diff --git a/.github/workflows/main-cmake.yml b/.github/workflows/main-cmake.yml
index c8739ae58c5..d3803a3a702 100644
--- a/.github/workflows/main-cmake.yml
+++ b/.github/workflows/main-cmake.yml
@@ -39,8 +39,8 @@ jobs:
           - "MacOS Clang"
 
         # This is where we list the bulk of the options for each configuration.
-        # The key-value pair values are usually appropriate for being CMake or
-        # Autotools configure values, so be aware of that.
+        # The key-value pair values are usually appropriate for being CMake
+        # configure values, so be aware of that.
 
         include:
 
diff --git a/.github/workflows/tarball.yml b/.github/workflows/tarball.yml
index 11a3894f35f..3935d9892e4 100644
--- a/.github/workflows/tarball.yml
+++ b/.github/workflows/tarball.yml
@@ -97,10 +97,10 @@ jobs:
           path: hdfsrc
           ref: '${{needs.check_commits.outputs.branch_ref }}'
 
-      - name: Install Autotools Dependencies (Linux, serial)
+      - name: Install Linux Dependencies (Linux, serial)
         run: |
              sudo apt update
-             sudo apt install automake autoconf libtool libtool-bin gzip dos2unix
+             sudo apt install gzip dos2unix
 
       - name: Retrieve version
         id: version
diff --git a/.github/workflows/vol_adios2.yml b/.github/workflows/vol_adios2.yml
index 835e7e020fe..e92a1472195 100644
--- a/.github/workflows/vol_adios2.yml
+++ b/.github/workflows/vol_adios2.yml
@@ -23,7 +23,7 @@ jobs:
       - name: Install dependencies
         run: |
           sudo apt-get update
-          sudo apt-get install automake autoconf libtool libtool-bin libopenmpi-dev
+          sudo apt-get install libopenmpi-dev
 
       - name: Checkout HDF5
         uses: actions/checkout@v4.1.7
diff --git a/.github/workflows/vol_ext_passthru.yml b/.github/workflows/vol_ext_passthru.yml
index 629f24cab11..b72d98f8a03 100644
--- a/.github/workflows/vol_ext_passthru.yml
+++ b/.github/workflows/vol_ext_passthru.yml
@@ -19,7 +19,7 @@ jobs:
       - name: Install dependencies
         run: |
           sudo apt-get update
-          sudo apt-get install automake autoconf libtool libtool-bin libopenmpi-dev
+          sudo apt-get install libopenmpi-dev
 
       - name: Checkout HDF5
         uses: actions/checkout@v4.1.7
diff --git a/.github/workflows/vol_rest.yml b/.github/workflows/vol_rest.yml
index 3e5d0713016..0887614a596 100644
--- a/.github/workflows/vol_rest.yml
+++ b/.github/workflows/vol_rest.yml
@@ -39,7 +39,7 @@ jobs:
       - name: Install dependencies
         run: |
           sudo apt-get update
-          sudo apt-get install automake autoconf libtool libtool-bin libcurl4-openssl-dev libyajl-dev
+          sudo apt-get install libcurl4-openssl-dev libyajl-dev
 
       - name: Checkout HDF5
         uses: actions/checkout@v4.1.7
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 4803ffefa8f..97c5b5d42e8 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -119,7 +119,6 @@ Please make sure that you check the items applicable to your pull request:
 * Code
   * [ ] Does the pull request have a corresponding GitHub issue and clear purpose?
   * [ ] Does the pull request follow HDF5 best practices (naming conventions, code portability, code structure, etc.)? <<TODO: link to the document>>
-  * [ ] If changes were done to Autotools build, were they added to CMake and vice versa?
   * [ ] Is the pull request applicable to any other branches? If yes, which ones? Please document it in the GitHub issue.
   * [ ] Is the new code sufficiently documented for future maintenance?
   * [ ] Does the new feature require a change to an existing API? See "API Compatibility Macros" document (https://hdfgroup.github.io/hdf5/develop/d7/d26/api-compat-macros.html)
diff --git a/README.md b/README.md
index 0bcf1efa6fc..e06bc46ecf6 100644
--- a/README.md
+++ b/README.md
@@ -14,7 +14,6 @@
 ![HDF5 Logo][u3]
 
 [![develop cmake build status](https://img.shields.io/github/actions/workflow/status/HDFGroup/hdf5/cmake.yml?branch=develop&label=HDF5%20develop%20CMake%20CI)](https://github.com/HDFGroup/hdf5/actions/workflows/cmake.yml?query=branch%3Adevelop)
-[![develop autotools build status](https://img.shields.io/github/actions/workflow/status/HDFGroup/hdf5/autotools.yml?branch=develop&label=HDF5%20develop%20Autotools%20CI)](https://github.com/HDFGroup/hdf5/actions/workflows/autotools.yml?query=branch%3Adevelop)
 [![HDF-EOS5 build status](https://img.shields.io/github/actions/workflow/status/HDFGroup/hdf5/hdfeos5.yml?branch=develop&label=HDF-EOS5)](https://github.com/HDFGroup/hdf5/actions/workflows/hdfeos5.yml?query=branch%3Adevelop)
 [![netCDF build status](https://img.shields.io/github/actions/workflow/status/HDFGroup/hdf5/netcdf.yml?branch=develop&label=netCDF)](https://github.com/HDFGroup/hdf5/actions/workflows/netcdf.yml?query=branch%3Adevelop)
 [![h5py build status](https://img.shields.io/github/actions/workflow/status/HDFGroup/hdf5/h5py.yml?branch=develop&label=h5py)](https://github.com/HDFGroup/hdf5/actions/workflows/h5py.yml?query=branch%3Adevelop)
diff --git a/doxygen/dox/HDF5CompressionTroubleshooting.dox b/doxygen/dox/HDF5CompressionTroubleshooting.dox
index 97efb29af19..be7cb89fe3c 100644
--- a/doxygen/dox/HDF5CompressionTroubleshooting.dox
+++ b/doxygen/dox/HDF5CompressionTroubleshooting.dox
@@ -71,23 +71,7 @@ Everywhere in this document, the term \b szip refers to the \b szip filter and t
 \b gzip and \b szip require the \b libz.a(so,dylib,lib) and \b libsz.a(so,dylib,lib)/libaec.a(so,dylib,lib)
 libraries, respectively, to be present on the system and to be enabled during HDF5 configuration with
 this autotools configure command:
-\code
-    ./configure –with-zlib=/path… –with-szlib=/path… <other flags>
-\endcode
-There is one important difference in the behavior of GNU Autotools configure between \b gzip and \b szip.
-On Unix systems,\b  gzip compression is enabled automatically if the \b zlib library is present on the system
-in default locations without explicitly specifying <code>–with-zlib=/path</code>. For example, if
-<code>libz.so</code> is installed under <code>/usr/lib</code> with the
-header under <code>/usr/include</code> or under <code>/usr/local/lib</code> with the header under
-<code>/usr/local/include</code>, the following HDF5 configure command will find the \b gzip library and will
-configure the compression filter in: 
-\code
-    ./configure
-\endcode
-With GNU Autotools configure will not fail if libraries supporting the requested compression method are not found, for example,
-because a specified path was not correct, or the library is missing.
-
-Or CMake configure command:
+CMake configure command:
 \code
     cmake -G "Unix Makefiles" -DHDF5_ENABLE_ZLIB_SUPPORT=ON -DHDF5_ENABLE_SZIP_SUPPORT=ON -D<other flags>
 \endcode
diff --git a/doxygen/dox/branches-explained.dox b/doxygen/dox/branches-explained.dox
index 46f9c00b70b..7aeafeec2ef 100644
--- a/doxygen/dox/branches-explained.dox
+++ b/doxygen/dox/branches-explained.dox
@@ -31,7 +31,7 @@ support.
 \section sec_branchexpl_release Release branches
 Release branches are used to prepare a new production release. They are primarily used to allow for
 last minute dotting of i's and crossing of t's 
-(things like setting the release version, finalizing release notes, and generating Autotools files)
+(things like setting the release version, finalizing release notes, and generating files)
 and do not include new development. 
