access to either file, you may request a copy from
 # help@hdfgroup.org.
 #
@@ -70,20 +70,20 @@ echo ""
 
 # Positive tests for h52gif
 echo "**validate the h52gif tool processes input correctly..."
-TESTING "./h52gif h52giftst.h5 image1.gif -i image" 
+TESTING "./h52gif h52giftst.h5 image1.gif -i image"
 TOOLTEST ./h52gif $TESTFILE1 image1.gif -i image
 echo ""
 
 # Negative tests.
 echo "**verify that the h52gif tool handles error conditions correctly..."
 # nonexisting dataset name
-TESTING "./h52gif h52giftst.h5 image.gif -i nosuch_image" 
-TOOLTESTFAIL "./h52gif $TESTFILE1 image.gif -i nosuch_image" 
+TESTING "./h52gif h52giftst.h5 image.gif -i nosuch_image"
+TOOLTESTFAIL "./h52gif $TESTFILE1 image.gif -i nosuch_image"
 # this test should have failed but it did not. Comment it out for now.
-#TESTING "./h52gif h52giftst.h5 image.gif -i palette" 
-#TOOLTESTFAIL "./h52gif $TESTFILE1 image.gif -i palette" 
-TESTING "./h52gif h52giftst.h5 image24.gif -i image24bitpixel" 
-TOOLTESTFAIL "./h52gif $TESTFILE3 image24.gif -i image24bitpixel" 
+#TESTING "./h52gif h52giftst.h5 image.gif -i palette"
+#TOOLTESTFAIL "./h52gif $TESTFILE1 image.gif -i palette"
+TESTING "./h52gif h52giftst.h5 image24.gif -i image24bitpixel"
+TOOLTESTFAIL "./h52gif $TESTFILE3 image24.gif -i image24bitpixel"
 echo ""
 
 # all done. summarize results.
diff --git a/hl/tools/gif2h5/hdf2gif.c b/hl/tools/gif2h5/hdf2gif.c
index 402314a..d14a4cb 100644
--- a/hl/tools/gif2h5/hdf2gif.c
+++ b/hl/tools/gif2h5/hdf2gif.c
@@ -6,7 +6,7 @@
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
  * the COPYING file, which can be found at the root of the source code       *
- * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * distribution tree, or in https://www.hdfgroup.org/licenses.               *
  * If you do not have access to either file, you may request a copy from     *
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
@@ -18,6 +18,9 @@
 #include "h5tools.h"
 #include "h5tools_utils.h"
 
+/* Name of tool */
+#define PROGRAMNAME "hdf2gif"
+
 #define IMAGE_WIDTH_MAX  65535 /* unsigned 16bits integer */
 #define IMAGE_HEIGHT_MAX 65535 /* unsigned 16bits integer */
 
@@ -40,13 +43,18 @@ usage(void)
     printf("h52gif expects *at least* one h5_image.\n");
 }
 
+static void
+leave(int ret)
+{
+    h5tools_close();
+    HDexit(ret);
+}
+
 FILE *fpGif = NULL;
 int
 main(int argc, char **argv)
 {
-    GIFBYTE *   Image;
-    void *      edata;
-    H5E_auto2_t func;
+    GIFBYTE *Image;
 
     /* compression structs */
     GIFCHAR *HDFName = NULL;
@@ -72,22 +80,21 @@ main(int argc, char **argv)
     char *image_name    = NULL;
     int   idx;
 
-    /* Disable error reporting */
-    H5Eget_auto2(H5E_DEFAULT, &func, &edata);
-    H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
+    h5tools_setprogname(PROGRAMNAME);
+    h5tools_setstatus(EXIT_SUCCESS);
 
     /* Initialize h5tools lib */
     h5tools_init();
 
     if (argv[1] && (strcmp("-V", argv[1]) == 0)) {
         print_version("gif2h5");
-        exit(EXIT_SUCCESS);
+        h5tools_setstatus(EXIT_SUCCESS);
     }
 
     if (argc < 4) {
         /* they didn't supply at least one image -- bail */
         usage();
-        return EXIT_FAILURE;
+        h5tools_setstatus(EXIT_FAILURE);
     }
 
     HDFName = argv[1];
@@ -140,9 +147,11 @@ main(int argc, char **argv)
             goto out;
         }
 
-        /* read image */
-        if (H5IMget_image_info(fid, image_name, &width, &height, &planes, interlace, &npals) < 0)
+        /* get image's information */
+        if (H5IMget_image_info(fid, image_name, &width, &height, &planes, interlace, &npals) < 0) {
+            fprintf(stderr, "Unable to get information of the image. Aborting.\n");
             goto out;
+        }
 
         if (width > IMAGE_WIDTH_MAX || height > IMAGE_HEIGHT_MAX) {
             fprintf(stderr, "HDF5 image is too large. Limit is %d by %d.\n", IMAGE_WIDTH_MAX,
@@ -158,12 +167,16 @@ main(int argc, char **argv)
 
         Image = (GIFBYTE *)malloc((size_t)width * (size_t)height);
 
