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

9 files changed, 690 insertions, 386 deletions

diff --git a/doxygen/dox/DDLBNF110.dox b/doxygen/dox/DDLBNF110.dox
index f7e4267..6d6b67e 100644
--- a/doxygen/dox/DDLBNF110.dox
+++ b/doxygen/dox/DDLBNF110.dox
@@ -126,7 +126,7 @@ This section contains a brief explanation of the symbols used in the DDL.
 
 <reference> ::= H5T_REFERENCE { <ref_type> }
 
-<ref_type> ::= H5T_STD_REF_OBJECT | H5T_STD_REF_DSETREG | H5T_STD_REF | UNDEFINED
+<ref_type> ::= H5T_STD_REF_OBJECT | H5T_STD_REF_DSETREG
 
 <compound_type> ::= H5T_COMPOUND {
                         <member_type_def>+
diff --git a/doxygen/dox/Overview.dox b/doxygen/dox/Overview.dox
index 040769c..64e80c7 100644
--- a/doxygen/dox/Overview.dox
+++ b/doxygen/dox/Overview.dox
@@ -23,7 +23,7 @@ documents cover a mix of tasks, concepts, and reference, to help a specific
 \par Versions
      Version-specific documentation (see the version in the title area) can be found
      here:
-     - HDF5 <code>develop</code> branch (this site)
+     - HDF5 <code>1.12</code> branch (this site)
      - <a href="https://docs.hdfgroup.org/hdf5/v1_12/index.html">HDF5 1.12.x</a>
      - <a href="https://docs.hdfgroup.org/hdf5/v1_10/index.html">HDF5 1.10.x</a>
      - <a href="https://docs.hdfgroup.org/hdf5/v1_8/index.html">HDF5 1.8.x</a>
@@ -36,10 +36,6 @@ documents cover a mix of tasks, concepts, and reference, to help a specific
 \par Offline reading
      You can <a href="hdf5-doc.tgz">download</a> it as a tgz archive for offline reading.
 
-\par History
-     A snapshot (~April 2017) of the pre-Doxygen HDF5 documentation can be found
-     <a href="https://docs.hdfgroup.org/archive/support/HDF5/doc/index.html">here</a>.
-
 \par ToDo List
      There is plenty of <a href="./todo.html">unfinished business</a>.
 
diff --git a/doxygen/dox/RFC.dox b/doxygen/dox/RFC.dox
index c16dcea..3cda309 100644
--- a/doxygen/dox/RFC.dox
+++ b/doxygen/dox/RFC.dox
@@ -88,4 +88,4 @@
 <tr> <td>2004-08-11</td> <td>\ref_rfc20040811</td> <td></td> </tr>
 </table>
 
-*/
\ No newline at end of file
+*/
diff --git a/doxygen/dox/ReferenceManual.dox b/doxygen/dox/ReferenceManual.dox
index ad10ba1..7900925 100644
--- a/doxygen/dox/ReferenceManual.dox
+++ b/doxygen/dox/ReferenceManual.dox
@@ -1,53 +1,32 @@
 /** \page RM HDF5 Reference Manual
 
-The functions provided by the HDF5 C-API are grouped into the following
+The functions provided by the HDF5 API are grouped into the following
 \Emph{modules}:
 
 <table>
 <tr><th>Modules</th></tr>
 <tr valign="top">
 <td>
-
 <table>
-<tr><td style="border: none;">
-\li \ref H5A "Attributes (H5A)"
-\li \ref H5D "Datasets (H5D)"
-\li \ref H5S "Dataspaces (H5S)"
-\li \ref H5T "Datatypes (H5T)"
-\li \ref H5E "Error Handling (H5E)"
-\li \ref H5ES "Event Sets (H5ES)"
-\li \ref H5F "Files (H5F)"
-\li \ref H5Z "Filters (H5Z)"
-\li \ref H5G "Groups (H5G)"
-</td><td style="border: none;">
-\li \ref H5I "Identifiers (H5I)"
-\li \ref H5 "Library General (H5)"
-\li \ref H5L "Links (H5L)"
-\li \ref H5M "Maps (H5M)"
-\li \ref H5O "Objects (H5O)"
-\li \ref H5P "Property Lists (H5P)"
-\li \ref H5PL "Dynamically-loaded Plugins (H5PL)"
-\li \ref H5R "References (H5R)"
-\li \ref H5VL "Virtual Object Layer (H5VL)"
-</td><td style="border: none;">
-\li \ref high_level
-    <ul>
-    <li>\ref H5LT "Lite (H5LT, H5LD)"
-    <li>\ref H5IM "Images (H5IM)"
-    <li>\ref H5TB "Table (H5TB)"
-    <li>\ref H5PT "Packet Table (H5PT)"
-    <li>\ref H5DS "Dimension Scale (H5DS)"
-    <li>\ref H5DO "Optimizations (H5DO)"
-    <li>\ref H5LR "Extensions (H5LR, H5LT)"
-    </ul>
-</td></tr>
-<tr><td colspan="3" style="border: none;">
-\a Core \a library: \ref H5 \ref H5A \ref H5D \ref H5E \ref H5ES \ref H5F \ref H5G \ref H5I \ref H5L
-\ref H5M \ref H5O \ref H5P \ref H5PL \ref H5R \ref H5S \ref H5T \ref H5VL \ref H5Z
-</td></tr>
-<tr><td colspan="3" style="border: none;">
-\a High-level \a library: \ref H5LT \ref H5IM \ref H5TB \ref H5PT \ref H5DS \ref H5DO \ref H5LR
-</td></tr>
+<tr valign="top"><td style="border: none;">
+\include{doc} core_menu.md
+</td>
+</tr>
+<tr valign="top"><td style="border: none;">
+<!--  High-level library -->
+\include{doc} high_level_menu.md
+</td>
+</tr>
+<tr valign="top"><td style="border: none;">
+<!--  Fortran library -->
+\include{doc} fortran_menu.md
+</td>
+</tr>
+<tr valign="top"><td style="border: none;">
+<!--  Java library -->
+\include{doc} java_menu.md
+</td>
+</tr>
 <tr>
 <td><a href="./deprecated.html">Deprecated functions</a></td>
 <td>Functions with \ref ASYNC</td>
diff --git a/doxygen/dox/Specifications.dox b/doxygen/dox/Specifications.dox
index 5a36d61..e352f40 100644
--- a/doxygen/dox/Specifications.dox
+++ b/doxygen/dox/Specifications.dox
@@ -2,20 +2,20 @@
 
 \section DDL
 
-\li \ref DDLBNF110 "DDL in BNF through HDF5 1.10"
-\li \ref DDLBNF112 "DDL in BNF for HDF5 1.12 and above"
+\li \ref DDLBNF110
+\li \ref DDLBNF112
 
 \section File Format
 
-\li \ref FMT1 "HDF5 File Format Specification Version 1.0"
-\li \ref FMT11 "HDF5 File Format Specification Version 1.1"
-\li \ref FMT2 "HDF5 File Format Specification Version 2.0"
-\li \ref FMT3 "HDF5 File Format Specification Version 3.0"
+\li \ref FMT1
+\li \ref FMT11
+\li \ref FMT2
+\li \ref FMT3
 
 \section Other
 
-\li \ref IMG "HDF5 Image and Palette Specification Version 1.2"
-\li \ref TBL "HDF5 Table Specification Version 1.0"
+\li \ref IMG
+\li \ref TBL
 \li <a href="https://support.hdfgroup.org/HDF5/doc/HL/H5DS_Spec.pdf">
       HDF5 Dimension Scale Specification</a>
 
diff --git a/doxygen/dox/TechnicalNotes.dox b/doxygen/dox/TechnicalNotes.dox
index 9bd2802..bca81e4 100644
--- a/doxygen/dox/TechnicalNotes.dox
+++ b/doxygen/dox/TechnicalNotes.dox
@@ -1,13 +1,13 @@
 /** \page TN Technical Notes
 
-\li \link api-compat-macros API Compatibility Macros \endlink
-\li \ref APPDBG "Debugging HDF5 Applications"
-\li \ref FMTDISC "File Format Walkthrough"
-\li \ref FILTER "Filters"
-\li \ref IOFLOW "HDF5 Raw I/O Flow Notes"
-\li \ref TNMDC "Metadata Caching in HDF5"
-\li \ref MT "Thread Safe library"
-\li \ref VFL "Virtual File Layer"
+\li \ref api-compat-macros
+\li \ref APPDBG
+\li \ref FMTDISC
+\li \ref FILTER
+\li \ref IOFLOW
+\li \ref TNMDC
+\li \ref MT
+\li \ref VFL
 
