Merge UG from 1.10 and add prelim vol section (#1980)

* Merge UG from 1.10 and add prelim vol section

* Spelling fixes

* Merge format and autotools javadoc from 1.10

10 files changed, 253 insertions, 184 deletions

diff --git a/doxygen/examples/H5.format.1.0.html b/doxygen/examples/H5.format.1.0.html
index ff21315..4eb0548 100644
--- a/doxygen/examples/H5.format.1.0.html
+++ b/doxygen/examples/H5.format.1.0.html
@@ -139,7 +139,7 @@
 
     <p>This document describes the lower-level data objects;
       the higher-level objects and their properties are described
-      in the <a href="H5.user.html"><cite>HDF5 User's Guide</cite></a>.
+      in the <a href="H5.user.html"><cite>HDF5 User Guide</cite></a>.
 
 
 <!--
diff --git a/doxygen/examples/H5.format.1.1.html b/doxygen/examples/H5.format.1.1.html
index 0ae31df..9d03a76 100644
--- a/doxygen/examples/H5.format.1.1.html
+++ b/doxygen/examples/H5.format.1.1.html
@@ -172,7 +172,7 @@ TABLE.list TD { border:none; }
 
     <p>This document describes the lower-level data objects;
       the higher-level objects and their properties are described
-      in the <a href="H5.user.html"><cite>HDF5 User's Guide</cite></a>.
+      in the <a href="H5.user.html"><cite>HDF5 User Guide</cite></a>.
 
     <P>Three levels of information comprise the file format.
       Level 0 contains basic information for identifying and
diff --git a/doxygen/examples/H5.format.2.0.html b/doxygen/examples/H5.format.2.0.html
index 4a5fe37..242fdea 100644
--- a/doxygen/examples/H5.format.2.0.html
+++ b/doxygen/examples/H5.format.2.0.html
@@ -357,7 +357,7 @@ div {   page-break-inside:avoid;
 
     <p>This document describes the lower-level data objects;
       the higher-level objects and their properties are described
-      in the <a href="UG/HDF5_Users_Guide-Responsive HTML5/index.html"><cite>HDF5 User&rsquo;s Guide</cite></a>.</p>
+      in the <a href="UG/HDF5_User_Guide-Responsive HTML5/index.html"><cite>HDF5 User Guide</cite></a>.</p>
 
     <p>Three levels of information comprise the file format.
       Level 0 contains basic information for identifying and
@@ -12861,9 +12861,9 @@ Pipeline Message</a></h4>
       datatypes).</p>
       <p>In 1.8.x versions of the library, attributes can be larger
       than 64KB. See the
-      <a href="UG/HDF5_Users_Guide-Responsive%20HTML5/index.html#t=HDF5_Users_Guide%2FAttributes%2FHDF5_Attributes.htm%3Frhtocid%3Dtoc8.2_1%23TOC_8_5_Special_Issuesbc-13">
+      <a href="UG/HDF5_Users_Guide-Responsive%20HTML5/index.html#t=HDF5_User_Guide%2FAttributes%2FHDF5_Attributes.htm%3Frhtocid%3Dtoc8.2_1%23TOC_8_5_Special_Issuesbc-13">
       &ldquo;Special Issues&rdquo;</a> section of the Attributes chapter
-      in the <cite>HDF5 User&rsquo;s Guide</cite> for more information.</p>
+      in the <cite>HDF5 User Guide</cite> for more information.</p>
       <p>Note: Attributes on an object must have unique names:
       the HDF5 Library currently enforces this by causing the
       creation of an attribute with a duplicate name to fail.
diff --git a/doxygen/examples/H5.format.html b/doxygen/examples/H5.format.html
index cbcb387..378f7a3 100644
--- a/doxygen/examples/H5.format.html
+++ b/doxygen/examples/H5.format.html
@@ -418,7 +418,7 @@
 
     <p>This document describes the lower-level data objects;
       the higher-level objects and their properties are described
-      in the <a href="UG/HDF5_Users_Guide-Responsive HTML5/index.html"><cite>HDF5 User&rsquo;s Guide</cite></a>.</p>
+      in the <a href="UG/HDF5_User_Guide-Responsive HTML5/index.html"><cite>HDF5 User Guide</cite></a>.</p>
 