-        if (H5IMread_image(fid, image_name, Image) < 0)
+        if (H5IMread_image(fid, image_name, Image) < 0) {
+            fprintf(stderr, "Unable to read the image. Aborting.\n");
             goto out;
+        }
 
         if (npals) {
-            if (H5IMget_palette_info(fid, image_name, 0, pal_dims) < 0)
+            if (H5IMget_palette_info(fid, image_name, 0, pal_dims) < 0) {
+                fprintf(stderr, "Unable to get information of the palette. Aborting.\n");
                 goto out;
+            }
 
             pal = (GIFBYTE *)malloc((size_t)pal_dims[0] * (size_t)pal_dims[1]);
 
@@ -308,9 +321,7 @@ main(int argc, char **argv)
     if (image_name != NULL)
         free(image_name);
 
-    H5Eset_auto2(H5E_DEFAULT, func, edata);
-
-    return EXIT_SUCCESS;
+    leave(h5tools_getstatus());
 
 out:
 
@@ -319,7 +330,6 @@ out:
     if (image_name != NULL)
         free(image_name);
 
-    H5Eset_auto2(H5E_DEFAULT, func, edata);
-
-    return EXIT_FAILURE;
+    h5tools_setstatus(EXIT_FAILURE);
+    leave(h5tools_getstatus());
 }
diff --git a/hl/tools/gif2h5/hdfgifwr.c b/hl/tools/gif2h5/hdfgifwr.c
index 4619b99..21b14d1 100644
--- a/hl/tools/gif2h5/hdfgifwr.c
+++ b/hl/tools/gif2h5/hdfgifwr.c
@@ -6,7 +6,7 @@
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
  * the COPYING file, which can be found at the root of the source code       *
- * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * distribution tree, or in https://www.hdfgroup.org/licenses.               *
  * If you do not have access to either file, you may request a copy from     *
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
@@ -68,45 +68,6 @@ static void char_init(), char_out(), flush_char();
 
 static byte pc2nc[256];
 
-/*************************************************************/
-int
-hdfWriteGIF(FILE *fp, byte *pic, int ptype, int w, int h, byte *rmap, byte *gmap, byte *bmap, byte *pc2ncmap,
-            int numcols, int colorstyle, int BitsPerPixel)
-{
-    int   InitCodeSize;
-    int   i;
-    byte *pic8 = pic;
-
-    /* Shut compiler up... */
-    ptype      = ptype;
-    rmap       = rmap;
-    gmap       = gmap;
-    bmap       = bmap;
-    numcols    = numcols;
-    colorstyle = colorstyle;
-
-    for (i = 0; i < 256; i++) {
-        pc2nc[i] = pc2ncmap[i];
-    }
-
-    if (BitsPerPixel <= 1)
-        InitCodeSize = 2;
-    else
-        InitCodeSize = BitsPerPixel;
-
-    if (!fp) {
-        fprintf(stderr, "WriteGIF: file not open for writing\n");
-        return (1);
-    }
-
-    compress(InitCodeSize + 1, fp, pic8, w * h);
-
-    if (ferror(fp))
-        return -1;
-
-    return 0;
-}
-
 /***********************************************************************/
 static unsigned long cur_accum = 0;
 static int           cur_bits  = 0;
@@ -122,8 +83,8 @@ static int maxbits = XV_BITS;         /* user settable max # bits/code */
 static int maxcode;                   /* maximum code, given n_bits */
 static int maxmaxcode = 1 << XV_BITS; /* NEVER generate this */
 
-static count_int      htab[HSIZE];
-static unsigned short codetab[HSIZE];
+static count_int *     htab;
+static unsigned short *codetab;
 
 #define HashTabOf(i) htab[i]
 #define CodeTabOf(i) codetab[i]
@@ -172,6 +133,57 @@ static FILE *g_outfile;
 static int ClearCode;
 static int EOFCode;
 
+/*************************************************************/
+int
+hdfWriteGIF(FILE *fp, byte *pic, int ptype, int w, int h, const byte *rmap, const byte *gmap,
+            const byte *bmap, const byte *pc2ncmap, int numcols, int colorstyle, int BitsPerPixel)
+{
+    int   InitCodeSize;
+    int   i;
+    byte *pic8 = pic;
+
+    if (!(htab = calloc(HSIZE, sizeof(count_int)))) {
+        fprintf(stderr, "Out of memory");
+        return 1;
+    }
+    if (!(codetab = calloc(HSIZE, sizeof(unsigned short)))) {
+        fprintf(stderr, "Out of memory");
+        return 1;
+    }
+
+    /* Shut compiler up... */
+    (void)ptype;
+    (void)rmap;
+    (void)gmap;
+    (void)bmap;
+    (void)numcols;
+    (void)colorstyle;
+
+    for (i = 0; i < 256; i++) {
+        pc2nc[i] = pc2ncmap[i];
+    }
+
+    if (BitsPerPixel <= 1)
+        InitCodeSize = 2;
+    else
+        InitCodeSize = BitsPerPixel;
+
+    if (!fp) {
+        fprintf(stderr, "WriteGIF: file not open for writing\n");
+        return 1;
+    }
+
+    compress(InitCodeSize + 1, fp, pic8, w * h);
+
+    free(htab);
+    free(codetab);
+
+    if (ferror(fp))
+        return -1;
+
+    return 0;
+}
+
 /********************************************************/
 static void
 compress(int init_bits, FILE *outfile, byte *data, int len)
@@ -194,15 +206,13 @@ compress(int init_bits, FILE *outfile, byte *data, int len)
     /* initialize 'compress' globals */
     maxbits    = XV_BITS;
     maxmaxcode = 1 << XV_BITS;
-    memset(htab, 0, sizeof(htab));
-    memset(codetab, 0, sizeof(codetab));
-    hsize     = HSIZE;
-    free_ent  = 0;
-    clear_flg = 0;
-    in_count  = 1;
-    out_count = 0;
-    cur_accum = 0;
-    cur_bits  = 0;
+    hsize      = HSIZE;
+    free_ent   = 0;
+    clear_flg  = 0;
+    in_count   = 1;
+    out_count  = 0;
+    cur_accum  = 0;
+    cur_bits   = 0;
 