 They are created from the maintenance branch at the time of the maintenance release and have 
 names like hdf5_1_10_N, where N is the minor release number. Once the release is  done it is
diff --git a/doxygen/dox/file-locking.dox b/doxygen/dox/file-locking.dox
index aacf2135b04..5af369e840c 100644
--- a/doxygen/dox/file-locking.dox
+++ b/doxygen/dox/file-locking.dox
@@ -172,12 +172,6 @@ You can set the file locking defaults at configure time. This sets the defaults
 for the associated properties in the fapl. Users can override the configure
 defaults using #H5Pset_file_locking or the <code>HDF5_USE_FILE_LOCKING</code>
 environment variable.
-
-<h4>Autotools</h4>
-\li <code>--enable-file-locking=(yes</td><td>no</td><td>best-effort)</code> sets the file locking behavior.
-    <code>on</code> and <code>off</code> should be self-explanatory. <code>best-effort</code> turns file locking
-    on but ignores file locks when they are disabled (default: <code>best-effort</code>).
-
 <h4>CMake</h4>
 \li set <code>IGNORE_DISABLED_FILE_LOCK</code> to <code>ON</code> to ignore file locks when they
 \li  are disabled on the file system (default: <code>ON</code>).
diff --git a/test/test_abort_fail.sh.in b/test/test_abort_fail.sh.in
deleted file mode 100644
index f4873f53184..00000000000
--- a/test/test_abort_fail.sh.in
+++ /dev/null
@@ -1,65 +0,0 @@
-#! /bin/sh
-#
-# Copyright by The HDF Group.
-# All rights reserved.
-#
-# This file is part of HDF5.  The full HDF5 copyright notice, including
-# terms governing use, modification, and redistribution, is contained in
-# the LICENSE file, which can be found at the root of the source code
-# 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.
-#
-# Test to verify that the assertion/abort failure is fixed when the application
-# does not close the file. (See HDFFV-10160)
-#
-# Test to verify that the infinite loop closing library/abort failure is fixed
-# when the application creates and removes dense attributes (See HDFFV-10659)
-
-srcdir=@srcdir@
-
-nerrors=0
-
-##############################################################################
-##############################################################################
-###			  T H E   T E S T S                                            ###
-##############################################################################
-##############################################################################
-#
-#
-echo "Testing file not closed assertion/abort failure"
-TEST_NAME=filenotclosed     # The test name
-TEST_BIN=`pwd`/$TEST_NAME   # The path of the test binary
-#
-# Run the test
-$RUNSERIAL $TEST_BIN >/dev/null 2>&1
-exitcode=$?
-if [ $exitcode -eq 0 ]; then
-    echo "Test PASSED"
-else
-    echo "Test FAILED"
- 	nerrors="`expr $nerrors + 1`"
-fi
-#
-#
-echo "Testing infinite loop closing library/abort failure"
-TEST_NAME=del_many_dense_attrs  # The test name
-TEST_BIN=`pwd`/$TEST_NAME 	    # The path of the test binary
-# Run the test
-$RUNSERIAL $TEST_BIN >/dev/null 2>&1
-exitcode=$?
-if [ $exitcode -eq 0 ]; then
-    echo "Test PASSED"
-else
-    echo "Test FAILED"
- 	nerrors="`expr $nerrors + 1`"
-fi
-#
-#
-if test $nerrors -eq 0 ; then
-    echo "All tests for abort failure passed."
-    exit 0
-else
-    echo "Tests for abort failure failed with $nerrors errors."
-    exit 1
-fi
diff --git a/test/test_check_version.sh.in b/test/test_check_version.sh.in
deleted file mode 100644
index 6bd268b745d..00000000000
--- a/test/test_check_version.sh.in
+++ /dev/null
@@ -1,258 +0,0 @@
-#! /bin/sh
-#
-# Copyright by The HDF Group.
-# All rights reserved.
-#
-# This file is part of HDF5.  The full HDF5 copyright notice, including
-# terms governing use, modification, and redistribution, is contained in
-# the LICENSE file, which can be found at the root of the source code
-# distribution tree, or in https://www.hdfgroup.org/licenses.
-# If you do not have access to either file, you may request a copy from
-# help@hdfgroup.org.
-
-#
-# Tests for the H5check_version function.
-#
-
-srcdir=@srcdir@
-
-# Variables filled in by the configure process.
-# Determine the configure options of the hdf5 library and executables.
-Shared_Lib=@enable_shared@
-Static_Lib=@enable_static@
-Static_exec=@STATIC_EXEC@
-h5haveexitcode=yes    # default is yes
-
-CMP='cmp -s'
-DIFF='diff -c'
-RM='rm -f'
-
-# Function definitions
-#
-# Show the purpose of this test script and a note about the abort messages.
-PURPOSE() {
-    echo "Tests for the H5check_version function."
-    echo "Note that abort messages may appear due to the expected termination"
-    echo "of the program when it is tested with mis-matched version numbers."
-}
-
-# Print a line-line message left justified in a field of 70 characters.
-#
-LINEMSG() {
-   SPACES="                                                               "
-   echo "$* $SPACES" | cut -c1-70 | tr -d '\012'
-}
-
-
-# Print a "SKIP" message
-SKIP() {
-    LINEMSG $*
-    echo  " -SKIP-"
-}
-
-
-# Print warning message of version mismatch.
-WarnMesg(){
-    echo "Warning! ***HDF5 library version mismatched error***"
-    echo "The HDF5 header files used to compile this application do not match"
-    echo "the version used by the HDF5 library to which this application is linked."
-    echo "Data corruption or segmentation faults may occur if the application continues."
-    echo "This can happen when an application was compiled by one version of HDF5 but"
-    echo "linked with a different version of static or shared HDF5 library."
-    echo "You should recompile the application or check your shared library related"
-    echo "settings such as 'LD_LIBRARY_PATH'."
-    echo "You can, at your own risk, disable this warning by setting the environment"
-    echo "variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'."
-    echo "Setting it to 2 or higher will suppress the warning messages totally."
-    echo "Headers are $xxh5versmajor.$xxh5versminor.$xxh5versrelease, library is $h5versmajor.$h5versminor.$h5versrelease"
-    test -n "$H5_HAVE_EMBEDDED_LIBINFO" && cat $h5libsettings
-    echo "Bye..."
-}
-
-
-# Print warning message2 of version mismatch.
-WarnMesg2(){
-    echo "Warning! ***HDF5 library version mismatched error***"
-    echo "The HDF5 header files used to compile this application do not match"
-    echo "the version used by the HDF5 library to which this application is linked."
-    echo "Data corruption or segmentation faults may occur if the application continues."
-    echo "This can happen when an application was compiled by one version of HDF5 but"
-    echo "linked with a different version of static or shared HDF5 library."
-    echo "You should recompile the application or check your shared library related"
-    echo "settings such as 'LD_LIBRARY_PATH'."
-    echo "'HDF5_DISABLE_VERSION_CHECK' environment variable is set to 1, application will"
-    echo "continue at your own risk."
-    echo "Headers are $xxh5versmajor.$xxh5versminor.$xxh5versrelease, library is $h5versmajor.$h5versminor.$h5versrelease"
-    test -n "$H5_HAVE_EMBEDDED_LIBINFO" && cat $h5libsettings
-}
-
-
-# Run a test and print PASS or *FAIL*.  If a test fails then increment
-# the `nerrors' global variable and (if $verbose is set) display the
-# difference between the actual output and the expected output. The
-# expected output generated according to the parameter values and compared
-# against actual output.
-# The expected and actual output files are removed unless $HDF5_NOCLEANUP
-# has a non-zero value.
-# $1: the set value of $HDF5_DISABLE_VERSION_CHECK. (unset means not to set
-#     it at all.
-# $2: Change the version number(s) to cause a mismatch. (none means no
-#     mismatch).
-#
-# Expected results:
-#         Value of $HDF5_DISABLE_VERSION_CHECK
-#        unset    ""    -1    0    1    2    3
-# Matched    OK    OK    OK    OK    OK    OK    OK
-# Mismatched    W/A    W/A    W/A    W/A    W2/OK    OK    W2/OK
-# Result codes:
-# OK:    No warning, exit 0.
-# W/A:   Warning, abort and exit non-0.
-# W2/OK: Different Warning, exit 0.