  */
 
diff --git a/doxygen/dox/UsersGuide.dox b/doxygen/dox/UsersGuide.dox
new file mode 100644
index 0000000..6b44d21
--- /dev/null
+++ b/doxygen/dox/UsersGuide.dox
@@ -0,0 +1,400 @@
+/** \page UG HDF5 User Guide
+
+<center>
+HDF5 Release 1.12
+
+\image html HDFG-logo.png "The HDF Group"
+
+</center>
+
+\ref sec_data_model
+\li \ref subsec_data_model_intro
+\li \ref subsec_data_model_abstract
+    <ul>
+        <li> \ref subsubsec_data_model_abstract_file
+        <li> \ref subsubsec_data_model_abstract_group
+        <li> \ref subsubsec_data_model_abstract_dataset
+        <li> \ref subsubsec_data_model_abstract_space
+        <li> \ref subsubsec_data_model_abstract_type
+        <li> \ref subsubsec_data_model_abstract_attr
+        <li> \ref subsubsec_data_model_abstract_plist
+        <li> \ref subsubsec_data_model_abstract_link
+    </ul>
+\li \ref subsec_data_model_storage
+    <ul>
+        <li> \ref subsubsec_data_model_storage_spec
+        <li> \ref subsubsec_data_model_storage_imple
+    </ul>
+\li \ref subsec_data_model_structure
+    <ul>
+        <li> \ref subsubsec_data_model_structure_file
+        <li> \ref subsubsec_data_model_structure_path
+        <li> \ref subsubsec_data_model_structure_example
+    </ul>
+
+\ref sec_program
+\li \ref subsec_program_intro
+\li \ref subsec_program_model
+    <ul>
+        <li> \ref subsubsec_program_model_create
+        <li> \ref subsubsec_program_model_dset
+        <li> \ref subsubsec_program_model_close
+        <li> \ref subsubsec_program_model_data
+        <li> \ref subsubsec_program_model_partial
+        <li> \ref subsubsec_program_model_info
+        <li> \ref subsubsec_program_model_compound
+        <li> \ref subsubsec_program_model_extend
+        <li> \ref subsubsec_program_model_group
+        <li> \ref subsubsec_program_model_attr
+    </ul>
+\li \ref subsec_program_transfer_pipeline
+
+\ref sec_file
+\li \ref subsec_file_intro
+\li \ref subsec_file_access_modes
+\li \ref subsec_file_creation_access
+\li \ref subsec_file_drivers
+\li \ref subsec_file_program_model
+    <ul>
+        <li> \ref subsubsec_file_program_model_create
+        <li> \ref subsubsec_file_program_model_open
+        <li> \ref subsubsec_file_program_model_close
+    </ul>
+\li \ref subsec_file_h5dump
+\li \ref subsec_file_summary
+\li \ref subsec_file_create
+\li \ref subsec_file_closes
+\li \ref subsec_file_property_lists
+    <ul>
+        <li> \ref subsubsec_file_property_lists_create
+        <li> \ref subsubsec_file_property_lists_props
+        <li> \ref subsubsec_file_property_lists_access
+    </ul>
+\li \ref subsec_file_alternate_drivers
+    <ul>
+        <li> \ref subsubsec_file_alternate_drivers_id
+        <li> \ref subsubsec_file_alternate_drivers_sec2
+        <li> \ref subsubsec_file_alternate_drivers_direct
+        <li> \ref subsubsec_file_alternate_drivers_log
+        <li> \ref subsubsec_file_alternate_drivers_win
+        <li> \ref subsubsec_file_alternate_drivers_stdio
+        <li> \ref subsubsec_file_alternate_drivers_mem
+        <li> \ref subsubsec_file_alternate_drivers_family
+        <li> \ref subsubsec_file_alternate_drivers_multi
+        <li> \ref subsubsec_file_alternate_drivers_split
+        <li> \ref subsubsec_file_alternate_drivers_par
+    </ul>
+\li \ref subsec_file_examples
+    <ul>
+        <li> \ref subsubsec_file_examples_trunc
+        <li> \ref subsubsec_file_examples_props
+        <li> \ref subsubsec_file_examples_access
+    </ul>
+\li \ref subsec_file_multiple
+
+\ref sec_group
+\li \ref subsec_group_intro
+\li \ref subsec_group_descr
+    <ul>
+        <li> \ref subsubsec_group_descr_object
+        <li> \ref subsubsec_group_descr_model
+        <li> \ref subsubsec_group_descr_path
+        <li> \ref subsubsec_group_descr_impl
+    </ul>
+\li \ref subsec_group_h5dump
+\li \ref subsec_group_function
+\li \ref subsec_group_program
+    <ul>
+        <li> \ref subsubsec_group_program_create
+        <li> \ref subsubsec_group_program_open
+        <li> \ref subsubsec_group_program_dataset
+        <li> \ref subsubsec_group_program_close
+        <li> \ref subsubsec_group_program_links
+        <li> \ref subsubsec_group_program_info
+        <li> \ref subsubsec_group_program_objs
+        <li> \ref subsubsec_group_program_all
+    </ul>
+\li \ref subsec_group_examples
+
+\ref sec_dataset
+\li \ref subsec_dataset_intro
+\li \ref subsec_dataset_function
+\li \ref subsec_dataset_program
+    <ul>
+        <li> \ref subsubsec_dataset_program_general
+        <li> \ref subsubsec_dataset_program_create
+        <li> \ref subsubsec_dataset_program_transfer
+        <li> \ref subsubsec_dataset_program_read
+    </ul>
+\li \ref subsec_dataset_transfer Data Transfer
+    <ul>
+        <li> \ref subsubsec_dataset_transfer_pipe
+        <li> \ref subsubsec_dataset_transfer_filter
+        <li> \ref subsubsec_dataset_transfer_drive
+        <li> \ref subsubsec_dataset_transfer_props
+        <li> \ref subsubsec_dataset_transfer_store
+        <li> \ref subsubsec_dataset_transfer_partial
+    </ul>
+\li \ref subsec_dataset_allocation
+    <ul>
+        <li> \ref subsubsec_dataset_allocation_store
+        <li> \ref subsubsec_dataset_allocation_delete
+        <li> \ref subsubsec_dataset_allocation_release
+        <li> \ref subsubsec_dataset_allocation_ext
+    </ul>
+\li \ref subsec_dataset_filters
+    <ul>
+        <li> \ref subsubsec_dataset_filters_nbit
+        <li> \ref subsubsec_dataset_filters_scale
+        <li> \ref subsubsec_dataset_filters_szip
+    </ul>
+
+\ref sec_datatype
+\li \ref subsec_datatype_intro
+\li \ref subsec_datatype_model
+    <ul>
+        <li> \ref subsubsec_datatype_model_class
+        <li> \ref subsubsec_datatype_model_predefine
+    </ul>
+\li \ref subsec_datatype_usage
+    <ul>
+        <li> \ref subsubsec_datatype_usage_object
+        <li> \ref subsubsec_datatype_usage_create
+        <li> \ref subsubsec_datatype_usage_transfer
+        <li> \ref subsubsec_datatype_usage_discover
+        <li> \ref subsubsec_datatype_usage_user
+    </ul>
+\li \ref subsec_datatype_function
+\li \ref subsec_datatype_program
+    <ul>
+        <li> \ref subsubsec_datatype_program_discover
+        <li> \ref subsubsec_datatype_program_define
+    </ul>
+\li \ref subsec_datatype_other
+    <ul>
+        <li> \ref subsubsec_datatype_other_strings
+        <li> \ref subsubsec_datatype_other_refs
+        <li> \ref subsubsec_datatype_other_enum
+        <li> \ref subsubsec_datatype_other_opaque
+        <li> \ref subsubsec_datatype_other_bitfield
+    </ul>
+\li \ref subsec_datatype_fill
+\li \ref subsec_datatype_complex
+    <ul>
+        <li> \ref subsubsec_datatype_complex_create
+        <li> \ref subsubsec_datatype_complex_analyze
+    </ul>
+\li \ref subsec_datatype_life
+\li \ref subsec_datatype_transfer
+\li \ref subsec_datatype_text
+
+\ref sec_dataspace
+\li \ref subsec_dataspace_intro
+\li \ref subsec_dataspace_function
+\li \ref subsec_dataspace_program
+    <ul>
+        <li> \ref subsubsec_dataspace_program_object
+        <li> \ref subsubsec_dataspace_program_model
+    </ul>
+\li \ref subsec_dataspace_transfer
+    <ul>
+        <li> \ref subsubsec_dataspace_transfer_select
+        <li> \ref subsubsec_dataspace_transfer_model
+    </ul>
+\li \ref subsec_dataspace_select
+\li \ref subsec_dataspace_refer
+    <ul>
+        <li> \ref subsubsec_dataspace_refer_use
+        <li> \ref subsubsec_dataspace_refer_create
+        <li> \ref subsubsec_dataspace_refer_read
+    </ul>
+\li \ref subsec_dataspace_sample
+
+\ref sec_attribute
+\li \ref subsec_attribute_intro
+\li \ref subsec_attribute_program
+    <ul>
+        <li> <!-- \subsubsection subsubsec_attribute_program_exist --> To Open and Read or Write an Existing Attribute </li>
+    </ul>
+\li \ref subsec_error_H5A
+\li \ref subsec_attribute_work
+    <ul>
+        <li> \ref subsubsec_attribute_work_struct
+        <li> \ref subsubsec_attribute_work_create
+        <li> \ref subsubsec_attribute_work_access
+        <li> \ref subsubsec_attribute_work_info
+        <li> \ref subsubsec_attribute_work_iterate
+        <li> \ref subsubsec_attribute_work_delete
+        <li> \ref subsubsec_attribute_work_close
+    </ul>
+\li \ref subsec_attribute_special
+
+\ref sec_error
+\li \ref subsec_error_intro
+\li \ref subsec_error_program
+\li \ref subsec_error_H5E
+\li \ref subsec_error_ops
+    <ul>
+        <li> \ref subsubsec_error_ops_stack
+        <li> \ref subsubsec_error_ops_print
+        <li> \ref subsubsec_error_ops_mute
+        <li> \ref subsubsec_error_ops_custom_print
+        <li> \ref subsubsec_error_ops_walk
+        <li> \ref subsubsec_error_ops_travers
+    </ul>
+\li \ref subsec_error_adv
+    <ul>
+        <li> \ref subsubsec_error_adv_more
+        <li> \ref subsubsec_error_adv_app
+    </ul>
+
+\ref sec_plist
+\li \ref subsec_plist_intro
+\li \ref subsec_plist_class
+    <ul>
+        <li> \ref subsubsec_plist_class
+        <li> \ref subsubsec_plist_lists
+        <li> \ref subsubsec_plist_props
+    </ul>
+\li \ref subsec_plist_program
+    <ul>
+        <li> \ref subsubsec_plist_default
+        <li> \ref subsubsec_plist_basic
+        <li> \ref subsubsec_plist_additional
+    </ul>
+\li \ref subsec_plist_generic
+\li \ref subsec_plist_H5P
+\li \ref subsec_plist_resources
+\li \ref subsec_plist_notes
+
+\ref sec_vol
+\li \ref subsec_vol_intro
+\li \ref subsec_vol_abstract_layer
+\li \ref subsec_vol_connect
+\li \ref subsec_vol_use
+
+\ref sec_map
+
+\ref sec_addition
+
+\page AR_UG Additional Resources
+
+\section sec_addition Additional Resources
+These documents provide additional information for the use and tuning of specific HDF5 features.
+ <table style=" border-spacing:0; padding-left:6.00pt; padding-top:6.00pt; padding-right:6.00pt; padding-bottom:6.00pt; float:aligncenter; width:100%; max-width:432.00pt;" cellspacing="0">
+  <caption x-list-start="1" style="font-size: 12.0pt;">Table of Additional resources</caption>
+  <tr style="height: 23.00pt;">
+  <th style="width: 234.000pt; border-top-style: solid; border-top-width: 1px; border-top-color: #228a22; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align : top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p>Document</p>
+</th>
+  <th style="width: 198.000pt; border-top-style: solid; border-top-width: 1px; border-top-color: #228a22; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align : top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p>Comments</p>
+</th>
+</tr>
+  <tr style="height: 23.00pt;">
+  <td style="width: 234.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p style="font-style: italic; color: #0000ff;"><span><a href="http://www.hdfgroup.org/HDF5/examples/">HDF5 Examples</a></span></p>
+</td>
+  <td style="width: 198.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p>Code examples by API. </p>
+</td>
+</tr>
+  <tr style="height: 36.00pt;">
+  <td style="width: 234.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p style="font-style: italic; color: #0000ff;"><span><a href="http://www.hdfgroup.org/HDF5/doc/Advanced/Chunking/index.html">Chunking in HDF5</a></span></p>
+</td>
+  <td style="width: 198.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p>Structuring the use of chunking and tuning it for performance.</p>
+</td>
+</tr>
+  <tr style="height: 36.00pt;">
+  <td style="width: 234.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p style="font-style: italic; color: #0000ff;"><span class="FM_LT_LinkText"><a href="http://www.hdfgroup.org/HDF5/doc/Advanced/DirectChunkWrite/UsingDirectChunkWrite.pdf">Using the Direct Chunk Write Function</a></span></p>
+</td>
+  <td style="width: 198.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p>Describes another way that chunks can be written to datasets.</p>
+</td>
+</tr>
+  <tr style="height: 88.00pt;">
+  <td style="width: 234.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p style="font-style: italic; color: #0000ff;"><span><a href="http://www.hdfgroup.org/HDF5/doc/Advanced/CommittedDatatypeCopying/CopyingCommittedDatatypesWithH5Ocopy.pdf">Copying Committed Datatypes with H5Ocopy</a></span></p>
+</td>