     <p>Three levels of information comprise the file format.
       Level 0 contains basic information for identifying and
@@ -14647,9 +14647,9 @@ Data Layout message.
           datatypes).</p>
         <p>In 1.8.x versions of the library, attributes can be larger
           than 64KB. See the
-          <a href="UG/HDF5_Users_Guide-Responsive%20HTML5/index.html#t=HDF5_Users_Guide%2FAttributes%2FHDF5_Attributes.htm%3Frhtocid%3Dtoc8.2_1%23TOC_8_5_Special_Issuesbc-13">
+          <a href="UG/HDF5_User_Guide-Responsive%20HTML5/index.html#t=HDF5_User_Guide%2FAttributes%2FHDF5_Attributes.htm%3Frhtocid%3Dtoc8.2_1%23TOC_8_5_Special_Issuesbc-13">
             &ldquo;Special Issues&rdquo;</a> section of the Attributes chapter
-          in the <cite>HDF5 User&rsquo;s Guide</cite> for more information.</p>
+          in the <cite>HDF5 User Guide</cite> for more information.</p>
         <p>Note: Attributes on an object must have unique names:
           the HDF5 Library currently enforces this by causing the
           creation of an attribute with a duplicate name to fail.
diff --git a/doxygen/examples/H5R_examples.c b/doxygen/examples/H5R_examples.c
deleted file mode 100644
index b40b992..0000000
--- a/doxygen/examples/H5R_examples.c
+++ /dev/null
@@ -1,171 +0,0 @@
-/* -*- c-file-style: "stroustrup" -*- */
-
-#include "hdf5.h"
-
-#include <assert.h>
-#include <stdio.h>
-#include <stdlib.h>
-
-int
-main(void)
-{
-    int ret_val = EXIT_SUCCESS;
-
-    //! <!-- [create] -->
-    {
-        __label__ fail_file, fail_fspace, fail_dset, fail_sel, fail_aspace, fail_attr, fail_awrite;
-        hid_t     file, fspace, dset, aspace, attr;
-        H5R_ref_t ref;
-
-        if ((file = H5Fcreate("reference.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) == H5I_INVALID_HID) {
-            ret_val = EXIT_FAILURE;
-            goto fail_file;
-        }
-        // create a region reference which selects all elements of the dataset at "/data"
-        if ((fspace = H5Screate_simple(2, (hsize_t[]){10, 20}, NULL)) == H5I_INVALID_HID) {
-            ret_val = EXIT_FAILURE;
-            goto fail_fspace;
-        }
-        if ((dset = H5Dcreate(file, "data", H5T_STD_I32LE, fspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) ==
-            H5I_INVALID_HID) {
-            ret_val = EXIT_FAILURE;
-            goto fail_dset;
-        }
-        if (H5Sselect_all(fspace) < 0 || H5Rcreate_region(file, "data", fspace, H5P_DEFAULT, &ref) < 0) {
-            ret_val = EXIT_FAILURE;
-            goto fail_sel;
-        }
-        // store the region reference in a scalar attribute of the root group called "region"
-        if ((aspace = H5Screate(H5S_SCALAR)) == H5I_INVALID_HID) {
-            ret_val = EXIT_FAILURE;
-            goto fail_aspace;
-        }
-        if ((attr = H5Acreate(file, "region", H5T_STD_REF, aspace, H5P_DEFAULT, H5P_DEFAULT)) ==
-            H5I_INVALID_HID) {
-            ret_val = EXIT_FAILURE;
-            goto fail_attr;
-        }
-        if (H5Awrite(attr, H5T_STD_REF, &ref) < 0) {
-            ret_val = EXIT_FAILURE;
-            goto fail_awrite;
-        }
-
-fail_awrite:
-        H5Aclose(attr);
-fail_attr:
-        H5Sclose(aspace);
-fail_aspace:
-        H5Rdestroy(&ref);
-fail_sel:
-        H5Dclose(dset);
-fail_dset:
-        H5Sclose(fspace);
-fail_fspace:
-        H5Fclose(file);
-fail_file:;
-    }
-    //! <!-- [create] -->
-
-    //! <!-- [read] -->
-    {
-        __label__ fail_file, fail_attr, fail_aread;
-        hid_t     file, attr;
-        H5R_ref_t ref;
-
-        if ((file = H5Fopen("reference.h5", H5F_ACC_RDONLY, H5P_DEFAULT)) == H5I_INVALID_HID) {
-            ret_val = EXIT_FAILURE;
-            goto fail_file;
-        }
-
-        // read the dataset region reference from the attribute
-        if ((attr = H5Aopen(file, "region", H5P_DEFAULT)) == H5I_INVALID_HID) {
-            ret_val = EXIT_FAILURE;
-            goto fail_attr;
-        }
-        if (H5Aread(attr, H5T_STD_REF, &ref) < 0) {
-            ret_val = EXIT_FAILURE;
-            goto fail_aread;
-        }
-        assert(H5Rget_type(&ref) == H5R_DATASET_REGION2);
-
-        // get an HDF5 path name for the dataset of the region reference
-        {
-            char buf[255];
-            if (H5Rget_obj_name(&ref, H5P_DEFAULT, buf, 255) < 0) {
-                ret_val = EXIT_FAILURE;
-            }
-            printf("Object name: \"%s\"\n", buf);
-        }
-
-        H5Rdestroy(&ref);
-fail_aread:
-        H5Aclose(attr);
-fail_attr:
-        H5Fclose(file);
-fail_file:;
-    }
-    //! <!-- [read] -->
-
-    //! <!-- [update] -->
-    {
-        __label__ fail_file, fail_attr, fail_ref;
-        hid_t     file, attr;
-        H5R_ref_t ref;
-
-        if ((file = H5Fopen("reference.h5", H5F_ACC_RDWR, H5P_DEFAULT)) == H5I_INVALID_HID) {
-            ret_val = EXIT_FAILURE;
-            goto fail_file;
-        }
-
-        // H5T_STD_REF is a generic reference type
-        // we can "update" the attribute value to refer to the attribute itself
-        if ((attr = H5Aopen(file, "region", H5P_DEFAULT)) == H5I_INVALID_HID) {
-            ret_val = EXIT_FAILURE;
-            goto fail_attr;
-        }
-        if (H5Rcreate_attr(file, "data", "region", H5P_DEFAULT, &ref) < 0) {
-            ret_val = EXIT_FAILURE;
-            goto fail_ref;
-        }
-
-        assert(H5Rget_type(&ref) == H5R_ATTR);
-
-        if (H5Awrite(attr, H5T_STD_REF, &ref) < 0) {
-            ret_val = EXIT_FAILURE;
-        }
-
-        H5Rdestroy(&ref);
-fail_ref:
-        H5Aclose(attr);
-fail_attr:
-        H5Fclose(file);
-fail_file:;
-    }
-    //! <!-- [update] -->
-
-    //! <!-- [delete] -->
-    {
-        __label__ fail_file, fail_ref;
-        hid_t     file;
-        H5R_ref_t ref;
-
-        // create an HDF5 object reference to the root group
-        if ((file = H5Fopen("reference.h5", H5F_ACC_RDONLY, H5P_DEFAULT)) == H5I_INVALID_HID) {
-            ret_val = EXIT_FAILURE;
-            goto fail_file;
-        }
-        if (H5Rcreate_object(file, ".", H5P_DEFAULT, &ref) < 0) {
-            ret_val = EXIT_FAILURE;
-            goto fail_ref;
-        }
-
-        // H5Rdestroy() releases all resources associated with an HDF5 reference
-        H5Rdestroy(&ref);
-fail_ref:
-        H5Fclose(file);
-fail_file:;
-    }
-    //! <!-- [delete] -->
-
-    return ret_val;
-}
diff --git a/doxygen/examples/ThreadSafeLibrary.html b/doxygen/examples/ThreadSafeLibrary.html
index 97f7742..5824dc6 100644
--- a/doxygen/examples/ThreadSafeLibrary.html
+++ b/doxygen/examples/ThreadSafeLibrary.html
@@ -20,9 +20,9 @@ The following code is placed at the beginning of H5private.h:
 </blockquote>
 