-#
-# Implemented only exit code matching. Still need to match output.
-TESTING() {
-    DEBUGPRINT command is $0 $*
-    TEST_NAME=tcheck_version                  # The test name
-    TEST_BIN=`pwd`/$TEST_NAME # The path of the test binary
-
-    expect=${TEST_NAME}_expect.out
-    actual=${TEST_NAME}_actual.out
-    actual_err=${TEST_NAME}_actual.err
-    arguments=
-
-    h5DisableVersion="$1"
-    wrongversionnumbers="$2"
-    xxh5versmajor=$h5versmajor
-    xxh5versminor=$h5versminor
-    xxh5versrelease=$h5versrelease
-
-    if [ "$h5DisableVersion" = unset ]; then
-    envcmd=""        # noop
-    else
-    envcmd="env HDF5_DISABLE_VERSION_CHECK=$h5DisableVersion"
-    fi
-
-    if [ "$wrongversionnumbers" = none ]; then
-    # OK: No warning, exit 0
-    cp /dev/null $expect
-    expect_code=0
-    else
-    arguments=-t"$wrongversionnumbers"
-    # calculate mismatched version numbers by listing.
-    case $wrongversionnumbers in
-        "M")    xxh5versmajor=`expr $h5versmajor + 1`
-            ;;
-        "m")    xxh5versminor=`expr $h5versminor + 1`
-            ;;
-        "r")    xxh5versrelease=`expr $h5versrelease + 1`
-            ;;
-    esac
-    case "$h5DisableVersion" in
-        1)
-        # W2/OK: Different Warning, exit 0.
-        WarnMesg2 > $expect
-        expect_code=0
-        ;;
-        [2-9]|[1-9][0-9]*)
-        # OK: No warning, exit 0
-        cp /dev/null $expect
-        expect_code=0
-        ;;
-        *)    # W/A:   Warning, abort and exit non-0.
-        WarnMesg > $expect
-        expect_code=6    # Signal Abort exit code (128+6)
-        ;;
-    esac
-    fi
-
-    # Run test.
-    LINEMSG $envcmd $TEST_NAME $arguments
-    (
-      $envcmd $RUNSERIAL $TEST_BIN  $arguments
-    ) >$actual 2>$actual_err
-    ret_code=$?
-    cat $actual_err >> $actual
-
-    if [ $h5haveexitcode = 'yes' -a \( $expect_code -ne $ret_code \) ]; then
-    echo "*FAILED*"
-    echo "    Expected exit code ($expect_code) differs from actual code ($ret_code)"
-    nerrors="`expr $nerrors + 1`"
-    elif $CMP $expect $actual; then
-    echo " PASSED"
-    else
-    echo "*FAILED*"
-    echo "    Expected result differs from actual result"
-    nerrors="`expr $nerrors + 1`"
-    test yes = "$verbose" && $DIFF $expect $actual |sed 's/^/    /'
-    fi
-
-    # Clean up output file.
-    # Also clean the core file generated by H5check_version's abort.
-    if test -z "$HDF5_NOCLEANUP"; then
-    $RM $expect $actual $actual_err
-    $RM core
-    fi
-}
-
-
-# Echo parameters for debugging if verbose mode is on.
-DEBUGPRINT() {
-    if [ -n "$debugmode" ]; then
-    echo $*
-    fi
-}
-
-
-# MAIN Body
-nerrors=0
-verbose=yes    # default on
-debugmode=    # default off
-H5_HAVE_EMBEDDED_LIBINFO=`grep '#define H5_HAVE_EMBEDDED_LIBINFO ' ../src/H5pubconf.h`
-h5libsettings=../src/libhdf5.settings
-
-PURPOSE
-
-# Figure out library version numbers from the header file.
-h5versmajor=`grep '#define H5_VERS_MAJOR' $srcdir/../src/H5public.h | awk '{print $3}'`
-h5versminor=`grep '#define H5_VERS_MINOR' $srcdir/../src/H5public.h | awk '{print $3}'`
-h5versrelease=`grep '#define H5_VERS_RELEASE' $srcdir/../src/H5public.h | awk '{print $3}'`
-DEBUGPRINT $h5versmajor.$h5versminor.$h5versrelease
-case "$h5versmajor$h5versminor$h5versrelease" in
-    [0-9]*)     # good. noop.
-        ;;
-    *)
-        echo "Illegal library version numbers($h5versmajor.$h5versminor.$h5versrelease)"
-        echo "Test aborted"
-        exit 1
-        ;;
-esac
-
-# RUNSERIAL is used. Check if it can return exit code from executalbe correctly.
-if [ -n "$RUNSERIAL_NOEXITCODE" ]; then
-    echo "***Warning*** Serial Exit Code is not passed back to shell correctly."
-    echo "***Warning*** Exit code checking is skipped."
-    h5haveexitcode=no
-fi
-
-# Three Categories of tests:
-# Normal: where the version numbers all matched (wrong_version == none).
-# Mismatched version numbers (could be Major or minor version
-#    or release numbers or a combination of all three.)
-# Test all the above with different values of the environment variable,
-# HDF5_DISABLE_VERSION_CHECK, as unset, "", -1, 0, 1, 2, 3
-
-for val_disable_version_check in unset "" -1 0 1 2 3; do
-    for wrong_version in none M m; do
-    TESTING "$val_disable_version_check" "$wrong_version"
-    done
-done
-
-
-# Check and report results.
-if [ $nerrors -gt 0 ]; then
-    echo "***$nerrors errors encountered***"
-    exit 1
-else
-    echo "No error encountered"
-    exit 0
-fi
diff --git a/test/test_error.sh.in b/test/test_error.sh.in
deleted file mode 100644
index 63682057d41..00000000000
--- a/test/test_error.sh.in
+++ /dev/null
@@ -1,125 +0,0 @@
-#! /bin/sh
-#
-# Copyright by The HDF Group.
-# All rights reserved.
-#
-# This file is part of HDF5.  The full HDF5 copyright notice, including
-# terms governing use, modification, and redistribution, is contained in
-# the LICENSE file, which can be found at the root of the source code
-# 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.
-#
-# Tests for test_error and err_compat
-
-srcdir=@srcdir@
-
-# Check if backward compatibility options are enabled
-DEPRECATED_SYMBOLS="@DEPRECATED_SYMBOLS@"
-
-CMP='cmp -s'
-DIFF='diff -c'
-
-# Skip plugin module to test missing filter
-# Also reset the VOL connector to only use the native connector, because of the
-#       error stack checking.   QAK - 2019/03/09
-ENVCMD="env HDF5_PLUGIN_PRELOAD=:: HDF5_VOL_CONNECTOR=native"
-
-nerrors=0
-verbose=yes
-
-test -d ./testfiles || mkdir ./testfiles
-
-# Print a line-line message left justified in a field of 70 characters
-# beginning with the word "Testing".
-#
-TESTING() {
-    SPACES="                                                               "
-    echo "Testing $* $SPACES" | cut -c1-70 | tr -d '\012'
-}
-
-# Run a test and print PASS or *FAIL*.  If a test fails then increment
-# the `nerrors' global variable and (if $verbose is set) display the
-# difference between the actual output and the expected output. The
-# expected output is given as the first argument to this function and
-# the actual output file is calculated by replacing the `.ddl' with
-# `.out'.  The actual output is not removed if $HDF5_NOCLEANUP has a
-# non-zero value.
-#
-TEST() {
-   TEST_ERR=$1                  # The test name
-   TEST_ERR_BIN=`pwd`/$TEST_ERR # The path of the test binary
-
-   expect1="$srcdir/testfiles/$1_1"
-   expect2="$srcdir/testfiles/$1_2"
-   actual="./`basename $1`.out"
-   actual_err="./`basename $1`.err"
-   actual_ext="./`basename $1`.ext"
-   shift
-
-   # Run test.
-   TESTING $TEST_ERR
-   (
-      # Skip the plugin for testing missing filter.