+  <td style="width: 198.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p>Describes how to copy to another file a dataset that uses a committed datatype or an object with an attribute that uses a committed datatype so that the committed datatype in the destination file can be used by multiple objects.</p>
+</td>
+</tr>
+  <tr style="height: 36.00pt;">
+  <td style="width: 234.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p style="font-style: italic; color: #0000ff;"><span><a href="http://www.hdfgroup.org/HDF5/doc/Advanced/MetadataCache/index.html">Metadata Caching in HDF5</a></span></p>
+</td>
+  <td style="width: 198.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p>Managing the HDF5 metadata cache and tuning it for performance.</p>
+</td>
+</tr>
+  <tr style="height: 49.00pt;">
+  <td style="width: 234.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p style="font-style: italic; color: #0000ff;"><span><a href="http://www.hdfgroup.org/HDF5/doc/Advanced/DynamicallyLoadedFilters/HDF5DynamicallyLoadedFilters.pdf">HDF5 Dynamically Loaded Filters</a></span></p>
+</td>
+  <td style="width: 198.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p>Describes how an HDF5 application can apply a filter that is not registered with the HDF5 Library.</p>
+</td>
+</tr>
+  <tr style="height: 62.00pt;">
+  <td style="width: 234.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p style="font-style: italic; color: #0000ff;"><span><a href="http://www.hdfgroup.org/HDF5/doc/Advanced/FileImageOperations/HDF5FileImageOperations.pdf">HDF5 File Image Operations</a></span></p>
+</td>
+  <td style="width: 198.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p>Describes how to work with HDF5 files in memory. Disk I/O is not required when file images are opened, created, read from, or written to.</p>
+</td>
+</tr>
+  <tr style="height: 62.00pt;">
+  <td style="width: 234.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p style="font-style: italic; color: #0000ff;"><span><a href="http://www.hdfgroup.org/HDF5/doc/Advanced/ModifiedRegionWrites/ModifiedRegionWrites.pdf">Modified Region Writes</a></span></p>
+</td>
+  <td style="width: 198.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p>Describes how to set write operations for in-memory files so that only modified regions are written to storage. Available when the Core (Memory) VFD is used.</p>
+</td>
+</tr>
+  <tr style="height: 36.00pt;">
+  <td style="width: 234.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p style="font-style: italic; color: #0000ff;"><span><a href="http://www.hdfgroup.org/HDF5/doc/Advanced/UsingIdentifiers/index.html">Using Identifiers</a></span></p>
+</td>
+  <td style="width: 198.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p>Describes how identifiers behave and how they should be treated.</p>
+</td>
+</tr>
+  <tr style="height: 36.00pt;">
+  <td style="width: 234.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p style="font-style: italic; color: #0000ff;"><span><a href="http://www.hdfgroup.org/HDF5/doc/Advanced/UsingUnicode/index.html">Using UTF-8 Encoding in HDF5 Applications</a></span></p>
+</td>
+  <td style="width: 198.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p>Describes the use of UTF-8 Unicode character encodings in HDF5 applications.</p>
+</td>
+</tr>
+  <tr style="height: 49.00pt;">
+  <td style="width: 234.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p style="font-style: italic; color: #0000ff;"><span><a href="http://www.hdfgroup.org/HDF5/doc/Advanced/FreeingMemory/FreeingMemoryAllocatedByTheHdf5Library.pdf">Freeing Memory Allocated by the HDF5 Library</a></span></p>
+</td>
+  <td style="width: 198.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p>Describes how inconsistent memory management can cause heap corruption or resource leaks and possible solutions.</p>
+</td>
+</tr>
+  <tr style="height: 23.00pt;">
+  <td style="width: 234.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p style="font-style: italic; color: #0000ff;"><span><a href="http://www.hdfgroup.org/HDF5/doc/Glossary.html">HDF5 Glossary</a></span></p>
+</td>
+  <td style="width: 198.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p>A glossary of terms.</p>
+</td>
+</tr>
+ </table>
+
+Previous Chapter \ref sec_plist
+
+\par Don't like what you see? - You can help to improve this User Guide
+     Complete the survey linked near the top of this page!\n
+     We treat documentation like code: Fork the
+     <a href="https://github.com/HDFGroup/hdf5">HDF5 repo</a>, make changes, and create a
+     <a href="https://github.com/HDFGroup/hdf5/pulls">pull request</a> !\n
+
+*/
\ No newline at end of file
diff --git a/doxygen/dox/high_level/extension.dox b/doxygen/dox/high_level/extension.dox
index c81ac6e..e8471b9 100644
--- a/doxygen/dox/high_level/extension.dox
+++ b/doxygen/dox/high_level/extension.dox
@@ -1,60 +1,48 @@
 /** \defgroup H5LR Extensions
  *
- * <em>Working with region references, hyperslab selections, 
+ * <em>Working with region references, hyperslab selections,
  * and bit-fields (H5LR, H5LT)</em>
  *
- * The following reference manual entries describe high-level HDF5 C and Fortran APIs 
- * for working with region references, hyperslab selections, and bit-fields. 
- * These functions were created as part of a project supporting 
+ * The following reference manual entries describe high-level HDF5 C and Fortran APIs
+ * for working with region references, hyperslab selections, and bit-fields.
+ * These functions were created as part of a project supporting
  * NPP/NPOESS Data Production and Exploitation (
  * <a href="https://support.hdfgroup.org/projects/jpss/documentation">
- * project </a>, 
- * <a href="https://gamma.hdfgroup.org/ftp/pub/outgoing/NPOESS/source">
- * software </a>). 
- * While they were written to facilitate access to NPP, NPOESS, and JPSS 
- * data in the HDF5 format, these functions may be useful to anyone working 
+ * project</a>, software).
+ * While they were written to facilitate access to NPP, NPOESS, and JPSS
+ * data in the HDF5 format, these functions may be useful to anyone working
  * with region references, hyperslab selections, or bit-fields.
  *
- * Note that these functions are not part of the standard HDF5 distribution; 
- * the 
- * <a href="https://gamma.hdfgroup.org/ftp/pub/outgoing/NPOESS/source">
- * software </a> 
- * must be separately downloaded and installed.
+ * Note that these functions are not part of the standard HDF5 distribution;
+ * the software must be separately downloaded and installed.
  *
- * A comprehensive guide to this library, 
- * <a href="https://support.hdfgroup.org/projects/jpss/documentation/HL/UG/NPOESS_HL-UG.pdf"> 
+ * A comprehensive guide to this library,
+ * <a href="https://support.hdfgroup.org/projects/jpss/documentation/HL/UG/NPOESS_HL-UG.pdf">
  * <em>User Guide to the HDF5 High-level Library for Handling Region References and Hyperslab Selections</em></a>
- * is available at 
+ * is available at
  * https://support.hdfgroup.org/projects/jpss/documentation/HL/UG/NPOESS_HL-UG.pdf.
  *
  * - \ref H5LRcopy_reference
- *        \n Copies data from the specified dataset to a new location and 
- *        creates a reference to it.
+ *        \n Copies data from the specified dataset to a new location and creates a reference to it.
  * - \ref H5LRcopy_region
- *        \n  Copies data from a referenced region to a region in a 
- *        destination dataset.
+ *        \n  Copies data from a referenced region to a region in a destination dataset.
  * - \ref H5LRcreate_ref_to_all
- *        \n  Creates a dataset with the region references to the data in all 
- *        datasets located under a specified group in a file or creates a 
- *        dataset with object references to all objects (groups or datasets) 
+ *        \n  Creates a dataset with the region references to the data in all datasets located under a
+ *        specified group in a file or creates a dataset with object references to all objects (groups or datasets) 
  *        located under a specified group in a file.
  * - \ref H5LRcreate_region_references
- *        \n Creates an array of region references using an array of paths to 
+ *        \n Creates an array of region references using an array of paths to
  *        datasets and an array of corresponding hyperslab descriptions.
  * - \ref H5LRget_region_info
  *        \n Retrieves information about the data a region reference points to.
  * - \ref H5LRmake_dataset
- *        \n Creates and writes a dataset containing a list of 
- *        region references.
+ *        \n Creates and writes a dataset containing a list of region references.
  * - \ref H5LRread_region
- *        \n  Retrieves raw data pointed to by a region reference to 
- *        an application buffer.
+ *        \n  Retrieves raw data pointed to by a region reference to an application buffer.
  * - \ref H5LTcopy_region
- *        \n Copies data from a specified region in a source dataset 
- *        to a specified region in a destination dataset.
+ *        \n Copies data from a specified region in a source dataset to a specified region in a destination dataset.
  * - \ref H5LTread_bitfield_value
- *        \n Retrieves the values of quality flags for each element 
- *        to the application provided buffer.
+ *        \n Retrieves the values of quality flags for each element to the application provided buffer.
  * - \ref H5LTread_region
  *        \n Reads selected data to an application buffer.
  *
@@ -77,24 +65,24 @@
  * \param[in] path          Path to the dataset being created
  * \param[in] type_id       Datatype of the dataset
  * \param[in] buf_size      Size of the \p loc_id_ref and \p buf arrays
- * \param[in] loc_id_ref    Array of object identifiers; each identifier 
- *                          describes to which HDF5 file the corresponding 
+ * \param[in] loc_id_ref    Array of object identifiers; each identifier
+ *                          describes to which HDF5 file the corresponding
  *                          region reference belongs to
  * \param[in] buf           Array of region references
  *
  * \return \herr_t
  *
- * \details Given an array of size \p buf_size of region references \p buf, 
- *          the function will create a dataset with path \p path, at location 
- *          specified by \p loc_id and of a datatype specified by \p type_id, 
- *          and will write data associated with each region reference in the order 
- *          corresponding to the order of the region references in the buffer. 
- *          It is assumed that all referenced hyperslabs have the same dimensionality, 
- *          and only the size of the slowest changing dimension may differ. 
- *          Each reference in the \p buf array belongs to the file identified 
+ * \details Given an array of size \p buf_size of region references \p buf,
+ *          the function will create a dataset with path \p path, at location
+ *          specified by \p loc_id and of a datatype specified by \p type_id,
+ *          and will write data associated with each region reference in the order
+ *          corresponding to the order of the region references in the buffer.
+ *          It is assumed that all referenced hyperslabs have the same dimensionality,
+ *          and only the size of the slowest changing dimension may differ.
+ *          Each reference in the \p buf array belongs to the file identified
  *          by the corresponding object identifiers in the array \p loc_id_ref.
  *
- *          If \p path does not exist in \p loc_id then the function will 
+ *          If \p path does not exist in \p loc_id then the function will
  *          create the path specified by \p path automatically.
  *
  * \version 1.1 Fortran wrapper introduced in this release.
@@ -103,10 +91,10 @@
  *
  */
 H5_HLRDLL herr_t H5LRmake_dataset(hid_t loc_id,
-				 const char *path, 
-				 hid_t type_id, const size_t buf_size,
-				 const hid_t *loc_id_ref,
-				 const hdset_reg_ref_t *buf);
+                 const char *path,
+                 hid_t type_id, const size_t buf_size,
+                 const hid_t *loc_id_ref,
+                 const hdset_reg_ref_t *buf);
 