     /* Set up the necessary values */
     out_count = 0;
diff --git a/hl/tools/gif2h5/writehdf.c b/hl/tools/gif2h5/writehdf.c
index 0cf3926..6ec6af4 100644
--- a/hl/tools/gif2h5/writehdf.c
+++ b/hl/tools/gif2h5/writehdf.c
@@ -6,7 +6,7 @@
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
  * the COPYING file, which can be found at the root of the source code       *
- * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * distribution tree, or in https://www.hdfgroup.org/licenses.               *
  * If you do not have access to either file, you may request a copy from     *
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
diff --git a/hl/tools/h5watch/CMakeLists.txt b/hl/tools/h5watch/CMakeLists.txt
index 9329c97..be983ba 100644
--- a/hl/tools/h5watch/CMakeLists.txt
+++ b/hl/tools/h5watch/CMakeLists.txt
@@ -11,7 +11,8 @@ set (H5WATCH_SOURCES
 #-- Add h5watch program
 if (NOT ONLY_SHARED_LIBS)
   add_executable (h5watch ${H5WATCH_SOURCES})
-  target_include_directories (h5watch PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_compile_options(h5watch PRIVATE "${HDF5_CMAKE_C_FLAGS}")
+  target_include_directories (h5watch PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   TARGET_C_PROPERTIES (h5watch STATIC)
   target_link_libraries (h5watch PRIVATE ${HDF5_HL_LIB_TARGET} ${HDF5_LIB_TARGET} ${HDF5_TOOLS_LIB_TARGET})
   set_target_properties (h5watch PROPERTIES FOLDER tools/hl)
@@ -19,20 +20,33 @@ if (NOT ONLY_SHARED_LIBS)
 endif ()
 if (BUILD_SHARED_LIBS)
   add_executable (h5watch-shared ${H5WATCH_SOURCES})
-  target_include_directories (h5watch-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_compile_options(h5watch-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}")
+  target_include_directories (h5watch-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   TARGET_C_PROPERTIES (h5watch-shared SHARED)
   target_link_libraries (h5watch-shared PRIVATE ${HDF5_HL_LIBSH_TARGET} ${HDF5_LIBSH_TARGET} ${HDF5_TOOLS_LIBSH_TARGET})
   set_target_properties (h5watch-shared PROPERTIES FOLDER tools/hl)
   set (H5_DEP_EXECUTABLES ${H5_DEP_EXECUTABLES} h5watch-shared)
 endif ()
 
+#-----------------------------------------------------------------------------
+# Add Target to clang-format
+#-----------------------------------------------------------------------------
+if (HDF5_ENABLE_FORMATTERS)
+  if (NOT ONLY_SHARED_LIBS)
+    clang_format (HDF5_HL_TOOLS_H5WATCH_FORMAT h5watch)
+  else ()
+    clang_format (HDF5_HL_TOOLS_H5WATCH_FORMAT h5watch-shared)
+  endif ()
+endif ()
+
 if (BUILD_TESTING AND HDF5_TEST_SWMR AND HDF5_TEST_SERIAL)
   #-- Add swmr_check_compat_vfd program
   set (hl_swmr_check_compat_vfd_SOURCES
       ${HDF5_HL_TOOLS_H5WATCH_SOURCE_DIR}/swmr_check_compat_vfd.c
   )
   add_executable (hl_swmr_check_compat_vfd ${hl_swmr_check_compat_vfd_SOURCES})
-  target_include_directories (hl_swmr_check_compat_vfd PRIVATE "${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_compile_options(hl_swmr_check_compat_vfd PRIVATE "${HDF5_CMAKE_C_FLAGS}")
+  target_include_directories (hl_swmr_check_compat_vfd PRIVATE "${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   if (NOT ONLY_SHARED_LIBS)
     TARGET_C_PROPERTIES (hl_swmr_check_compat_vfd STATIC)
     target_link_libraries (hl_swmr_check_compat_vfd PRIVATE ${HDF5_LIB_TARGET})
@@ -42,12 +56,20 @@ if (BUILD_TESTING AND HDF5_TEST_SWMR AND HDF5_TEST_SERIAL)
   endif ()
   set_target_properties (hl_swmr_check_compat_vfd PROPERTIES FOLDER tools/hl)
 