-      $ENVCMD $RUNSERIAL $TEST_ERR_BIN
-   ) >$actual 2>$actual_err
-
-   # Check for core dump
-   if [ $? != 0 ]; then
-       nerrors=`expr $nerrors + 1`
-   fi
-
-   # Extract file name, line number, version and thread IDs because they may be different
-   sed -e 's/ thread [0-9]*//' -e 's/: .*\.c /: (file name) /' \
-	-e 's/line [0-9]*/line (number)/' \
-        -e 's/v[1-9]*\.[0-9]*\./version (number)\./' \
-	-e 's/[1-9]*\.[0-9]*\.[0-9]*[^)]*/version (number)/' \
-        -e 's/H5Eget_auto[1-2]*/H5Eget_auto(1 or 2)/' \
-        -e 's/H5Eset_auto[1-2]*/H5Eset_auto(1 or 2)/' \
-	$actual_err > $actual_ext
-   cat $actual_ext >> $actual
-
-   if $CMP $expect1 $actual; then
-      echo " PASSED"
-   elif $CMP $expect2 $actual; then
-      echo " PASSED"
-   else
-      echo "*FAILED*"
-      echo "    Expected result differs from actual result"
-      nerrors="`expr $nerrors + 1`"
-      test yes = "$verbose" && $DIFF $expect1 $actual |sed 's/^/    /'
-   fi
-
-   # Clean up output file
-   if test -z "$HDF5_NOCLEANUP"; then
-      rm -f $actual $actual_err $actual_ext
-   fi
-}
-
-# Print a "SKIP" message
-SKIP() {
-    TESTING $@
-    echo  " -SKIP-"
-}
-
-##############################################################################
-##############################################################################
-###			  T H E   T E S T S                                ###
-##############################################################################
-##############################################################################
-
-# test for err_compat
-if test $DEPRECATED_SYMBOLS != "yes"; then
-SKIP err_compat
-else
-TEST err_compat
-fi
-
-# test for error_test.  Skip the plugin for testing missing filter.
-TEST error_test
-
-if test $nerrors -eq 0 ; then
-   echo "All Error API tests passed."
-fi
-
-exit $nerrors
diff --git a/test/test_external_env.sh.in b/test/test_external_env.sh.in
deleted file mode 100644
index 86d2fd5870d..00000000000
--- a/test/test_external_env.sh.in
+++ /dev/null
@@ -1,41 +0,0 @@
-#! /bin/sh
-#
-# Copyright by The HDF Group.
-# All rights reserved.
-#
-# This file is part of HDF5.  The full HDF5 copyright notice, including
-# terms governing use, modification, and redistribution, is contained in
-# the LICENSE file, which can be found at the root of the source code
-# distribution tree, or in https://www.hdfgroup.org/licenses.
-# If you do not have access to either file, you may request a copy from
-# help@hdfgroup.org.
-#
-# Test for external file with environment variable: HDF5_EXTFILE_PREFIX
-
-srcdir=@srcdir@
-
-nerrors=0
-
-##############################################################################
-##############################################################################
-###			  T H E   T E S T S                                ###
-##############################################################################
-##############################################################################
-
-# test for external file with HDF5_EXTFILE_PREFIX
-echo "Testing external file with HDF5_EXTFILE_PREFIX"
-TEST_NAME=external_env                         # The test name
-TEST_BIN=`pwd`/$TEST_NAME                      # The path of the test binary
-ENVCMD="env HDF5_EXTFILE_PREFIX=\${ORIGIN}"    # The environment variable & value
-#
-# Run the test
-# echo "$ENVCMD $RUNSERIAL $TEST_BIN"
-$ENVCMD $RUNSERIAL $TEST_BIN
-exitcode=$?
-if [ $exitcode -eq 0 ]; then
-    echo "Test prefix for HDF5_EXTFILE_PREFIX PASSED"
-else
-    nerrors="`expr $nerrors + 1`"
-    echo "***Error encountered for HDF5_EXTFILE_PREFIX test***"
-fi
-exit $nerrors
diff --git a/test/test_libinfo.sh.in b/test/test_libinfo.sh.in
deleted file mode 100644
index 89f852f2173..00000000000
--- a/test/test_libinfo.sh.in
+++ /dev/null
@@ -1,117 +0,0 @@
-#! /bin/sh
-#
-# Copyright by The HDF Group.
-# All rights reserved.
-#
-# This file is part of HDF5.  The full HDF5 copyright notice, including
-# terms governing use, modification, and redistribution, is contained in
-# the LICENSE file, which can be found at the root of the source code
-# 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.
-
-
-#
-# Tests for the embedded library information feature.
-# Part 1:
-# Verify the HDF5 library does contains an exact copy of the content of the
-# libhdf5.settings file.
-# Part 2:
-# If executable is linked with the static hdf5 library (how to determine?),
-# verify an executable indeed contains an exact copy of the content of the
-# libhdf5.settings file.
-#
-
-srcdir=@srcdir@
-
-# Determine the configure options of the hdf5 library and executables.
-
-Shared_Lib=@enable_shared@
-Static_Lib=@enable_static@
-Static_exec=@STATIC_EXEC@
-
-
-# Print a line-line message left justified in a field of 70 characters.
-#
-LINEMSG() {
-   SPACES="                                                               "
-   echo "Check file $* $SPACES" | cut -c1-70 | tr -d '\012'
-}
-
-
-# Print a "SKIP" message
-SKIP() {
-    LINEMSG $*
-    echo  " -SKIP-"
-}
-
-# Function definitions
-CHECK_LIBINFO(){
-    LINEMSG $1
-    # Some systems, like Mac, the strings command inspects library files. Older
-    # versions of strings may not know newer library format, resulting in
-    # command errors. Make it read the file as stdin to avoid the problem.
-    if strings < $1 | grep "SUMMARY OF THE HDF5 CONFIGURATION" > /dev/null; then
-	echo " PASSED"
-    else
-	echo " FAILED"
-	nerrors=`expr $nerrors + 1`
-    fi
-}
-
-
-# MAIN Body
-nerrors=0
-H5_HAVE_EMBEDDED_LIBINFO=`grep '#define H5_HAVE_EMBEDDED_LIBINFO ' ../src/H5pubconf.h`
-
-# Skip the rest if embedded-libinfo is not enabled.
-if [ -z "$H5_HAVE_EMBEDDED_LIBINFO" ]; then
-    echo "embedded-libinfo is not enabled. Test skipped."
-    exit 0
-fi
-
-# The location of HDF library file(s) depends on whether shared lib is
-# built too.
-if [ -n $Shared_Lib ]; then
-   h5libdir=../src/.libs
-   shlib=$(grep dlname ../src/libhdf5.la | sed -e "s/dlname='//" -e "s/'//")
-else
-   h5libdir=../src
-fi
-
-h5libsettings=../src/libhdf5.settings
-
-# Part 1:
-# Verify the HDF5 library does contains an exact copy of the content of the
-# libhdf5.settings file.
-# Check dynamic library file if built.
-if [ x-$Shared_Lib = x-yes ]; then
-    CHECK_LIBINFO ${h5libdir}/${shlib}
-else
-    SKIP shlib
-fi
-
-# Though rare, libhdf5.a may not have been built.
-if [ x-$Static_Lib = x-yes ]; then
-    CHECK_LIBINFO ${h5libdir}/libhdf5.a
-else
-    SKIP ${h5libdir}/libhdf5.a
-fi
-
-# Check if executables has the lib information only if shared lib is not
-# built or static-exec is used.  (Don't care static-exec since it affects
-# tools binary only.)
-if [ x-$Shared_Lib != x-yes ]; then
-    CHECK_LIBINFO testhdf5
-else
-    SKIP testhdf5
-fi
-
-
-if [ $nerrors -gt 0 ]; then
-    echo "***$nerrors errors encountered***"
-    exit 1
-else
-    echo "No error encountered"
-    exit 0
-fi
diff --git a/test/test_links_env.sh.in b/test/test_links_env.sh.in
deleted file mode 100644
index a81aec2343e..00000000000
--- a/test/test_links_env.sh.in
+++ /dev/null
@@ -1,41 +0,0 @@
-#! /bin/sh
-#
-# Copyright by The HDF Group.
-# All rights reserved.
-#
-# This file is part of HDF5.  The full HDF5 copyright notice, including
-# terms governing use, modification, and redistribution, is contained in
-# the LICENSE file, which can be found at the root of the source code
-# 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.