 /*-------------------------------------------------------------------------
  *
@@ -119,49 +107,46 @@ H5_HLRDLL herr_t H5LRmake_dataset(hid_t loc_id,
  * --------------------------------------------------------------------------
  * \ingroup H5LR
  *
- * \brief Creates an array of region references using an array of paths to 
+ * \brief Creates an array of region references using an array of paths to
  *        datasets and an array of corresponding hyperslab descriptions.
  *
  * \param[in] obj_id        File identifier for the HDF5 file containing
  *                          the referenced regions or an object identifier
  *                          for any object in that file
- * \param[in] num_elem      Number of elements in the \p path and 
- *                          \p buf arrays
- * \param[in] path          Array of pointers to strings, which contain 
- *                          the paths to the target datasets for the 
- *                          region references
+ * \param[in] num_elem      Number of elements in the \p path and \p buf arrays
+ * \param[in] path          Array of pointers to strings, which contain
+ *                          the paths to the target datasets for the region references
  * \param[in] block_coord   Array of hyperslab coordinate
- * \param[out] buf          Buffer for returning an array of region 
- *                          references
+ * \param[out] buf          Buffer for returning an array of region references
  *
  * \return \herr_t
  *
  * \note    **Motivation:**
- * \note    H5LRcreate_region_references() is useful when creating 
+ * \note    H5LRcreate_region_references() is useful when creating
  *          large numbers of similar region references.
  *
- * \details H5LRcreate_region_references() creates a list of region references 
- *          given an array of paths to datasets and another array listing the 
+ * \details H5LRcreate_region_references() creates a list of region references
+ *          given an array of paths to datasets and another array listing the
  *          corner coordinates of the corresponding hyperslabs.
  *
  *          \p path parameter is an array of pointers to strings.
  *
- *          \p num_elem specifies the number of region references to be created, 
+ *          \p num_elem specifies the number of region references to be created,
  *          thus specifying the size of the \p path and \p _buf arrays.
  *
- *          Buffer \p block_coord has size 2*rank and is the coordinates of the 
- *          starting point following by the coordinates of the ending point of 
- *          the hyperslab, repeated \p num_elem times for each hyperslab. 
- *          For example, creating two region references to two hyperslabs, 
- *          one with a rectangular hyperslab region starting at element (2,2) 
- *          to element (5,4) and the second rectangular region starting at 
- *          element (7,7) to element (9,10), results in \p block_coord 
+ *          Buffer \p block_coord has size 2*rank and is the coordinates of the
+ *          starting point following by the coordinates of the ending point of
+ *          the hyperslab, repeated \p num_elem times for each hyperslab.
+ *          For example, creating two region references to two hyperslabs,
+ *          one with a rectangular hyperslab region starting at element (2,2)
+ *          to element (5,4) and the second rectangular region starting at
+ *          element (7,7) to element (9,10), results in \p block_coord
  *          being {2,2,5,4, 7,7,9,10}.
  *
- *          The rank of the hyperslab will be the same as the rank of the 
- *          target dataset. H5LRcreate_region_references() will retrieve 
- *          the rank for each dataset and will use those values to interpret 
- *          the values in the buffer. Please note that rank may vary from one 
+ *          The rank of the hyperslab will be the same as the rank of the
+ *          target dataset. H5LRcreate_region_references() will retrieve
+ *          the rank for each dataset and will use those values to interpret
+ *          the values in the buffer. Please note that rank may vary from one
  *          dataset to another.
  *
  * \version 1.1 Fortran wrapper introduced in this release.
@@ -170,43 +155,39 @@ H5_HLRDLL herr_t H5LRmake_dataset(hid_t loc_id,
  *
  */
 H5_HLRDLL herr_t H5LRcreate_region_references(hid_t obj_id,
-					     size_t num_elem,
-					     const char **path,
-					     const hsize_t *block_coord,
-					     hdset_reg_ref_t *buf);
+                      size_t num_elem,
+                      const char **path,
+                      const hsize_t *block_coord,
+                      hdset_reg_ref_t *buf);
 