+  #-----------------------------------------------------------------------------
+  # Add Target to clang-format
+  #-----------------------------------------------------------------------------
+  if (HDF5_ENABLE_FORMATTERS)
+    clang_format (HDF5_HL_TOOLS_H5WATCH_hl_swmr_check_compat_vfd_FORMAT hl_swmr_check_compat_vfd)
+  endif ()
+
   #-- Add extend_dset program
   set (extend_dset_SOURCES
       ${HDF5_HL_TOOLS_H5WATCH_SOURCE_DIR}/extend_dset.c
   )
   add_executable (extend_dset ${extend_dset_SOURCES})
-  target_include_directories (extend_dset PRIVATE "${HDF5_HL_SRC_DIR}/test;${HDF5_HL_SRC_DIR}/src;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_compile_options(extend_dset PRIVATE "${HDF5_CMAKE_C_FLAGS}")
+  target_include_directories (extend_dset PRIVATE "${HDF5_HL_SRC_DIR}/test;${HDF5_HL_SRC_DIR}/src;${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   if (NOT ONLY_SHARED_LIBS)
     TARGET_C_PROPERTIES (extend_dset STATIC)
     target_link_libraries (extend_dset PRIVATE ${HDF5_HL_LIB_TARGET} ${HDF5_TEST_LIB_TARGET} ${HDF5_LIB_TARGET} ${HDF5_TOOLS_LIB_TARGET})
@@ -57,8 +79,16 @@ if (BUILD_TESTING AND HDF5_TEST_SWMR AND HDF5_TEST_SERIAL)
   endif ()
   set_target_properties (extend_dset PROPERTIES FOLDER tools/hl)
 
+  #-----------------------------------------------------------------------------
+  # Add Target to clang-format
+  #-----------------------------------------------------------------------------
+  if (HDF5_ENABLE_FORMATTERS)
+    clang_format (HDF5_HL_TOOLS_H5WATCH_extend_dset_FORMAT extend_dset)
+  endif ()
+
   add_executable (h5watchgentest ${HDF5_HL_TOOLS_H5WATCH_SOURCE_DIR}/h5watchgentest.c)
-  target_include_directories (h5watchgentest PRIVATE "${HDF5_HL_SRC_DIR}/src;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_compile_options(h5watchgentest PRIVATE "${HDF5_CMAKE_C_FLAGS}")
+  target_include_directories (h5watchgentest PRIVATE "${HDF5_HL_SRC_DIR}/src;${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   if (NOT ONLY_SHARED_LIBS)
     TARGET_C_PROPERTIES (h5watchgentest STATIC)
     target_link_libraries (h5watchgentest PRIVATE ${HDF5_HL_LIB_TARGET} ${HDF5_LIB_TARGET})
@@ -68,6 +98,13 @@ if (BUILD_TESTING AND HDF5_TEST_SWMR AND HDF5_TEST_SERIAL)
   endif ()
   set_target_properties (h5watchgentest PROPERTIES FOLDER generator/tools/hl)
 
+  #-----------------------------------------------------------------------------
+  # Add Target to clang-format
+  #-----------------------------------------------------------------------------
+  if (HDF5_ENABLE_FORMATTERS)
+    clang_format (HDF5_HL_TOOLS_H5WATCH_h5watchgentest_FORMAT h5watchgentest)
+  endif ()
+
   if (HDF5_TEST_TOOLS)
     include (CMakeTests.cmake)
   endif ()
diff --git a/hl/tools/h5watch/CMakeTests.cmake b/hl/tools/h5watch/CMakeTests.cmake
index 19d47cb..60c099b 100644
--- a/hl/tools/h5watch/CMakeTests.cmake
+++ b/hl/tools/h5watch/CMakeTests.cmake
@@ -5,7 +5,7 @@
 # This file is part of HDF5.  The full HDF5 copyright notice, including
 # terms governing use, modification, and redistribution, is contained in
 # the COPYING file, which can be found at the root of the source code
-# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.
+# distribution tree, or in https://www.hdfgroup.org/licenses.
 # If you do not have access to either file, you may request a copy from
 # help@hdfgroup.org.
 #
diff --git a/hl/tools/h5watch/Makefile.am b/hl/tools/h5watch/Makefile.am
index 0bf265e..5112965 100644
--- a/hl/tools/h5watch/Makefile.am
+++ b/hl/tools/h5watch/Makefile.am
@@ -6,7 +6,7 @@
 # This file is part of HDF5.  The full HDF5 copyright notice, including
 # terms governing use, modification, and redistribution, is contained in
 # the COPYING file, which can be found at the root of the source code
-# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.
+# distribution tree, or in https://www.hdfgroup.org/licenses.
 # If you do not have access to either file, you may request a copy from
 # help@hdfgroup.org.
 ##
diff --git a/hl/tools/h5watch/Makefile.in b/hl/tools/h5watch/Makefile.in
index 3822dda..ed7b7ea 100644
--- a/hl/tools/h5watch/Makefile.in
+++ b/hl/tools/h5watch/Makefile.in
@@ -22,7 +22,7 @@
 # This file is part of HDF5.  The full HDF5 copyright notice, including
 # terms governing use, modification, and redistribution, is contained in
 # the COPYING file, which can be found at the root of the source code
-# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.
+# distribution tree, or in https://www.hdfgroup.org/licenses.
 # If you do not have access to either file, you may request a copy from
 # help@hdfgroup.org.
 #
@@ -118,6 +118,7 @@ am__aclocal_m4_deps = $(top_srcdir)/m4/aclocal_cxx.m4 \
 	$(top_srcdir)/m4/ax_check_junit.m4 \
 	$(top_srcdir)/m4/ax_java_options.m4 \
 	$(top_srcdir)/m4/ax_jni_include_dir.m4 \
+	$(top_srcdir)/m4/ax_prog_doxygen.m4 \
 	$(top_srcdir)/m4/ax_prog_jar.m4 \
 	$(top_srcdir)/m4/ax_prog_java.m4 \
 	$(top_srcdir)/m4/ax_prog_java_works.m4 \
@@ -437,7 +438,7 @@ AMTAR = @AMTAR@
 