 <p>
-<code>H5_HAVE_THREADSAFE</code> is defined when the HDF-5 library is
+<code>H5_HAVE_THREADSAFE</code> is defined when the HDF5 library is
 compiled with the --enable-threadsafe configuration option. In general,
-code for the non-threadsafe version of HDF-5 library are placed within
+code for the non-threadsafe version of HDF5 library are placed within
 the <code>#else</code> part of the conditional compilation. The exception
 to this rule are the changes to the <code>FUNC_ENTER</code> (in
 H5private.h), <code>HRETURN</code> and <code>HRETURN_ERROR</code> (in
@@ -438,7 +438,7 @@ described in Appendix D and may be found in <code>H5TS.c</code>.
 
 <p>
 Except where stated, all tests involve 16 simultaneous threads that make
-use of HDF-5 API calls without any explicit synchronization typically
+use of HDF5 API calls without any explicit synchronization typically
 required in a non-threadsafe environment.
 </p>
 
@@ -453,7 +453,7 @@ dataset's named value.
 
 <p>
 The main thread would join with all 16 threads and attempt to match the
-resulting HDF-5 file with expected results - that each dataset contains
+resulting HDF5 file with expected results - that each dataset contains
 the correct value (0 for <i>zero</i>, 1 for <i>one</i> etc ...) and all
 datasets were correctly created.
 </p>
@@ -473,7 +473,7 @@ name.
 