 /**
  * --------------------------------------------------------------------------
  * \ingroup H5LR
  *
- * \brief Copies data from the specified dataset to a new location and 
- *        creates a reference to it.
+ * \brief Copies data from the specified dataset to a new location and creates a reference to it.
  *
- * \param[in] obj_id        Identifier of any object in a file an 
- *                          HDF5 reference belongs to
+ * \param[in] obj_id        Identifier of any object in a file an HDF5 reference belongs to
  * \param[in] ref           Reference to the datasets region
- * \param[in] file          Name of the destination file 
+ * \param[in] file          Name of the destination file
  * \param[in] path          Full path to the destination dataset
- * \param[in] block_coord   Hyperslab coordinates in the destination 
- *                          dataset
- * \param[out] ref_new      Region reference to the new location of 
- *                          data
+ * \param[in] block_coord   Hyperslab coordinates in the destination dataset
+ * \param[out] ref_new      Region reference to the new location of data
  *
  * \return \herr_t
  *
- * \details Given a data set pointed to by a region reference, the function 
- *          H5LRcopy_reference() will copy the hyperslab data referenced by 
- *          a datasets region reference into existing dataset specified by 
- *          its path \p path in the file with the name \p file, and to location 
- *          specified by the hyperslab coordinates \p block_coord. It will 
- *          create the region reference \p ref_new to point to the new location. 
- *          The number of elements in the old and newly specified regions has 
+ * \details Given a data set pointed to by a region reference, the function
+ *          H5LRcopy_reference() will copy the hyperslab data referenced by
+ *          a datasets region reference into existing dataset specified by
+ *          its path \p path in the file with the name \p file, and to location
+ *          specified by the hyperslab coordinates \p block_coord. It will
+ *          create the region reference \p ref_new to point to the new location.
+ *          The number of elements in the old and newly specified regions has
  *          to be the same.
  *
- *          Buffer \p block_coord has size 2*rank and is the coordinates of 
- *          the starting point following by the coordinates of the ending 
- *          point of the hyperslab. For example, to extract a rectangular 
- *          hyperslab region starting at element (2,2) to element (5,4) 
+ *          Buffer \p block_coord has size 2*rank and is the coordinates of
+ *          the starting point following by the coordinates of the ending
+ *          point of the hyperslab. For example, to extract a rectangular
+ *          hyperslab region starting at element (2,2) to element (5,4)
  *          then \p block_coord would be {2, 2, 5, 4}.
  *
  * \version 1.1 Fortran wrapper introduced in this release.
@@ -215,41 +196,39 @@ H5_HLRDLL herr_t H5LRcreate_region_references(hid_t obj_id,
  *
  */
 H5_HLRDLL herr_t H5LRcopy_reference(hid_t obj_id, hdset_reg_ref_t *ref, const char *file,
-				    const char *path, const hsize_t *block_coord, 
-				    hdset_reg_ref_t *ref_new);
+                     const char *path, const hsize_t *block_coord,
+                     hdset_reg_ref_t *ref_new);
 
 /**
  * --------------------------------------------------------------------------
  * \ingroup H5LR
  *
- * \brief Copies data from a referenced region to a region in a 
- *        destination dataset.
+ * \brief Copies data from a referenced region to a region in a destination dataset.
  *
- * \param[in] obj_id        Identifier of any object in a file 
+ * \param[in] obj_id        Identifier of any object in a file
  *                          dataset region reference belongs to
  * \param[in] ref           Dataset region reference
- * \param[in] file          Name of the destination file 
+ * \param[in] file          Name of the destination file
  * \param[in] path          Full path to the destination dataset
- * \param[in] block_coord   Hyperslab coordinates in the destination 
- *                          dataset
+ * \param[in] block_coord   Hyperslab coordinates in the destination dataset
  *
  * \return \herr_t
  *
- * \details Given a dataset region reference \p ref in a source file 
- *          specified by an identifier of any object in that file 
- *          \p obj_id, the function will write data to the existing 
- *          dataset \p path in file \p file to the simple hyperslab 
+ * \details Given a dataset region reference \p ref in a source file
+ *          specified by an identifier of any object in that file
+ *          \p obj_id, the function will write data to the existing
+ *          dataset \p path in file \p file to the simple hyperslab
  *          specified by \p block_coord.
  *
- *          Buffer \p block_coord has size 2*rank and is the coordinates 
- *          of the starting point following by the coordinates of the 
- *          ending point of the hyperslab. For example, to specify a 
- *          rectangular hyperslab destination region starting at element 
+ *          Buffer \p block_coord has size 2*rank and is the coordinates
+ *          of the starting point following by the coordinates of the
+ *          ending point of the hyperslab. For example, to specify a
+ *          rectangular hyperslab destination region starting at element
  *          (2,2) to element (5,4) then \p block_coord would be {2, 2, 5, 4}.
  *
- *          If \p path does not exist in the destination file (as may be 
- *          the case when writing to a new file) then the dataset will be 
- *          copied directly to the \p path and \p block_coord will be 
+ *          If \p path does not exist in the destination file (as may be
+ *          the case when writing to a new file) then the dataset will be
+ *          copied directly to the \p path and \p block_coord will be
  *          disregarded.
  *
  * \version 1.1 Fortran wrapper introduced in this release.
@@ -258,71 +237,66 @@ H5_HLRDLL herr_t H5LRcopy_reference(hid_t obj_id, hdset_reg_ref_t *ref, const ch
  *
  */
 H5_HLRDLL herr_t H5LRcopy_region(hid_t obj_id,
-				hdset_reg_ref_t *ref,
-				const char *file,
-				const char *path,
-				const hsize_t *block_coord);
+                 hdset_reg_ref_t *ref,
+                 const char *file,
+                 const char *path,
+                 const hsize_t *block_coord);
 