 # H5_CFLAGS holds flags that should be used when building hdf5,
 # but which should not be exported to h5cc for building other programs.
-# AM_CFLAGS is an automake construct which should be used by Makefiles 
+# AM_CFLAGS is an automake construct which should be used by Makefiles
 # instead of CFLAGS, as CFLAGS is reserved solely for the user to define.
 # This applies to FCFLAGS, CXXFLAGS, CPPFLAGS, and LDFLAGS as well.
 AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@
@@ -466,6 +467,7 @@ CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
 CFLAGS = @CFLAGS@
+CLANG_SANITIZE_CHECKS = @CLANG_SANITIZE_CHECKS@
 CODESTACK = @CODESTACK@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
@@ -482,11 +484,54 @@ DEFAULT_API_VERSION = @DEFAULT_API_VERSION@
 DEFS = @DEFS@
 DEPDIR = @DEPDIR@
 DEPRECATED_SYMBOLS = @DEPRECATED_SYMBOLS@
-DEV_WARNINGS = @DEV_WARNINGS@
+DESIRED_FILE_LOCKING = @DESIRED_FILE_LOCKING@
+DIAGS = @DIAGS@
 DIRECT_VFD = @DIRECT_VFD@
 DLLTOOL = @DLLTOOL@
+DOXYGEN_EXAMPLES_DIRECTORY = @DOXYGEN_EXAMPLES_DIRECTORY@
+DOXYGEN_EXTERNAL_SEARCH = @DOXYGEN_EXTERNAL_SEARCH@
+DOXYGEN_HTML_EXTRA_FILES = @DOXYGEN_HTML_EXTRA_FILES@
+DOXYGEN_HTML_EXTRA_STYLESHEET = @DOXYGEN_HTML_EXTRA_STYLESHEET@
+DOXYGEN_HTML_FOOTER = @DOXYGEN_HTML_FOOTER@
+DOXYGEN_HTML_HEADER = @DOXYGEN_HTML_HEADER@
+DOXYGEN_INCLUDE_ALIASES = @DOXYGEN_INCLUDE_ALIASES@
+DOXYGEN_INPUT_DIRECTORY = @DOXYGEN_INPUT_DIRECTORY@
+DOXYGEN_LAYOUT_FILE = @DOXYGEN_LAYOUT_FILE@
+DOXYGEN_MACRO_EXPANSION = @DOXYGEN_MACRO_EXPANSION@
+DOXYGEN_OPTIMIZE_OUTPUT_FOR_C = @DOXYGEN_OPTIMIZE_OUTPUT_FOR_C@
+DOXYGEN_OUTPUT_DIRECTORY = @DOXYGEN_OUTPUT_DIRECTORY@
+DOXYGEN_PACKAGE = @DOXYGEN_PACKAGE@
+DOXYGEN_PAPER_SIZE = @DOXYGEN_PAPER_SIZE@
+DOXYGEN_PROJECT_BRIEF = @DOXYGEN_PROJECT_BRIEF@
+DOXYGEN_PROJECT_LOGO = @DOXYGEN_PROJECT_LOGO@
+DOXYGEN_SEARCHENGINE_URL = @DOXYGEN_SEARCHENGINE_URL@
+DOXYGEN_SERVER_BASED_SEARCH = @DOXYGEN_SERVER_BASED_SEARCH@
+DOXYGEN_VERSION_STRING = @DOXYGEN_VERSION_STRING@
 DSYMUTIL = @DSYMUTIL@
 DUMPBIN = @DUMPBIN@
+DX_CONFIG = @DX_CONFIG@
+DX_DOCDIR = @DX_DOCDIR@
+DX_DOT = @DX_DOT@
+DX_DOXYGEN = @DX_DOXYGEN@
+DX_DVIPS = @DX_DVIPS@
+DX_EGREP = @DX_EGREP@
+DX_ENV = @DX_ENV@