-#
-# Test for external link with environment variable: HDF5_EXT_PREFIX
-
-srcdir=@srcdir@
-
-nerrors=0
-
-##############################################################################
-##############################################################################
-###              T H E   T E S T S                                ###
-##############################################################################
-##############################################################################
-
-# test for external links with HDF5_EXT_PREFIX
-echo "Testing external link with HDF5_EXT_PREFIX"
-TEST_NAME=links_env         # The test name
-TEST_BIN=`pwd`/$TEST_NAME     # The path of the test binary
-ENVCMD="env HDF5_EXT_PREFIX=.:tmp_links_env"     # The environment variable & value
-#
-# Run the test
-echo "$ENVCMD $RUNSERIAL $TEST_BIN"
-$ENVCMD $RUNSERIAL $TEST_BIN
-exitcode=$?
-if [ $exitcode -eq 0 ]; then
-    echo "Test for HDF5_EXT_PREFIX PASSED"
-else
-    nerrors="`expr $nerrors + 1`"
-    echo "***Error encountered for HDF5_EXT_PREFIX test***"
-fi
-exit $nerrors
diff --git a/test/test_mirror.sh.in b/test/test_mirror.sh.in
deleted file mode 100644
index 6ad2a901bea..00000000000
--- a/test/test_mirror.sh.in
+++ /dev/null
@@ -1,110 +0,0 @@
-#! /bin/bash
-#
-# Copyright by The HDF Group.
-# All rights reserved.
-#
-# This file is part of HDF5.  The full HDF5 copyright notice, including
-# terms governing use, modification, and redistribution, is contained in
-# the LICENSE file, which can be found at the root of the source code
-# distribution tree, or in https://www.hdfgroup.org/licenses.
-# If you do not have access to either file, you may request a copy from
-# help@hdfgroup.org.
-#
-# Tests for the Mirror VFD feature.
-#
-
-###############################################################################
-## test parameters
-###############################################################################
-
-nerrors=0
-
-SERVER_VERBOSITY="--verbosity=1"
-# Choose random ephemeral port number
-RANDOM_PORT=$[ $RANDOM % 16384 + 49152 ]
-echo "Using port: $RANDOM_PORT"
-SERVER_PORT="--port=$RANDOM_PORT"
-
-
-###############################################################################
-## Main
-###############################################################################
-
-## TODO: arguments for main port, port range, verbosity?
-# Parse options (none accepted at this time)
-while [ $# -gt 0 ]; do
-    case "$1" in
-    *)  # unknown option
-        echo "$0: Unknown option ($1)"
-        exit 1
-        ;;
-    esac
-done
-
-RUN_DIR=mirror_vfd_test
-MIRROR_UTILS=../utils/mirror_vfd # TODO: presupposes from test/
-
-# Start clean
-if test -d $RUN_DIR ; then
-    rm -rf $RUN_DIR
-fi
-mkdir $RUN_DIR
-
-# Copy program files into dedicated test directory
-for FILE in $MIRROR_UTILS/mirror_* ; do
-    case "$FILE" in
-        *.o) continue ;; # Don't copy .o files
-    esac
-    cp $FILE $RUN_DIR
-done
-cp mirror_vfd $RUN_DIR
-
-# With the --disable-shared option, program files are built in their main
-# directories; otherwise they are built in dir/.libs with a corresponding
-# wrapper script. Copy these libs builds if appropriate.
-if [ -f $MIRROR_UTILS/.libs/mirror_server ] ; then
-    RUN_LIBS=$RUN_DIR/.libs
-    # Delete previous .libs directory, to remove any generated libtool files
-    if test -d $RUN_LIBS ; then
-        rm -rf $RUN_LIBS
-    fi
-    mkdir $RUN_LIBS
-    for FILE in $MIRROR_UTILS/.libs/mirror_* ; do
-        case "$FILE" in
-            *.o) continue ;; # Don't copy .o files
-        esac
-        cp $FILE $RUN_LIBS
-    done
-    cp .libs/mirror_vfd $RUN_LIBS
-fi
-
-cd $RUN_DIR
-
-echo "Launching Mirror Server"
-SERVER_ARGS="$SERVER_PORT $SERVER_VERBOSITY"
-./mirror_server $SERVER_ARGS &
-
-./mirror_vfd $SERVER_PORT
-nerrors=$?
-
-echo "Stopping Mirror Server"
-./mirror_server_stop $SERVER_PORT
-
-# Wait for background server process to exit
-wait
-
-###############################################################################
-## Report and exit
-###############################################################################
-cd ..
-if test $nerrors -eq 0 ; then
-    echo "Mirror VFD tests passed."
-    if test -z "$HDF5_NOCLEANUP" ; then
-        rm -rf $RUN_DIR
-    fi
-    exit 0
-else
-    echo "Mirror VFD tests FAILED."
-    exit 1
-fi
-
diff --git a/test/test_plugin.sh.in b/test/test_plugin.sh.in
deleted file mode 100644
index 82fcd525f9e..00000000000
--- a/test/test_plugin.sh.in
+++ /dev/null
@@ -1,140 +0,0 @@
-#!/usr/bin/env bash
-#
-# Copyright by The HDF Group.
-# All rights reserved.
-#
-# This file is part of HDF5.  The full HDF5 copyright notice, including
-# terms governing use, modification, and redistribution, is contained in
-# the LICENSE file, which can be found at the root of the source code
-# distribution tree, or in https://www.hdfgroup.org/licenses.
-# If you do not have access to either file, you may request a copy from
-# help@hdfgroup.org.
-#
-# This shell script is for testing filter, VFD, and VOL plugins.
-#
-srcdir=@srcdir@
-TOP_BUILDDIR=@top_builddir@
-
-EXIT_SUCCESS=0
-EXIT_FAILURE=1
-
-CP="cp -rp"     # Use -p to preserve mode,ownership, timestamps
-RM="rm -rf"
-
-nerrors=0
-verbose=yes
-exit_code=$EXIT_SUCCESS
-
-# Test binary names
-FILTER_TEST_NAME=filter_plugin
-FILTER_TEST_BIN=`pwd`/$FILTER_TEST_NAME
-
-VFD_TEST_NAME=vfd_plugin
-VFD_TEST_BIN=`pwd`/$VFD_TEST_NAME
-
-VOL_TEST_NAME=vol_plugin
-VOL_TEST_BIN=`pwd`/$VOL_TEST_NAME
-
-# Paths to actual plugins ("libraries" in test directory are just stubs)
-FROM_DIR=`pwd`/.libs
-case $(uname) in
-    CYGWIN* )
-        NULL_VFD_PLUGIN="$FROM_DIR/cygnull_vfd_plugin*"
-        NULL_VOL_PLUGIN="$FROM_DIR/cygnull_vol_connector*"
-        PLUGINS_FOR_DIR1="$FROM_DIR/cygfilter_plugin1* $FROM_DIR/cygfilter_plugin3*"
-        PLUGINS_FOR_DIR2="$FROM_DIR/cygfilter_plugin2* $FROM_DIR/cygfilter_plugin4*"
-        ;;
-    *)
-        NULL_VFD_PLUGIN="$FROM_DIR/libnull_vfd_plugin*"
-        NULL_VOL_PLUGIN="$FROM_DIR/libnull_vol_connector*"
-        PLUGINS_FOR_DIR1="$FROM_DIR/libfilter_plugin1* $FROM_DIR/libfilter_plugin3*"
-        PLUGINS_FOR_DIR2="$FROM_DIR/libfilter_plugin2* $FROM_DIR/libfilter_plugin4*"
-        ;;
-esac
-
-# Directories where we'll copy plugins
-TEMP_PLUGIN_DIR=temp_plugins
-TEMP_FILTER_DIR1=temp_filter_plugin_dir1
-TEMP_FILTER_DIR2=temp_filter_plugin_dir2
-
-# Function to print a line-line message left justified in a field of
-# 70 characters beginning with the word "Testing".