 /**
  * --------------------------------------------------------------------------
  * \ingroup H5LR
  *
- * \brief Creates a dataset with the region references to the data 
- *        in all datasets located under a specified group in a file 
- *        or creates a dataset with object references to all objects 
+ * \brief Creates a dataset with the region references to the data
+ *        in all datasets located under a specified group in a file
+ *        or creates a dataset with object references to all objects
  *        (groups or datasets) located under a specified group in a file.
  *
  * \fg_loc_id
- * \param[in] group_path    Absolute or relative path to the group 
- *                          at which traversal starts
- * \param[in] ds_path       Absolute or relative path to the dataset 
- *                          with region references to be created
- * \param[in] index_type    Index_type; 
- *                          see valid values below in description
- * \param[in] order         Order in which index is traversed; 
- *                          see valid values below in description
- * \param[in] ref_type      Reference type;
- *                          see valid values below in description
+ * \param[in] group_path    Absolute or relative path to the group at which traversal starts
+ * \param[in] ds_path       Absolute or relative path to the dataset with region references to be created
+ * \param[in] index_type    Index_type; see valid values below in description
+ * \param[in] order         Order in which index is traversed; see valid values below in description
+ * \param[in] ref_type      Reference type; see valid values below in description
  *
  * \return \herr_t
  *
- * \details H5LRcreate_ref_to_all() creates a dataset with the 
- *          region references to the data in all datasets located 
- *          under a specified group in a file or creates a dataset with 
- *          object references to all objects (groups or datasets) located 
+ * \details H5LRcreate_ref_to_all() creates a dataset with the
+ *          region references to the data in all datasets located
+ *          under a specified group in a file or creates a dataset with
+ *          object references to all objects (groups or datasets) located
  *          under a specified group in a file.
  *
- *          Given a dataset path \p ds_path in a file specified by the 
- *          \p loc_id identifier, the function H5LRcreate_ref_to_all() 
- *          will create a contiguous one-dimensional dataset with the 
- *          region references or object references depending on the value 
- *          of the \p ref_type parameter. When \p ref_type is 
- *          #H5R_DATASET_REGION, each region reference points to all data 
- *          in a dataset encountered by an internally called H5Lvisit() 
- *          routine, which starts at the group specified by the \p loc_id 
+ *          Given a dataset path \p ds_path in a file specified by the
+ *          \p loc_id identifier, the function H5LRcreate_ref_to_all()
+ *          will create a contiguous one-dimensional dataset with the
+ *          region references or object references depending on the value
+ *          of the \p ref_type parameter. When \p ref_type is
+ *          #H5R_DATASET_REGION, each region reference points to all data
+ *          in a dataset encountered by an internally called H5Lvisit()
+ *          routine, which starts at the group specified by the \p loc_id
  *          and \p group_path parameters. In a like manner, when
- *          \p ref_type is #H5R_OBJECT, each object reference points to 
+ *          \p ref_type is #H5R_OBJECT, each object reference points to
  *          an object (a group or a dataset) encountered by H5Lvisit().
  *
- *          If \p ds_path does not exist in \p loc_id then the function 
+ *          If \p ds_path does not exist in \p loc_id then the function
  *          will create the path specified by \p ds_path automatically.
  *
- *          \p index_type specifies the index to be used. 
+ *          \p index_type specifies the index to be used.
  *          Valid values include the following:
  *          - #H5_INDEX_NAME        Alphanumeric index on name
  *          - #H5_INDEX_CRT_ORDER   Index on creation order
  *
- *          \p order specifies the order in which objects are to be 
- *          inspected along the index specified in \p index_type. 
+ *          \p order specifies the order in which objects are to be
+ *          inspected along the index specified in \p index_type.
  *          Valid values include the following:
  *          - #H5_ITER_INC      Increasing order
  *          - #H5_ITER_DEC      Decreasing order
  *          - #H5_ITER_NATIVE   Fastest available order
  *
- *          For more detailed information on these two parameters, 
- *          see H5Lvisit().
+ *          For more detailed information on these two parameters,
+ *          @see H5Lvisit().
  *
- *          \p ref_type specifies the type of the reference to be used. 
+ *          \p ref_type specifies the type of the reference to be used.
  *          Valid values include the following:
  *          - #H5R_DATASET_REGION   Dataset region reference
  *          - #H5R_OBJECT           Object reference
@@ -333,7 +307,7 @@ H5_HLRDLL herr_t H5LRcopy_region(hid_t obj_id,
  *
  */
 H5_HLRDLL herr_t H5LRcreate_ref_to_all(hid_t loc_id, const char *group_path,
-					 const char *ds_path, H5_index_t index_type, H5_iter_order_t order, H5R_type_t ref_type);
+                  const char *ds_path, H5_index_t index_type, H5_iter_order_t order, H5R_type_t ref_type);
 
 /*-------------------------------------------------------------------------
  *
@@ -352,30 +326,27 @@ H5_HLRDLL herr_t H5LRcreate_ref_to_all(hid_t loc_id, const char *group_path,
  * \param[in] obj_id        File identifier for the HDF5 file containing
  *                          the dataset with the referenced region or an
  *                          object identifier for any object in that file
- * \param[in] ref           Region reference specifying data to be read
- *                          in
- * \param[in] mem_type      Memory datatype of data read from referenced 
+ * \param[in] ref           Region reference specifying data to be read in
+ * \param[in] mem_type      Memory datatype of data read from referenced
  *                          region into the application buffer
- * \param[in,out] numelem   Number of elements to be read into buffer 
- *                          \p buf
- * \param[out] buf          Buffer in which data is returned to the 
- *                          application
+ * \param[in,out] numelem   Number of elements to be read into buffer \p buf
+ * \param[out] buf          Buffer in which data is returned to the application
  *
  * \return \herr_t
  *
- * \details H5LRread_region() reads data pointed to by the region 
+ * \details H5LRread_region() reads data pointed to by the region
  *          reference \p ref into the buffer \p buf.
  *
- *          \p numelem specifies the number of elements to be read 
- *          into \p buf. When the size of the reference region is unknown, 
- *          H5LRread_region() can be called with \p buf set to NULL; 
- *          the number of elements in the referenced region will be returned 
+ *          \p numelem specifies the number of elements to be read
+ *          into \p buf. When the size of the reference region is unknown,
+ *          H5LRread_region() can be called with \p buf set to NULL;
+ *          the number of elements in the referenced region will be returned
  *          in \p numelem.
  *
- *          The buffer buf must be big enough to hold \p numelem elements 
- *          of type \p mem_type. For example, if data is read from the referenced 
- *          region into an integer buffer, \p mem_type should be #H5T_NATIVE_INT 
- *          and the buffer must be at least \c sizeof(int) * \p numelem  bytes 
+ *          The buffer buf must be big enough to hold \p numelem elements
+ *          of type \p mem_type. For example, if data is read from the referenced
+ *          region into an integer buffer, \p mem_type should be #H5T_NATIVE_INT
+ *          and the buffer must be at least \c sizeof(int) * \p numelem  bytes
  *          in size. This buffer must be allocated by the application.
  *
  * \version 1.1 Fortran wrapper introduced in this release.
@@ -384,10 +355,10 @@ H5_HLRDLL herr_t H5LRcreate_ref_to_all(hid_t loc_id, const char *group_path,
  *
  */
 H5_HLRDLL herr_t H5LRread_region(hid_t obj_id,
-				const hdset_reg_ref_t *ref, 
-				hid_t mem_type,
-				size_t *numelem,
-				void *buf );
+                 const hdset_reg_ref_t *ref,
+                 hid_t mem_type,
+                 size_t *numelem,
+                 void *buf );
 