+DX_FLAG_chi = @DX_FLAG_chi@
+DX_FLAG_chm = @DX_FLAG_chm@
+DX_FLAG_doc = @DX_FLAG_doc@
+DX_FLAG_dot = @DX_FLAG_dot@
+DX_FLAG_html = @DX_FLAG_html@
+DX_FLAG_man = @DX_FLAG_man@
+DX_FLAG_pdf = @DX_FLAG_pdf@
+DX_FLAG_ps = @DX_FLAG_ps@
+DX_FLAG_rtf = @DX_FLAG_rtf@
+DX_FLAG_xml = @DX_FLAG_xml@
+DX_HHC = @DX_HHC@
+DX_LATEX = @DX_LATEX@
+DX_MAKEINDEX = @DX_MAKEINDEX@
+DX_PDFLATEX = @DX_PDFLATEX@
+DX_PERL = @DX_PERL@
+DX_PROJECT = @DX_PROJECT@
 ECHO_C = @ECHO_C@
 ECHO_N = @ECHO_N@
 ECHO_T = @ECHO_T@
@@ -520,6 +565,7 @@ H5_CPPFLAGS = @H5_CPPFLAGS@
 H5_CXXFLAGS = @H5_CXXFLAGS@
 H5_FCFLAGS = @H5_FCFLAGS@
 H5_FORTRAN_SHARED = @H5_FORTRAN_SHARED@
+H5_IS_DARWIN = @H5_IS_DARWIN@
 H5_JAVACFLAGS = @H5_JAVACFLAGS@
 H5_JAVAFLAGS = @H5_JAVAFLAGS@
 H5_JNIFLAGS = @H5_JNIFLAGS@
@@ -530,6 +576,7 @@ HAVE_DMALLOC = @HAVE_DMALLOC@
 HAVE_Fortran_INTEGER_SIZEOF_16 = @HAVE_Fortran_INTEGER_SIZEOF_16@
 HAVE_LIBHDFS = @HAVE_LIBHDFS@
 HAVE_PTHREAD = @HAVE_PTHREAD@
+HDF5_DOXYGEN = @HDF5_DOXYGEN@
 HDF5_HL = @HDF5_HL@
 HDF5_INTERFACES = @HDF5_INTERFACES@
 HDF5_TESTS = @HDF5_TESTS@
@@ -542,6 +589,7 @@ HL = @HL@
 HL_FOR = @HL_FOR@
 HSIZE_T = @HSIZE_T@
 HSSIZE_T = @HSSIZE_T@
+IGNORE_DISABLED_FILE_LOCKS = @IGNORE_DISABLED_FILE_LOCKS@
 INSTALL = @INSTALL@
 INSTALL_DATA = @INSTALL_DATA@
 INSTALL_PROGRAM = @INSTALL_PROGRAM@
@@ -579,6 +627,7 @@ MAKEINFO = @MAKEINFO@
 MANIFEST_TOOL = @MANIFEST_TOOL@
 MAP_API = @MAP_API@
 MEMORYALLOCSANITYCHECK = @MEMORYALLOCSANITYCHECK@
+MIRROR_VFD = @MIRROR_VFD@
 MKDIR_P = @MKDIR_P@
 MPE = @MPE@
 NM = @NM@
@@ -615,6 +664,7 @@ PATH_SEPARATOR = @PATH_SEPARATOR@
 PREADWRITE = @PREADWRITE@
 PROFILING = @PROFILING@
 RANLIB = @RANLIB@
+RECURSIVE_RW_LOCKS = @RECURSIVE_RW_LOCKS@
 ROOT = @ROOT@
 ROS3_VFD = @ROS3_VFD@
 RUNPARALLEL = @RUNPARALLEL@
@@ -638,6 +688,7 @@ TIME = @TIME@
 TR = @TR@
 TRACE_API = @TRACE_API@
 UNAME_INFO = @UNAME_INFO@
+USE_FILE_LOCKING = @USE_FILE_LOCKING@
 USE_FILTER_DEFLATE = @USE_FILTER_DEFLATE@
 USE_FILTER_SZIP = @USE_FILTER_SZIP@
 USINGMEMCHECKER = @USINGMEMCHECKER@
@@ -730,15 +781,15 @@ LIBH5_HL = $(top_builddir)/hl/src/libhdf5_hl.la
 LIBH5F_HL = $(top_builddir)/hl/fortran/src/libhdf5hl_fortran.la
 LIBH5CPP_HL = $(top_builddir)/hl/c++/src/libhdf5_hl_cpp.la
 