 <p>
 The error stack implementation runs correctly if it reports 15 instances
-of the dataset name conflict error and finally generates a correct HDF-5
+of the dataset name conflict error and finally generates a correct HDF5
 containing that single dataset. Each thread should report its own stack
 of errors with a thread number associated with it.
 </p>
diff --git a/doxygen/examples/core_menu.md b/doxygen/examples/core_menu.md
new file mode 100644
index 0000000..8c82cc5
--- /dev/null
+++ b/doxygen/examples/core_menu.md
@@ -0,0 +1,65 @@
+<b>Core Library</b>
+
+- @ref H5A "Attributes (H5A)"
+<br />
+HDF5 attribute is a small metadata object describing the nature and/or intended usage of a primary data object.
+
+- @ref H5D "Datasets (H5D)"
+<br />
+Manage HDF5 datasets, including the transfer of data between memory and disk and the description of dataset properties.
+
+- @ref H5S "Dataspaces (H5S)"
+<br />
+HDF5 dataspaces describe the shape of datasets in memory or in HDF5 files.
+
+- @ref H5T "Datatypes (H5T)"
+<br />
+HDF5 datatypes describe the element type of HDF5 datasets and attributes.
+
+- @ref H5E "Error Handling (H5E)"
+<br />
+HDF5 library error reporting.
+
+- @ref H5F "Files (H5F)"
+<br />
+Manage HDF5 files.
+
+- @ref H5Z "Filters (H5Z)"
+<br />
+Manage HDF5 user-defined filters
+
+- @ref H5G "Groups (H5G)"
+<br />
+Manage HDF5 groups.
+
+- @ref H5I "Identifiers (H5I)"
+<br />
+Manage identifiers defined by the HDF5 library.
+
+- @ref H5 "Library General (H5)"
+<br />
+Manage the life cycle of HDF5 library instances.
+
+- @ref H5L "Links (H5L)"
+<br />
+Manage HDF5 links and link types.
+
+- @ref H5O "Objects (H5O)"
+<br />
+Manage HDF5 objects (groups, datasets, datatype objects).
+
+- @ref H5P "Property Lists (H5P)"
+<br />
+HDF5 property lists are the main vehicle to configure the behavior of HDF5 API functions.
+
+- @ref H5PL "Dynamically-loaded Plugins (H5PL)"
+<br />
+Manage the loading behavior of HDF5 plugins.
+
+- @ref H5R "References (H5R)"
+<br />
+Manage HDF5 references (HDF5 objects, attributes, and selections on datasets a.k.a. dataset regions).
+
+- @ref H5VL "VOL Connector (H5VL)"
+<br />
+Manage HDF5 VOL connector plugins.
diff --git a/doxygen/examples/fortran_menu.md b/doxygen/examples/fortran_menu.md
new file mode 100644
index 0000000..335a21a
--- /dev/null
+++ b/doxygen/examples/fortran_menu.md
@@ -0,0 +1,61 @@
+<b>Fortran Library</b>
+
+-  H5A "Attributes (H5A)"
+<br />
+HDF5 attribute is a small metadata object describing the nature and/or intended usage of a primary data object.
+
+-  H5D "Datasets (H5D)"
+<br />
+Manage HDF5 datasets, including the transfer of data between memory and disk and the description of dataset properties.
+
+-  H5S "Dataspaces (H5S)"
+<br />
+HDF5 dataspaces describe the shape of datasets in memory or in HDF5 files.
+
+-  H5T "Datatypes (H5T)"
+<br />
+HDF5 datatypes describe the element type of HDF5 datasets and attributes.
+
+-  H5E "Error Handling (H5E)"
+<br />
+HDF5 library error reporting.
+
+-  H5F "Files (H5F)"
+<br />
+Manage HDF5 files.
+
+-  H5Z "Filters (H5Z)"
+<br />
+Manage HDF5 user-defined filters
+
+-  H5G "Groups (H5G)"
+<br />
+Manage HDF5 groups.
+
+-  H5I "Identifiers (H5I)"
+<br />
+Manage identifiers defined by the HDF5 library.
+
+-  H5 "Library General (H5)"
+<br />
+Manage the life cycle of HDF5 library instances.
+
+-  H5L "Links (H5L)"
+<br />
+Manage HDF5 links and link types.
+
+-  H5O "Objects (H5O)"
+<br />
+Manage HDF5 objects (groups, datasets, datatype objects).
+
+-  H5P "Property Lists (H5P)"
+<br />
+HDF5 property lists are the main vehicle to configure the behavior of HDF5 API functions.