 /*-------------------------------------------------------------------------
  *
@@ -400,40 +371,33 @@ H5_HLRDLL herr_t H5LRread_region(hid_t obj_id,
  * --------------------------------------------------------------------------
  * \ingroup H5LR
  *
- * \brief Retrieves information about the data a region reference 
- *        points to.
+ * \brief Retrieves information about the data a region reference points to.
  *
- * \param[in] obj_id        Identifier of any object in an HDF5 file 
- *                          the region reference belongs to.
+ * \param[in] obj_id        Identifier of any object in an HDF5 file the region reference belongs to.
  * \param[in] ref           Region reference to query
- * \param[in,out] len       Size of the buffer to store \p path in. 
- *                          NOTE: if \p *path is not NULL then \p *len 
- *                          must be the appropriate length
+ * \param[in,out] len       Size of the buffer to store \p path in.
+ *                          NOTE: if \p *path is not NULL then \p *len must be the appropriate length
  * \param[out] path         Full path that a region reference points to
  * \param[out] rank         The number of dimensions of the dataset
- *                          dimensions of the dataset pointed by 
- *                          region reference.
- * \param[out] dtype        Datatype of the dataset pointed by the 
- *                          region reference.
+ *                          dimensions of the dataset pointed by region reference.
+ * \param[out] dtype        Datatype of the dataset pointed by the region reference.
  * \param[out] sel_type     Type of the selection (point or hyperslab)
- * \param[in,out] numelem   Number of coordinate blocks or 
- *                          selected elements.
- * \param[out] buf          Buffer containing description of the region 
- *                          pointed by region reference
+ * \param[in,out] numelem   Number of coordinate blocks or selected elements.
+ * \param[out] buf          Buffer containing description of the region pointed by region reference
  *
  * \return \herr_t
  *
- * \details H5LRget_region_info() queries information about the data 
- *          pointed by a region reference \p ref. It returns one of the 
- *          absolute paths to a dataset, length of the path, dataset’s rank 
- *          and datatype, description of the referenced region and type of 
- *          the referenced region. Any output argument can be NULL if that 
+ * \details H5LRget_region_info() queries information about the data
+ *          pointed by a region reference \p ref. It returns one of the
+ *          absolute paths to a dataset, length of the path, dataset’s rank
+ *          and datatype, description of the referenced region and type of
+ *          the referenced region. Any output argument can be NULL if that
  *          argument does not need to be returned.
  *
- *          The parameter \p obj_id is an identifier for any object in the 
- *          HDF5 file containing the referenced object. For example, it can 
- *          be an identifier of a dataset the region reference belongs to 
- *          or an identifier of an HDF5 file the dataset with region references 
+ *          The parameter \p obj_id is an identifier for any object in the
+ *          HDF5 file containing the referenced object. For example, it can
+ *          be an identifier of a dataset the region reference belongs to
+ *          or an identifier of an HDF5 file the dataset with region references
  *          is stored in.
  *
  *          The parameter \p ref is a region reference to query.
@@ -442,36 +406,36 @@ H5_HLRDLL herr_t H5LRread_region(hid_t obj_id,
  *          buffer of size \p len+1 to return an absolute path to a dataset
  *          the region reference points to.
  *
- *          The parameter \p len is a length of absolute path string plus 
- *          the \0 string terminator. If path parameter is NULL, actual 
- *          length of the path (+1 for \0 string terminator) is returned to 
- *          application and can be used to allocate buffer path of an 
+ *          The parameter \p len is a length of absolute path string plus
+ *          the \0 string terminator. If path parameter is NULL, actual
+ *          length of the path (+1 for \0 string terminator) is returned to
+ *          application and can be used to allocate buffer path of an
  *          appropriate length \p len.
  *
  *          The parameter \p sel_type describes the type of the selected
- *          region. Possible values can be #H5S_SEL_POINTS for point 
+ *          region. Possible values can be #H5S_SEL_POINTS for point
  *          selection and #H5S_SEL_HYPERSLABS for hyperslab selection.
  *
- *          The parameter \p numelem describes how many elements will be 
- *          placed in the buffer \p buf. The number should be interpreted 
+ *          The parameter \p numelem describes how many elements will be
+ *          placed in the buffer \p buf. The number should be interpreted
  *          using the value of \p sel_type.
  *
- *          If value of \p sel_type is #H5S_SEL_HYPERSLABS, the parameter 
- *          \p buf contains \p numelem blocks of the coordinates for each 
- *          simple hyperslab of the referenced region. Each block has 
- *          length \c 2*\p rank and is organized as follows: <"start" coordinate>, 
- *          immediately followed by <"opposite" corner coordinate>. 
- *          The total size of the buffer to hold the description of the 
- *          region will be \c 2*\p rank*\p numelem. If region reference 
- *          points to a contiguous sub-array, then the value of \p numelem 
- *          is 1 and the block contains coordinates of the upper left and 
+ *          If value of \p sel_type is #H5S_SEL_HYPERSLABS, the parameter
+ *          \p buf contains \p numelem blocks of the coordinates for each
+ *          simple hyperslab of the referenced region. Each block has
+ *          length \c 2*\p rank and is organized as follows: <"start" coordinate>,
+ *          immediately followed by <"opposite" corner coordinate>.
+ *          The total size of the buffer to hold the description of the
+ *          region will be \c 2*\p rank*\p numelem. If region reference
+ *          points to a contiguous sub-array, then the value of \p numelem
+ *          is 1 and the block contains coordinates of the upper left and
  *          lower right corners of the sub-array (or simple hyperslab).
  *
- *          If value of \p sel_type is #H5S_SEL_POINTS, the parameter \p buf 
- *          contains \p numelem blocks of the coordinates for each selected 
- *          point of the referenced region. Each block has length \p rank 
- *          and contains coordinates of the element. The total size of the 
- *          buffer to hold the description of the region will be 
+ *          If value of \p sel_type is #H5S_SEL_POINTS, the parameter \p buf
+ *          contains \p numelem blocks of the coordinates for each selected
+ *          point of the referenced region. Each block has length \p rank
+ *          and contains coordinates of the element. The total size of the
+ *          buffer to hold the description of the region will be
  *          \p rank* \p numelem.
  *
  *
@@ -481,14 +445,14 @@ H5_HLRDLL herr_t H5LRread_region(hid_t obj_id,
  *
  */
 H5_HLRDLL herr_t H5LRget_region_info(hid_t obj_id,
-				    const hdset_reg_ref_t *ref,  
-				    size_t *len, 
-				    char *path,
-				    int *rank,
-				    hid_t *dtype,
-				    H5S_sel_type *sel_type,
-				    size_t *numelem,
-				    hsize_t *buf );
+                     const hdset_reg_ref_t *ref,
+                     size_t *len, 
+                     char *path,
+                     int *rank,
+                     hid_t *dtype,
+                     H5S_sel_type *sel_type,
+                     size_t *numelem,
+                     hsize_t *buf );
 
 
 
@@ -503,35 +467,33 @@ H5_HLRDLL herr_t H5LRget_region_info(hid_t obj_id,
  * --------------------------------------------------------------------------
  * \ingroup H5LR
  *
- * \brief Copies data from a specified region in a source dataset 
+ * \brief Copies data from a specified region in a source dataset
  *        to a specified region in a destination dataset
  *
  * \param[in] file_src          Name of the source file
  * \param[in] path_src          Full path to the source dataset
- * \param[in] block_coord_src   Hyperslab coordinates in the 
- *                              source dataset
+ * \param[in] block_coord_src   Hyperslab coordinates in the source dataset
  * \param[in] file_dest         Name of the destination file
  * \param[in] path_dest         Full path to the destination dataset
- * \param[in] block_coord_dset  Hyperslab coordinates in the 
- *                              destination dataset
+ * \param[in] block_coord_dset  Hyperslab coordinates in the destination dataset
  *
  * \return \herr_t
  *
- * \details Given a path to a dataset \p path_src in a file with the 
- *          name \p file_src, and description of a simple hyperslab of 
- *          the source \p block_coord_src, the function will write data 
- *          to the dataset \p path_dest in file \p file_dest to the 
- *          simple hyperslab specified by \p block_coord_dset. 
- *          The arrays \p block_coord_src and \p block_coord_dset have 
- *          a length of 2*rank and are the coordinates of the starting 
- *          point following by the coordinates of the ending point of the 
- *          hyperslab. For example, to specify a rectangular hyperslab 
- *          destination region starting at element (2,2) to element (5,4) 
+ * \details Given a path to a dataset \p path_src in a file with the
+ *          name \p file_src, and description of a simple hyperslab of
+ *          the source \p block_coord_src, the function will write data
+ *          to the dataset \p path_dest in file \p file_dest to the
+ *          simple hyperslab specified by \p block_coord_dset.
+ *          The arrays \p block_coord_src and \p block_coord_dset have
+ *          a length of 2*rank and are the coordinates of the starting
+ *          point following by the coordinates of the ending point of the
+ *          hyperslab. For example, to specify a rectangular hyperslab
+ *          destination region starting at element (2,2) to element (5,4)
  *          then \p block_coord_dset would be {2, 2, 5, 4}.
  *
- *          If \p path_dest does not exist in the destination file 
- *          (as may be the case when writing to a new file) then the 
- *          dataset will be copied directly to the \p path_dest and 
+ *          If \p path_dest does not exist in the destination file
+ *          (as may be the case when writing to a new file) then the
+ *          dataset will be copied directly to the \p path_dest and
  *          \p block_coord_dset will be disregarded.
  *
  * \version 1.1 Fortran wrapper introduced in this release.
@@ -540,11 +502,11 @@ H5_HLRDLL herr_t H5LRget_region_info(hid_t obj_id,
  *
  */
 H5_HLRDLL herr_t H5LTcopy_region(const char *file_src,
-				const char *path_src,
-				const hsize_t *block_coord_src,
-				const char *file_dest,
-				const char *path_dest,
-				const hsize_t *block_coord_dset);
+                 const char *path_src,
+                 const hsize_t *block_coord_src,
+                 const char *file_dest,
+                 const char *path_dest,
+                 const hsize_t *block_coord_dset);
 