-#
-TESTING() {
-    SPACES="                                                               "
-    echo "Testing $* $SPACES" | cut -c1-70 | tr -d '\012'
-}
-
-#############
-# Main Body #
-#############
-
-# Create plugin directories
-test -d $TEMP_PLUGIN_DIR || mkdir -p $TEMP_PLUGIN_DIR
-if [ $? != 0 ]; then
-    echo "Failed to create plugin test directory ($TEMP_PLUGIN_DIR)"
-    exit $EXIT_FAILURE
-fi
-test -d $TEMP_FILTER_DIR1 || mkdir -p $TEMP_FILTER_DIR1
-if [ $? != 0 ]; then
-    echo "Failed to create filter plugin test directory ($TEMP_FILTER_DIR1)"
-    exit $EXIT_FAILURE
-fi
-test -d $TEMP_FILTER_DIR2 || mkdir -p $TEMP_FILTER_DIR2
-if [ $? != 0 ]; then
-    echo "Failed to create filter plugin test directory ($TEMP_FILTER_DIR2)"
-    exit $EXIT_FAILURE
-fi
-
-# Copy plugins for the tests
-$CP $NULL_VFD_PLUGIN $TEMP_PLUGIN_DIR
-if [ $? != 0 ]; then
-    echo "Failed to copy NULL VFD plugin ($NULL_VFD_PLUGIN) to test directory."
-    exit $EXIT_FAILURE
-fi
-$CP $NULL_VOL_PLUGIN $TEMP_PLUGIN_DIR
-if [ $? != 0 ]; then
-    echo "Failed to copy NULL VOL plugin ($NULL_VOL_PLUGIN) to test directory."
-    exit $EXIT_FAILURE
-fi
-$CP $PLUGINS_FOR_DIR1 $TEMP_FILTER_DIR1
-if [ $? != 0 ]; then
-    echo "Failed to copy filter plugins ($PLUGINS_FOR_DIR1) to test directory."
-    exit $EXIT_FAILURE
-fi
-$CP $PLUGINS_FOR_DIR2 $TEMP_FILTER_DIR2
-if [ $? != 0 ]; then
-    echo "Failed to copy filter plugins ($PLUGINS_FOR_DIR2) to test directory."
-    exit $EXIT_FAILURE
-fi
-
-# Set plugin path
-ENVCMD="env HDF5_PLUGIN_PATH=${TEMP_PLUGIN_DIR}:${TEMP_FILTER_DIR1}:${TEMP_FILTER_DIR2}:${HDF5_PLUGIN_PATH}"
-
-# Run the tests
-$ENVCMD $FILTER_TEST_BIN
-if [ $? != 0 ]; then
-    nerrors=`expr $nerrors + 1`
-fi
-$ENVCMD $VFD_TEST_BIN
-if [ $? != 0 ]; then
-    nerrors=`expr $nerrors + 1`
-fi
-$ENVCMD $VOL_TEST_BIN
-if [ $? != 0 ]; then
-    nerrors=`expr $nerrors + 1`
-fi
-
-# Print results
-if test $nerrors -ne 0 ; then
-    echo "$nerrors errors encountered"
-    exit_code=$EXIT_FAILURE
-else
-    echo "All plugin tests passed."
-    exit_code=$EXIT_SUCCESS
-fi
-
-# Clean up temporary files/directories and leave
-$RM $TEMP_PLUGIN_DIR $TEMP_FILTER_DIR1 $TEMP_FILTER_DIR2
-
-exit $exit_code
diff --git a/test/test_vds_env.sh.in b/test/test_vds_env.sh.in
deleted file mode 100644
index ea911185e0b..00000000000
--- a/test/test_vds_env.sh.in
+++ /dev/null
@@ -1,43 +0,0 @@
-#! /bin/sh
-#
-# Copyright by The HDF Group.
-# All rights reserved.
-#
-# This file is part of HDF5.  The full HDF5 copyright notice, including
-# terms governing use, modification, and redistribution, is contained in
-# the LICENSE file, which can be found at the root of the source code
-# distribution tree, or in https://www.hdfgroup.org/licenses.
-# If you do not have access to either file, you may request a copy from
-# help@hdfgroup.org.
-#
-# Test for external file with environment variable: HDF5_VDS_PREFIX
-
-srcdir=@srcdir@
-
-nerrors=0
-
-##############################################################################
-##############################################################################
-###              T H E   T E S T S                                ###
-##############################################################################
-##############################################################################
-
-# test for VDS with HDF5_VDS_PREFIX
-echo "Testing basic virtual dataset I/O via H5Pset_vds_prefix(): all selection with ENV prefix"
-TEST_NAME=vds_env                               # The test name
-TEST_BIN=`pwd`/$TEST_NAME                       # The path of the test binary
-ENVCMD="env HDF5_VDS_PREFIX=\${ORIGIN}/tmp_vds_env"     # Set the environment variable & value
-UNENVCMD="unset HDF5_VDS_PREFIX"                # Unset the environment variable & value
-#
-# Run the test
-# echo "$ENVCMD $RUNSERIAL $TEST_BIN"
-$ENVCMD $RUNSERIAL $TEST_BIN
-exitcode=$?
-if [ $exitcode -eq 0 ]; then
-    echo "Test prefix for HDF5_VDS_PREFIX PASSED"
-else
-    nerrors="`expr $nerrors + 1`"
-    echo "***Error encountered for HDF5_VDS_PREFIX test***"
-fi
-$UNENVCMD
-exit $nerrors
diff --git a/testpar/t_pread.c b/testpar/t_pread.c
index f0341191176..4e9105e85f4 100644
--- a/testpar/t_pread.c
+++ b/testpar/t_pread.c
@@ -1061,7 +1061,7 @@ main(int argc, char **argv)
      * We assume (but we'll check) that the h5jam utility
      * is in the directory as this executable.  If that
      * isn't true, then we can use a relative path that
-     * should be valid for the Autotools environment.
+     * should be valid for the environment.
      */
     test_argv0 = strdup(argv[0]);
 
diff --git a/tools/lib/Makefile.am b/tools/lib/Makefile.am
deleted file mode 100644
index f274932cc1b..00000000000
--- a/tools/lib/Makefile.am
+++ /dev/null
@@ -1,39 +0,0 @@
-#
-# Copyright by The HDF Group.
-# All rights reserved.
-#
-# This file is part of HDF5.  The full HDF5 copyright notice, including
-# terms governing use, modification, and redistribution, is contained in
-# the LICENSE file, which can be found at the root of the source code
-# 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.
-##
-## Makefile.am
-## Run automake to generate a Makefile.in from this file.
-#
-# HDF5 Library Makefile(.in)
-#
-
-include $(top_srcdir)/config/commence.am
-
-# Include files in /src directory
-AM_CPPFLAGS+=-I$(top_srcdir)/src
-
-# This is our main target, the h5tools library.
-noinst_LTLIBRARIES=libh5tools.la
-
-libh5tools_la_SOURCES=h5tools.c h5tools_dump.c h5tools_str.c h5tools_utils.c h5diff.c \
-    h5diff_array.c h5diff_attr.c h5diff_dset.c h5diff_util.c h5trav.c  \
-    h5tools_filters.c h5tools_ref.c h5tools_type.c io_timer.c
-
-# Test program.  Link using libhdf5 and libh5tools
-TEST_PROG=
-check_PROGRAMS=$(TEST_PROG)
-
-# Name libh5tools.la so that dependencies work out. Automake knows how
-# to build 'libh5tools.la', but not '../../tools/lib/libh5tools.la'.
-LDADD=libh5tools.la $(LIBHDF5)
-
-include $(top_srcdir)/config/conclude.am
-
diff --git a/tools/libtest/Makefile.am b/tools/libtest/Makefile.am
deleted file mode 100644
index 602e71e43d1..00000000000
--- a/tools/libtest/Makefile.am
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# Copyright by The HDF Group.
-# All rights reserved.
-#
-# This file is part of HDF5.  The full HDF5 copyright notice, including
-# terms governing use, modification, and redistribution, is contained in
-# the LICENSE file, which can be found at the root of the source code
-# 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.
-# If you do not have access to either file, you may request a copy from
-# help@hdfgroup.org.
-#
-## Makefile.am
-## Run automake to generate a Makefile.in from this file.