-# Note that in svn revision 19400 the '/' after DESTDIR in H5* variables below  
-# has been removed. According to the official description of DESTDIR by Gnu at 
-# http://www.gnu.org/prep/standards/html_node/DESTDIR.html, DESTDIR is 
-# prepended to the normal and complete install path that it precedes for the 
-# purpose of installing in a temporary directory which is useful for building 
-# rpms and other packages.  The '/' after ${DESTDIR} will be followed by another 
-# '/' at the beginning of the normal install path.  When DESTDIR is empty the  
-# path then begins with '//', which is incorrect and causes problems at least for 
-# Cygwin.   
+# Note that in svn revision 19400 the '/' after DESTDIR in H5* variables below
+# has been removed. According to the official description of DESTDIR by Gnu at
+# http://www.gnu.org/prep/standards/html_node/DESTDIR.html, DESTDIR is
+# prepended to the normal and complete install path that it precedes for the
+# purpose of installing in a temporary directory which is useful for building
+# rpms and other packages.  The '/' after ${DESTDIR} will be followed by another
+# '/' at the beginning of the normal install path.  When DESTDIR is empty the
+# path then begins with '//', which is incorrect and causes problems at least for
+# Cygwin.
 
 # Scripts used to build examples
 # If only shared libraries have been installed, have h5cc build examples with
@@ -784,7 +835,7 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
-chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST)
 TEST_EXTENSIONS = .sh
 SH_LOG_COMPILER = $(SHELL)
 AM_SH_LOG_FLAGS = 
@@ -1326,9 +1377,9 @@ uninstall-am: uninstall-binPROGRAMS
 # commands that should be executed even if a file with the same name already
 # exists.
 .PHONY: build-check-clean build-check-p build-check-s build-lib build-progs \
-        build-tests check-clean check-install check-p check-s check-vfd \
-        check-passthrough-vol install-doc lib progs tests uninstall-doc \
-        _exec_check-s _test help
+	build-tests check-clean check-install check-p check-s check-vfd \
+	check-passthrough-vol install-doc lib progs tests uninstall-doc \
+	_exec_check-s _test help trace doxygen
 
 help:
 	@$(top_srcdir)/bin/makehelp
diff --git a/hl/tools/h5watch/extend_dset.c b/hl/tools/h5watch/extend_dset.c
index 8677601..282f5c2 100644
--- a/hl/tools/h5watch/extend_dset.c
+++ b/hl/tools/h5watch/extend_dset.c
@@ -6,7 +6,7 @@
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
  * the COPYING file, which can be found at the root of the source code       *
- * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * distribution tree, or in https://www.hdfgroup.org/licenses.               *
  * If you do not have access to either file, you may request a copy from     *
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
diff --git a/hl/tools/h5watch/h5watch.c b/hl/tools/h5watch/h5watch.c
index 22ed314..a5e82ca 100644
--- a/hl/tools/h5watch/h5watch.c
+++ b/hl/tools/h5watch/h5watch.c
@@ -6,7 +6,7 @@
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
  * the COPYING file, which can be found at the root of the source code       *
- * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * distribution tree, or in https://www.hdfgroup.org/licenses.               *
  * If you do not have access to either file, you may request a copy from     *
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
@@ -43,7 +43,7 @@ static unsigned g_retry = DEFAULT_RETRY;  /* # of times to try opening the file
 static hbool_t  g_display_hex    = FALSE; /* display data in hexadecimal format : LATER */
 static hbool_t  g_user_interrupt = FALSE; /* Flag to indicate that user interrupted execution */
 
-static herr_t doprint(hid_t did, hsize_t *start, hsize_t *block, int rank);
+static herr_t doprint(hid_t did, const hsize_t *start, const hsize_t *block, int rank);
 static herr_t slicendump(hid_t did, hsize_t *prev_dims, hsize_t *cur_dims, hsize_t *start, hsize_t *block,
                          int rank, int subrank);
 static herr_t monitor_dataset(hid_t fid, char *dsetname);
@@ -95,7 +95,7 @@ static struct long_options l_opts[] = {{"help", no_arg, 'h'},         {"hel", no
  *-------------------------------------------------------------------------
  */
 static herr_t
-doprint(hid_t did, hsize_t *start, hsize_t *block, int rank)
+doprint(hid_t did, const hsize_t *start, const hsize_t *block, int rank)
 {
     h5tools_context_t ctx;                           /* print context  */
     h5tool_format_t   info;                          /* Format info for the tools library */
@@ -182,7 +182,7 @@ doprint(hid_t did, hsize_t *start, hsize_t *block, int rank)
     info.dset_format     = "DSET-%s ";
     info.dset_hidefileno = 0;
 
-    info.obj_format     = "-%lu:" H5_PRINTF_HADDR_FMT;
+    info.obj_format     = "-%lu:%" PRIuHADDR;
     info.obj_hidefileno = 0;
 
     info.dset_blockformat_pre = "%sBlk%lu: ";
@@ -340,7 +340,8 @@ monitor_dataset(hid_t fid, char *dsetname)
         if (i != ndims) {
             /* Printing changes in dimension sizes */
             for (u = 0; u < ndims; u++) {
-                HDfprintf(stdout, "dimension %u: %Hu->%Hu", (unsigned)u, prev_dims[u], cur_dims[u]);
+                HDfprintf(stdout, "dimension %d: %" PRIuHSIZE "->%" PRIuHSIZE "", u, prev_dims[u],
+                          cur_dims[u]);
                 if (cur_dims[u] > prev_dims[u])
                     HDfprintf(stdout, " (increases)\n");
                 else if (cur_dims[u] < prev_dims[u])
@@ -791,23 +792,17 @@ catch_signal(int H5_ATTR_UNUSED signo)
 int
 main(int argc, const char *argv[])
 {
-    char        drivername[50]; /* VFD name */
-    char *      fname = NULL;   /* File name */
-    char *      dname = NULL;   /* Dataset name */
-    void *      edata;          /* Error reporting */
-    H5E_auto2_t func;           /* Error reporting */
-    char *      x;              /* Temporary string pointer */
-    hid_t       fid  = -1;      /* File ID */
-    hid_t       fapl = -1;      /* File access property list */
+    char  drivername[50]; /* VFD name */
+    char *fname = NULL;   /* File name */
+    char *dname = NULL;   /* Dataset name */
+    char *x;              /* Temporary string pointer */
+    hid_t fid  = -1;      /* File ID */
+    hid_t fapl = -1;      /* File access property list */
 
     /* Set up tool name and exit status */
     h5tools_setprogname(PROGRAMNAME);
     h5tools_setstatus(EXIT_SUCCESS);
 
-    /* Disable error reporting */
-    H5Eget_auto2(H5E_DEFAULT, &func, &edata);
-    H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
-
     /* Initialize h5tools lib */
     h5tools_init();
 
@@ -832,6 +827,9 @@ main(int argc, const char *argv[])
         leave(EXIT_FAILURE);
     }
 