 /*-------------------------------------------------------------------------
  *
@@ -562,27 +524,25 @@ H5_HLRDLL herr_t H5LTcopy_region(const char *file_src,
  * \param[in] file          Name of file
  * \param[in] path          Full path to a dataset
  * \param[in] block_coord   Hyperslab coordinates
- * \param[in] mem_type      Memory datatype, describing the buffer 
- *                          the referenced data will be read into
- * \param[out] buf          Buffer containing data from the 
- *                          referenced region
+ * \param[in] mem_type      Memory datatype, describing the buffer the referenced data will be read into
+ * \param[out] buf          Buffer containing data from the referenced region
  *
  * \return \herr_t
  *
- * \details H5LTread_region() reads data from a region described by 
- *          the hyperslab coordinates in \p block_coord, located in 
- *          the dataset specified by its absolute path \p path in a 
- *          file specified by its name \p file. Data is read into a 
- *          buffer \p buf of the datatype that corresponds to the 
+ * \details H5LTread_region() reads data from a region described by
+ *          the hyperslab coordinates in \p block_coord, located in
+ *          the dataset specified by its absolute path \p path in a
+ *          file specified by its name \p file. Data is read into a
+ *          buffer \p buf of the datatype that corresponds to the
  *          HDF5 datatype specified by \p mem_type.
  *
- *          Buffer \p block_coord has size 2*rank and is the coordinates 
- *          of the starting point following by the coordinates of the 
- *          ending point of the hyperslab. For example, to extract a 
- *          rectangular hyperslab region starting at element (2,2) to 
+ *          Buffer \p block_coord has size 2*rank and is the coordinates
+ *          of the starting point following by the coordinates of the
+ *          ending point of the hyperslab. For example, to extract a
+ *          rectangular hyperslab region starting at element (2,2) to
  *          element (5,4) then \p block_coord would be {2, 2, 5, 4}.
  *
- *          Buffer \p buf should be big enough to hold selected elements 
+ *          Buffer \p buf should be big enough to hold selected elements
  *          of the type that corresponds to the \p mem_type
  *
  * \version 1.1 Fortran wrapper introduced in this release.
@@ -591,57 +551,55 @@ H5_HLRDLL herr_t H5LTcopy_region(const char *file_src,
  *
  */
 H5_HLRDLL herr_t  H5LTread_region(const char *file,
-				 const char *path,
-				 const hsize_t *block_coord,
-				 hid_t mem_type,
-				 void *buf );
+                  const char *path,
+                  const hsize_t *block_coord,
+                  hid_t mem_type,
+                  void *buf );
 
 /**
  * --------------------------------------------------------------------------
  * \ingroup H5LR
  *
- * \brief Retrieves the values of quality flags for each element 
+ * \brief Retrieves the values of quality flags for each element
  *        to the application provided buffer.
  *
  * \param[in] dset_id   Identifier of the dataset with bit-field values
  * \param[in] num_values    Number of the values to be extracted
- * \param[in] offset        Array of staring bits to be extracted from 
+ * \param[in] offset        Array of staring bits to be extracted from
  *                          the element; valid values: 0 (zero) through 7
- * \param[in] lengths       Array of the number of bits to be extracted 
- *                          for each value
- * \param[in] space         Dataspace identifier, describing the elements 
- *                          to be read from the dataset with bit-field 
- *                          values
+ * \param[in] lengths       Array of the number of bits to be extracted for each value
+ * \param[in] space         Dataspace identifier, describing the elements
+ *                          to be read from the dataset with bit-field values
  * \param[out] buf          Buffer to read the values in
  *
  * \return \herr_t
  *
- * \details H5LTread_bitfield_value() reads selected elements from a 
- *          dataset specified by its identifier \p dset_id, and unpacks 
+ * \details H5LTread_bitfield_value() reads selected elements from a
+ *          dataset specified by its identifier \p dset_id, and unpacks
  *          the bit-field values to a buffer \p buf.
  *
- *          The parameter \p space is a space identifier that indicates 
+ *          The parameter \p space is a space identifier that indicates
  *          which elements of the dataset should be read.
  *
- *          The parameter \p offset is an array of length \p num_values; 
+ *          The parameter \p offset is an array of length \p num_values;
  *          the i<sup>th</sup> element of the array holds the value of the
- *          starting bit of the i<sup>th</sup> bit-field value. 
+ *          starting bit of the i<sup>th</sup> bit-field value.
  *          Valid values are: 0 (zero) through 7.
  *
- *          The parameter \p lengths is an array of length \p num_values; 
- *          the i<sup>th</sup> element of the array holds the number of 
- *          bits to be extracted for the i<sup>th</sup> bit-field value. 
- *          Extracted bits will be interpreted as a base-2 integer value. 
- *          Each value will be converted to the base-10 integer value and 
- *          stored in the application buffer. 
- *
- *          Buffer \p buf is allocated by the application and should be big 
- *          enough to hold \c num_sel_elem * \p num_values elements of the 
- *          specified type, where \c num_sel_elem is a number of the elements 
- *          to be read from the dataset. Data in the buffer is organized 
- *          as \p num_values values for the first element, followed by the 
- *          \p num_values values for the second element, ... , followed by 
- *          the \p num_values values for the 
+ *          The parameter \p lengths is an array of length \p num_values;
+ *          the i<sup>th</sup> element of the array holds the number of
+ *          bits to be extracted for the i<sup>th</sup> bit-field value.
+ *          Extracted bits will be interpreted as a base-2 integer value.
+ *          Each value will be converted to the base-10 integer value and
+ *          stored in the application buffer.
+ *
+ *          Buffer \p buf is allocated by the application and should be big
+ *          enough to hold \c num_sel_elem * \p num_values elements of the
+ *          specified type, where \c num_sel_elem is a number of the elements
+ *          to be read from the dataset. Data in the buffer is organized
+ *          as \p num_values values for the first element, followed by the
+ *          \p num_values values for the second element, ... , followed by
+ *          the \p num_values values for the
  *          \c num_selected_elem<sup>th</sup> element.
  *
  * \version 1.1 Fortran wrapper introduced in this release.
@@ -650,5 +608,5 @@ H5_HLRDLL herr_t  H5LTread_region(const char *file,
  *
  */
 H5_HLRDLL herr_t H5LTread_bitfield_value(hid_t dset_id, int num_values, const unsigned *offset,
-					const unsigned *lengths, hid_t space, int *buf);
+                 const unsigned *lengths, hid_t space, int *buf);
 
diff --git a/doxygen/dox/high_level/high_level.dox b/doxygen/dox/high_level/high_level.dox
deleted file mode 100644
index c53d298..0000000
--- a/doxygen/dox/high_level/high_level.dox
+++ /dev/null
@@ -1,29 +0,0 @@
-/** \page high_level High-level library
- * The high-level HDF5 library includes several sets of convenience and standard-use APIs to 
- * facilitate common HDF5 operations.
- *
- * <ul>
- * <li>\ref H5LT "Lite (H5LT, H5LD)"
- * \n
- * Functions to simplify creating and manipulating datasets, attributes and other features
- * <li>\ref H5IM "Image (H5IM)"
- * \n
- * Creating and manipulating HDF5 datasets intended to be interpreted as images
- * <li>\ref H5TB "Table (H5TB)"
- * \n
- * Creating and manipulating HDF5 datasets intended to be interpreted as tables
- * <li>\ref H5PT "Packet Table (H5PT)"
- * \n
- * Creating and manipulating HDF5 datasets to support append- and read-only operations on table data
- * <li>\ref H5DS "Dimension Scale (H5DS)"
- * \n
- * Creating and manipulating HDF5 datasets that are associated with the dimension of another HDF5 dataset
- * <li>\ref H5DO "Optimizations (H5DO)"
- * \n
- * Bypassing default HDF5 behavior in order to optimize for specific use cases
- * <li>\ref H5LR "Extensions (H5LR, H5LT)"
- * \n
- * Working with region references, hyperslab selections, and bit-fields
- * </ul>
- * 
- */