-#
-# HDF5 Library Makefile(.in)
-#
-
-include $(top_srcdir)/config/commence.am
-
-# Include src, test, and tools/lib directories
-AM_CPPFLAGS+=-I$(top_srcdir)/src -I$(top_srcdir)/test -I$(top_srcdir)/tools/lib
-
-# All programs depend on the hdf5, hdf5 test, and h5tools libraries
-LDADD=$(LIBH5TOOLS) $(LIBH5TEST) $(LIBHDF5)
-
-
-# main target
-noinst_PROGRAMS=h5tools_test_utils
-# check_PROGRAMS=$(TEST_PROG)
-
-
-include $(top_srcdir)/config/conclude.am
diff --git a/tools/src/Makefile.am b/tools/src/Makefile.am
deleted file mode 100644
index 3d741cbe7e3..00000000000
--- a/tools/src/Makefile.am
+++ /dev/null
@@ -1,27 +0,0 @@
-#
-# Copyright by The HDF Group.
-# All rights reserved.
-#
-# This file is part of HDF5.  The full HDF5 copyright notice, including
-# terms governing use, modification, and redistribution, is contained in
-# the LICENSE file, which can be found at the root of the source code
-# 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.
-##
-## Makefile.am
-## Run automake to generate a Makefile.in from this file.
-##
-#
-# Tools HDF5 Makefile(.in)
-#
-
-include $(top_srcdir)/config/commence.am
-
-CONFIG=ordered
-
-# All subdirectories
-SUBDIRS=h5diff h5ls h5dump misc h5import h5repack h5jam h5copy \
-	h5format_convert h5stat h5perf
-
-include $(top_srcdir)/config/conclude.am
diff --git a/tools/src/h5copy/Makefile.am b/tools/src/h5copy/Makefile.am
deleted file mode 100644
index e12c2b16ede..00000000000
--- a/tools/src/h5copy/Makefile.am
+++ /dev/null
@@ -1,37 +0,0 @@
-#
-# Copyright by The HDF Group.
-# All rights reserved.
-#
-# This file is part of HDF5.  The full HDF5 copyright notice, including
-# terms governing use, modification, and redistribution, is contained in
-# the LICENSE file, which can be found at the root of the source code
-# 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.
-##
-## Makefile.am
-## Run automake to generate a Makefile.in from this file.
-#
-# HDF5 Library Makefile(.in)
-#
-
-include $(top_srcdir)/config/commence.am
-
-# Include src and tools/lib directories
-AM_CPPFLAGS+=-I$(top_srcdir)/src -I$(top_srcdir)/tools/lib
-
-# This is our main target, the h5copy tool
-bin_PROGRAMS=h5copy
-check_PROGRAMS=$(TEST_PROG)
-
-# Add h5copy specific linker flags here
-h5copy_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
-
-# All programs depend on the hdf5 and h5tools libraries
-LDADD=$(LIBH5TOOLS) $(LIBHDF5)
-
-# Temporary files.  *.h5 are generated by h5dumpgentest.  They should
-# copied to the testfiles/ directory if update is required.
-CHECK_CLEANFILES+=*.h5
-
-include $(top_srcdir)/config/conclude.am
diff --git a/tools/src/h5diff/Makefile.am b/tools/src/h5diff/Makefile.am
deleted file mode 100644
index 8782448f8f2..00000000000
--- a/tools/src/h5diff/Makefile.am
+++ /dev/null
@@ -1,43 +0,0 @@
-#
-# Copyright by The HDF Group.
-# All rights reserved.
-#
-# This file is part of HDF5.  The full HDF5 copyright notice, including
-# terms governing use, modification, and redistribution, is contained in
-# the LICENSE file, which can be found at the root of the source code
-# 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.
-##
-## Makefile.am
-## Run automake to generate a Makefile.in from this file.
-#
-# HDF5 Library Makefile(.in)
-#
-
-include $(top_srcdir)/config/commence.am
-
-# Include src and tools/lib directories
-AM_CPPFLAGS+=-I$(top_srcdir)/src -I$(top_srcdir)/tools/lib
-
-# Always build and test h5diff but build and test ph5diff only if parallel
-# is enabled.
-if BUILD_PARALLEL_CONDITIONAL
-  H5PDIFF=ph5diff
-endif
-
-# Our main target, h5diff
-bin_PROGRAMS=h5diff $(H5PDIFF)
-
-# Add h5diff specific linker flags here
-h5diff_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
-
-# Source files for the program
-h5diff_SOURCES=h5diff_main.c h5diff_common.c
-ph5diff_SOURCES=ph5diff_main.c h5diff_common.c
-
-# Programs depend on the main HDF5 library and tools library
-LDADD=$(LIBH5TOOLS) $(LIBHDF5)
-
-include $(top_srcdir)/config/conclude.am
-
diff --git a/tools/src/h5dump/Makefile.am b/tools/src/h5dump/Makefile.am
deleted file mode 100644
index 3b360a88fd4..00000000000
--- a/tools/src/h5dump/Makefile.am
+++ /dev/null
@@ -1,35 +0,0 @@
-#
-# Copyright by The HDF Group.
-# All rights reserved.
-#
-# This file is part of HDF5.  The full HDF5 copyright notice, including
-# terms governing use, modification, and redistribution, is contained in
-# the LICENSE file, which can be found at the root of the source code
-# 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.
-##
-## Makefile.am
-## Run automake to generate a Makefile.in from this file.
-#
-# HDF5 Library Makefile(.in)
-#
-
-include $(top_srcdir)/config/commence.am
-
-# Include files in /src directory and /tools/lib directory
-AM_CPPFLAGS+=-I$(top_srcdir)/src -I$(top_srcdir)/tools/lib
-
-# Our main target, the h5dump tool.
-bin_PROGRAMS=h5dump
-
-# Add h5dump specific linker flags here
-h5dump_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
-
-# All the programs depend on the hdf5 and h5tools libraries
-LDADD=$(LIBH5TOOLS) $(LIBHDF5)
-
-# Source files for the program
-h5dump_SOURCES=h5dump.c h5dump_ddl.c h5dump_xml.c
-
-include $(top_srcdir)/config/conclude.am
diff --git a/tools/src/h5format_convert/Makefile.am b/tools/src/h5format_convert/Makefile.am
deleted file mode 100644
index df29fa2f1c1..00000000000
--- a/tools/src/h5format_convert/Makefile.am
+++ /dev/null
@@ -1,35 +0,0 @@
-#
-# Copyright by The HDF Group.
-# All rights reserved.
-#
-# This file is part of HDF5.  The full HDF5 copyright notice, including
-# terms governing use, modification, and redistribution, is contained in
-# the LICENSE file, which can be found at the root of the source code
-# 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.
-##
-## Makefile.am
-## Run automake to generate a Makefile.in from this file.
-#
-# HDF5 Library Makefile(.in)
-#
-
-include $(top_srcdir)/config/commence.am
-
-# Include src directory
-AM_CPPFLAGS+=-I$(top_srcdir)/src -I$(top_srcdir)/tools/lib
-
-# These are our main targets, the tools
-bin_PROGRAMS=h5format_convert
-bin_SCRIPTS=
-
-# Add h5format_convert specific linker flags here
-h5format_convert_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
-
-# All programs rely on hdf5 library and h5tools library
-LDADD=$(LIBH5TOOLS) $(LIBHDF5)
-
-CLEANFILES=
-
-include $(top_srcdir)/config/conclude.am
diff --git a/tools/src/h5import/Makefile.am b/tools/src/h5import/Makefile.am
deleted file mode 100644
index 229d0e3b2ee..00000000000
--- a/tools/src/h5import/Makefile.am
+++ /dev/null
@@ -1,32 +0,0 @@
-#
-# Copyright by The HDF Group.
-# All rights reserved.
-#
-# This file is part of HDF5.  The full HDF5 copyright notice, including
-# terms governing use, modification, and redistribution, is contained in
-# the LICENSE file, which can be found at the root of the source code
-# 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.
-##
-## Makefile.am
-## Run automake to generate a Makefile.in from this file.
-#
-# HDF5 Library Makefile(.in)
-#
-
-include $(top_srcdir)/config/commence.am
-
-# Include src and tools/lib directories
-AM_CPPFLAGS+=-I$(top_srcdir)/src -I$(top_srcdir)/tools/lib
-
-# Our main targets
-bin_PROGRAMS=h5import
-
-# Add h5import specific linker flags here
-h5import_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
-
-# All programs depend on the main hdf5 library and the tools library
-LDADD=$(LIBH5TOOLS) $(LIBHDF5)
-
-include $(top_srcdir)/config/conclude.am
diff --git a/tools/src/h5jam/Makefile.am b/tools/src/h5jam/Makefile.am
deleted file mode 100644
index 1e9d122ce4a..00000000000
--- a/tools/src/h5jam/Makefile.am
+++ /dev/null
@@ -1,32 +0,0 @@
-#
-# Copyright by The HDF Group.