+    /* enable error reporting if command line option */
+    h5tools_error_report();
+
     /* Mostly copied from tools/h5ls coding & modified accordingly */
     /*
      * [OBJECT] is specified as
@@ -850,19 +848,24 @@ main(int argc, const char *argv[])
     if ((fname = HDstrdup(argv[opt_ind])) == NULL) {
         error_msg("memory allocation failed (file %s:line %d)\n", __FILE__, __LINE__);
         h5tools_setstatus(EXIT_FAILURE);
+        goto done;
     }
 
     /* Create a copy of file access property list */
-    if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
-        return -1;
+    if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
+        h5tools_setstatus(EXIT_FAILURE);
+        goto done;
+    }
 
     /* Set to use the latest library format */
-    if (H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0)
-        return -1;
+    if (H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) {
+        h5tools_setstatus(EXIT_FAILURE);
+        goto done;
+    }
 
     do {
         while (fname && *fname) {
-            fid = h5tools_fopen(fname, H5F_ACC_RDONLY | H5F_ACC_SWMR_READ, fapl, NULL, drivername,
+            fid = h5tools_fopen(fname, H5F_ACC_RDONLY | H5F_ACC_SWMR_READ, fapl, FALSE, drivername,
                                 sizeof drivername);
 
             if (fid >= 0) {
@@ -884,16 +887,14 @@ main(int argc, const char *argv[])
 
     if (fid < 0) {
         error_msg("unable to open file \"%s\"\n", fname);
-        if (fname)
-            HDfree(fname);
-        if (fapl >= 0)
-            H5Pclose(fapl);
-        leave(EXIT_FAILURE);
+        h5tools_setstatus(EXIT_FAILURE);
+        goto done;
     }
 
     if (!dname) {
         error_msg("no dataset specified\n");
         h5tools_setstatus(EXIT_FAILURE);
+        goto done;
     }
     else {
         *dname = '/';
@@ -901,16 +902,22 @@ main(int argc, const char *argv[])
         if ((dname = HDstrdup(dname)) == NULL) {
             error_msg("memory allocation failed (file %s:line %d)\n", __FILE__, __LINE__);
             h5tools_setstatus(EXIT_FAILURE);
+            goto done;
         }
         else {
             *x = '\0';
             /* Validate dataset */
-            if (check_dataset(fid, dname) < 0)
+            if (check_dataset(fid, dname) < 0) {
                 h5tools_setstatus(EXIT_FAILURE);
+                goto done;
+            }
             /* Validate input "fields" */
-            else if (g_list_of_fields && *g_list_of_fields)
-                if (process_cmpd_fields(fid, dname) < 0)
+            else if (g_list_of_fields && *g_list_of_fields) {
+                if (process_cmpd_fields(fid, dname) < 0) {
                     h5tools_setstatus(EXIT_FAILURE);
+                    goto done;
+                }
+            }
         }
     }
 
@@ -919,6 +926,7 @@ main(int argc, const char *argv[])
         if (monitor_dataset(fid, dname) < 0)
             h5tools_setstatus(EXIT_FAILURE);
 
+done:
     /* Free spaces */
     if (fname)
         HDfree(fname);
@@ -940,12 +948,11 @@ main(int argc, const char *argv[])
     }
 
     /* Close the file */
-    if (H5Fclose(fid) < 0) {
+    if (fid >= 0 && H5Fclose(fid) < 0) {
         error_msg("unable to close file\n");
         h5tools_setstatus(EXIT_FAILURE);
     }
 
-    H5Eset_auto2(H5E_DEFAULT, func, edata);
     /* exit */
     leave(h5tools_getstatus());
 } /* main() */
diff --git a/hl/tools/h5watch/h5watchgentest.c b/hl/tools/h5watch/h5watchgentest.c
index 255ad41..c83e485 100644
--- a/hl/tools/h5watch/h5watchgentest.c
+++ b/hl/tools/h5watch/h5watchgentest.c
@@ -6,7 +6,7 @@
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
  * the COPYING file, which can be found at the root of the source code       *
- * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * distribution tree, or in https://www.hdfgroup.org/licenses.               *
  * If you do not have access to either file, you may request a copy from     *
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
diff --git a/hl/tools/h5watch/swmr_check_compat_vfd.c b/hl/tools/h5watch/swmr_check_compat_vfd.c
index fb1c903..a2340bf 100644
--- a/hl/tools/h5watch/swmr_check_compat_vfd.c
+++ b/hl/tools/h5watch/swmr_check_compat_vfd.c
@@ -6,7 +6,7 @@
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
  * the COPYING file, which can be found at the root of the source code       *
- * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * distribution tree, or in https://www.hdfgroup.org/licenses.               *
  * If you do not have access to either file, you may request a copy from     *
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
diff --git a/hl/tools/h5watch/testh5watch.sh.in b/hl/tools/h5watch/testh5watch.sh.in
index 24ff6aa..67ffcc3 100644
--- a/hl/tools/h5watch/testh5watch.sh.in
+++ b/hl/tools/h5watch/testh5watch.sh.in
@@ -7,7 +7,7 @@
 # This file is part of HDF5.  The full HDF5 copyright notice, including
 # terms governing use, modification, and redistribution, is contained in
 # the COPYING file, which can be found at the root of the source code
-# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.
+# distribution tree, or in https://www.hdfgroup.org/licenses.
 # If you do not have access to either file, you may request a copy from
 # help@hdfgroup.org.
 #