+
+-  H5PL "Dynamically-loaded Plugins (H5PL)"
+<br />
+Manage the loading behavior of HDF5 plugins.
+
+-  H5R "References (H5R)"
+<br />
+Manage HDF5 references (HDF5 objects, attributes, and selections on datasets a.k.a. dataset regions).
diff --git a/doxygen/examples/high_level_menu.md b/doxygen/examples/high_level_menu.md
new file mode 100644
index 0000000..9e6f696
--- /dev/null
+++ b/doxygen/examples/high_level_menu.md
@@ -0,0 +1,30 @@
+<b>High-level library</b>
+<br />
+The high-level HDF5 library includes several sets of convenience and standard-use APIs to 
+facilitate common HDF5 operations.
+
+- @ref H5LT "Lite (H5LT, H5LD)"
+<br />
+Functions to simplify creating and manipulating datasets, attributes and other features
+
+- @ref H5IM "Image (H5IM)"
+<br />
+Creating and manipulating HDF5 datasets intended to be interpreted as images
+
+- @ref H5TB "Table (H5TB)"
+<br />
+Creating and manipulating HDF5 datasets intended to be interpreted as tables
+
+- @ref H5PT "Packet Table (H5PT)"
+<br />
+Creating and manipulating HDF5 datasets to support append- and read-only operations on table data
+
+- @ref H5DS "Dimension Scale (H5DS)"
+<br />
+Creating and manipulating HDF5 datasets that are associated with the dimension of another HDF5 dataset
+
+- @ref H5DO "Optimizations (H5DO)"
+<br />
+Bypassing default HDF5 behavior in order to optimize for specific use cases
+
+- @ref H5LR "Extensions (H5LR, H5LT)"
diff --git a/doxygen/examples/java_menu.md b/doxygen/examples/java_menu.md
new file mode 100644
index 0000000..1236838
--- /dev/null
+++ b/doxygen/examples/java_menu.md
@@ -0,0 +1,84 @@
+<b>Java Library</b>
+ @ref HDF5LIB
+ 
+- @ref JH5
+<br />
+This package is the Java interface for the HDF5 library.
+ 
+- @ref JH5A
+<br />
+This package is the Java interface for the HDF5 library attribute APIs.
+ 
+- @ref JH5D
+<br />
+This package is the Java interface for the HDF5 library dataset APIs.
+ 
+- @ref JH5S
+<br />
+This package is the Java interface for the HDF5 library dataspace APIs.
+ 
+- @ref JH5T
+<br />
+This package is the Java interface for the HDF5 library datatype APIs.
+ 
+- @ref JH5E
+<br />
+This package is the Java interface for the HDF5 library error APIs.
+ 
+- @ref JH5F
+<br />
+This package is the Java interface for the HDF5 library file APIs.
+ 
+- @ref JH5Z
+<br />
+This package is the Java interface for the HDF5 library filter APIs.
+ 
+- @ref JH5G
+<br />
+This package is the Java interface for the HDF5 library group APIs.
+ 
+- @ref JH5I
+<br />
+This package is the Java interface for the HDF5 library identifier APIs.
+ 
+- @ref JH5L
+<br />
+This package is the Java interface for the HDF5 library links APIs.
+ 
+- @ref JH5O
+<br />
+This package is the Java interface for the HDF5 library object APIs.
+ 
+- @ref JH5P
+<br />
+This package is the Java interface for the HDF5 library property list APIs.
+ 
+- @ref JH5PL
+<br />
+This package is the Java interface for the HDF5 library plugin APIs.
+ 
+- @ref JH5R
+<br />
+This package is the Java interface for the HDF5 library reference APIs.
+
+- @ref JH5VL
+<br />
+This package is the Java interface for the HDF5 library VOL connector APIs.
+
+- @ref HDF5CONST
+<br />
+This class contains C constants and enumerated types of HDF5 library.
+
+- @ref HDFNATIVE
+<br />
+This class encapsulates native methods to deal with arrays of numbers,
+ * converting from numbers to bytes and bytes to numbers.
+
+- @ref HDFARRAY
+<br />
+This is a class for handling multidimensional arrays for HDF.
+
+- @ref ERRORS
+<br />
+The class HDF5Exception returns errors from the Java HDF5 Interface.
+ 
\ No newline at end of file