-# All rights reserved.
-#
-# This file is part of HDF5.  The full HDF5 copyright notice, including
-# terms governing use, modification, and redistribution, is contained in
-# the LICENSE file, which can be found at the root of the source code
-# 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.
-##
-## Makefile.am
-## Run automake to generate a Makefile.in from this file.
-#
-# HDF5 Library Makefile(.in)
-#
-
-include $(top_srcdir)/config/commence.am
-
-# Include src and tools/lib directories
-AM_CPPFLAGS+=-I$(top_srcdir)/src -I$(top_srcdir)/tools/lib
-
-bin_PROGRAMS=h5jam h5unjam
-
-# Add h5jam and h5unjam specific linker flags here
-h5jam_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
-h5unjam_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
-
-# Link against the main HDF5 library and tools library
-LDADD=$(LIBH5TOOLS) $(LIBHDF5)
-
-include $(top_srcdir)/config/conclude.am
diff --git a/tools/src/h5ls/Makefile.am b/tools/src/h5ls/Makefile.am
deleted file mode 100644
index 9228a0acad2..00000000000
--- a/tools/src/h5ls/Makefile.am
+++ /dev/null
@@ -1,32 +0,0 @@
-#
-# Copyright by The HDF Group.
-# All rights reserved.
-#
-# This file is part of HDF5.  The full HDF5 copyright notice, including
-# terms governing use, modification, and redistribution, is contained in
-# the LICENSE file, which can be found at the root of the source code
-# 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.
-##
-## Makefile.am
-## Run automake to generate a Makefile.in from this file.
-#
-# HDF5 Library Makefile(.in)
-#
-
-include $(top_srcdir)/config/commence.am
-
-# Include src and tools/lib directories
-AM_CPPFLAGS+=-I$(top_srcdir)/src -I$(top_srcdir)/tools/lib
-
-# This is our main target, the h5ls tool
-bin_PROGRAMS=h5ls
-
-# Add h5ls specific linker flags here
-h5ls_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
-
-# All programs depend on the hdf5 and h5tools libraries
-LDADD=$(LIBH5TOOLS) $(LIBHDF5)
-
-include $(top_srcdir)/config/conclude.am
diff --git a/tools/src/h5perf/Makefile.am b/tools/src/h5perf/Makefile.am
deleted file mode 100644
index 6eed3b8975d..00000000000
--- a/tools/src/h5perf/Makefile.am
+++ /dev/null
@@ -1,61 +0,0 @@
-#
-# Copyright by The HDF Group.
-# All rights reserved.
-#
-# This file is part of HDF5.  The full HDF5 copyright notice, including
-# terms governing use, modification, and redistribution, is contained in
-# the LICENSE file, which can be found at the root of the source code
-# 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.
-##
-## Makefile.am
-## Run automake to generate a Makefile.in from this file.
-##
-#
-# HDF5 Library Performance Makefile(.in)
-#
-
-include $(top_srcdir)/config/commence.am
-
-AM_CPPFLAGS+=-I$(top_srcdir)/src -I$(top_srcdir)/test -I$(top_srcdir)/tools/lib
-
-# bin_PROGRAMS will be installed.
-if BUILD_PARALLEL_CONDITIONAL
-    bin_PROGRAMS=h5perf_serial h5perf
-else
-    bin_PROGRAMS=h5perf_serial
-endif
-
-# Add h5perf and h5perf_serial specific linker flags here
-h5perf_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
-h5perf_serial_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
-
-# Some programs are not built or run by default, but can be built by hand or by
-# specifying --enable-build-all at configure time.
-# Also, some of these programs should only be built in parallel.
-# Currently there is no such program.
-if BUILD_PARALLEL_CONDITIONAL
-    PARA_BUILD_ALL=
-endif
-if BUILD_ALL_CONDITIONAL
-    BUILD_ALL_PROGS=$(PARA_BUILD_ALL)
-endif
-
-# Define programs that will be run in 'make check'
-# List them in the order they should be run.
-# Parallel test programs.
-if BUILD_PARALLEL_CONDITIONAL
-    TEST_PROG_PARA=h5perf
-endif
-
-h5perf_SOURCES=pio_perf.c pio_engine.c
-h5perf_serial_SOURCES=sio_perf.c sio_engine.c
-
-# All of the programs depend on the main hdf5 library, and some of them
-# depend on test or tools library.
-LDADD=$(LIBHDF5)
-h5perf_LDADD=$(LIBH5TOOLS) $(LIBHDF5)
-h5perf_serial_LDADD=$(LIBH5TOOLS) $(LIBHDF5)
-
-include $(top_srcdir)/config/conclude.am
diff --git a/tools/src/h5repack/Makefile.am b/tools/src/h5repack/Makefile.am
deleted file mode 100644
index 52e1ca1f9c6..00000000000
--- a/tools/src/h5repack/Makefile.am
+++ /dev/null
@@ -1,44 +0,0 @@
-#
-# Copyright by The HDF Group.
-# All rights reserved.
-#
-# This file is part of HDF5.  The full HDF5 copyright notice, including
-# terms governing use, modification, and redistribution, is contained in
-# the LICENSE file, which can be found at the root of the source code
-# 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.
-##
-## Makefile.am
-## Run automake to generate a Makefile.in from this file.
-#
-# HDF5 Library Makefile(.in)
-#
-
-include $(top_srcdir)/config/commence.am
-
-# Include src, test, and tools/lib directories
-AM_CPPFLAGS+=-I$(top_srcdir)/src -I$(top_srcdir)/test -I$(top_srcdir)/tools/lib
-
-# A convenience library for the h5repack tool and the h5repack tests
-noinst_LTLIBRARIES=libh5repack.la
-
-libh5repack_la_SOURCES=h5repack.c h5repack_copy.c h5repack_filters.c \
-                       h5repack_opttable.c h5repack_parse.c h5repack_refs.c \
-                       h5repack_verify.c
-libh5repack_la_LDFLAGS = $(AM_LDFLAGS)
-libh5repack_la_LIBADD=$(LIBH5TOOLS) $(LIBHDF5)
-
-
-# Our main target, h5repack tool
-bin_PROGRAMS=h5repack
-
-h5repack_SOURCES=h5repack_main.c
-
-# Add h5repack specific linker flags here
-h5repack_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
-
-# Depend on the hdf5 library, the tools library, the h5repack library
-h5repack_LDADD=libh5repack.la $(LIBH5TOOLS) $(LIBHDF5)
-
-include $(top_srcdir)/config/conclude.am
diff --git a/tools/src/h5stat/Makefile.am b/tools/src/h5stat/Makefile.am
deleted file mode 100644
index f0d35431417..00000000000
--- a/tools/src/h5stat/Makefile.am
+++ /dev/null
@@ -1,36 +0,0 @@
-#
-# Copyright by The HDF Group.
-# All rights reserved.
-#
-# This file is part of HDF5.  The full HDF5 copyright notice, including
-# terms governing use, modification, and redistribution, is contained in
-# the LICENSE file, which can be found at the root of the source code
-# 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.
-##
-## Makefile.am
-## Run automake to generate a Makefile.in from this file.
-#
-# HDF5 Library Makefile(.in)
-#
-
-include $(top_srcdir)/config/commence.am
-
-# Include src directory
-AM_CPPFLAGS+=-I$(top_srcdir)/src -I$(top_srcdir)/tools/lib
-
-# These are our main targets, the tools
-bin_PROGRAMS=h5stat
-bin_SCRIPTS=
-
-# Add h5stat specific linker flags here
-h5stat_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
-
-# Tell automake to clean h5redeploy script
-CLEANFILES=
-
-# All programs rely on hdf5 library and h5tools library
-LDADD=$(LIBH5TOOLS) $(LIBHDF5)
-
-include $(top_srcdir)/config/conclude.am