Documentation fixes right in time for the holidays (#1321)

* Sketch of the H5S life cycle.

* Committing clang-format changes

* Fix H5S_UNLIMITED snafu.

* Updated RM template and RM page.

* Added H5S life cycle.

* Committing clang-format changes

* Added H5T life cycle.

* Committing clang-format changes

* Cleaner layout (?)

* Cleaned the H5F life cycle. Called out unfinished biz.

* Committing clang-format changes

* Remaining life cycle skeletons.

* Committing clang-format changes

* Committing clang-format changes

* Added H5Z life cycle.

* Committing clang-format changes

* Added H5G life cycle.

* Committing clang-format changes

* H5 and H5I life cycle updates.

* Committing clang-format changes

* Added H5PL life cycle.

* Committing clang-format changes

* Added H5L life cycle.

* Committing clang-format changes

* Fix for Chris' comment.

* Add a variable for Doxygen pre-processor definitions.

* Forgot to add the H5M API.

* Clarify the H5Z life cycle.

* Committing clang-format changes

* Add H5Zdevelop.h to Doxygen.in. Added H5I life cycle.

* Committing clang-format changes

* Clarified introduction and fixed missing label declaration.

* Added H5O life cycle.

* Committing clang-format changes

* H5O cleanup, part 1.

* Committing clang-format changes

* Cleaned up some of the endless repetition in H5O.

* Committing clang-format changes

* Cookbook & RFC draft layouts.

* Updated manifest.

* Updated the manifest, the example paths, and sketched the 1st recipe.

* Committing clang-format changes

* Outlined two more recipes.

* Committing clang-format changes

* More recipes and RFCs.

* Committing clang-format changes

* Draft of templatized RFC references.

* Another batch of RFC changes.

* Another batch of RFCs.

* Fixed reference.

* RFCs in reverse chronological order.

* First cut of RFCs.

* Fixed reference.

* Updated recipes.

* Updated recipes.

* More RFCs.

* Updated D*PL comments.

* Added H5P descriptions.

* Committing clang-format changes

* H5R life-cycle snapshot.

* Committing clang-format changes

* H5R life-cycle. Added line numbers to life-cycle examples.

* Committing clang-format changes

* Fixed formatting for H5Dchunk_iter().

* Added comment on collective mode requirement w/ compression.

* Simplified API compat. macro dox.

* More API vers. updates.

* Hide the async macro entrails.

* Latest VFD SWMR RFC.

* Create a tag file for permalinks.

* Added TODOs for metadoc.

* Removed duplication.

* Revised RM landing page.

* Trimmed more duplication.

* Committing clang-format changes

* Revised H5D.

* Committing clang-format changes

* Updated survey link.

* Added Doxygen RM entry template link.

* Added the "Multi-Thread HDF5" RFC.

* Added DOXYGEN_TAG_FILE.

* Added selection I/O RFC.

* Added the VFD Sub-filing RFC.

* Updated meta-documentation and added two old presentations.

* Added a few more RFCs (4).

* Fixed MANIFEST.

* Updated meta-documentation.

* Added Filters technical note.

* Fixed MANIFEST.

* Restore the path stripper.

* Experimental full-text search via Google.

* Better full-text search integration.

* Whoops. Forgot this one.

* Oh boy.

* Make CMake happy.

* Added "Debugging HDF5 Applications" technical note.

* Another batch of RFCs.

* Fixes for #1221.

* Updated overview.

* Fixed image dependencies.

* CMake updates.

* Fixed SET.

* Better?

* Update doxygen/dox/Overview.dox

* Fixed documentation errors. Added missing version info.

* Callback documentation updates.

* Fixed indexing errors in the outline.

* Doxygen-ized the HDF5 glossary.

* Fix a few minor typos
.

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>

3 files changed, 569 insertions, 7 deletions

diff --git a/doxygen/dox/About.dox b/doxygen/dox/About.dox
index 0b21fcc..a8b31d7 100644
--- a/doxygen/dox/About.dox
+++ b/doxygen/dox/About.dox
@@ -124,6 +124,4 @@ version.
 Talk to your friendly IT-team if you need write access, or you need someone to
 push an updated version for you!
 
-\todo Make the publication a GitHub action!
-
 */
\ No newline at end of file
diff --git a/doxygen/dox/Glossary.dox b/doxygen/dox/Glossary.dox
new file mode 100644
index 0000000..9ccd27d
--- /dev/null
+++ b/doxygen/dox/Glossary.dox
@@ -0,0 +1,565 @@
+/** \page GLS Glossary
+
+\section GLS_A A
+
+<DL>
+  <DT>Array datatype</DT>
+  <DD>A family of HDF5 datatypes whose elements are arrays of a fixed rank (≤
+  32) and fixed finite extent. All array elements must be of the same HDF5
+  datatype.</DD>
+</DL>
+
+<DL>
+  <DT>Array variable</DT>
+  <DD><P>A variable that can store (logically) dense, rectilinear, multidimensional
+      arrays of elements of a given HDF5 datatype.</P>
+    <P>The combination of array rank (dimensionality) and extent is called an
+    array variable's shape. This includes the degenerate array shapes of a
+    singleton (scalar) and the empty array (null).</P>
+    <P>The array element datatype is sometimes referred to as the array
+    variable's type, which is not entirely accurate because the array variable's
+    type is 'array of element type' rather than 'element type'.</P>
+    <P>In HDF5, there are two kinds of array variables, attributes and datasets,
+      and the distinction is functional (i.e., how they can be used) rather than
+      conceptual. Attributes are commonly used for descriptive "light-weight"
+      HDF5 object metadata while datasets are HDF5 objects used to store
+      "heavy-weight" problem-sized data.</P>
+  </DD>
+</DL>
+
+<DL>
+  <DT>Attribute</DT>
+  <DD><P>A named array variable that is associated with an HDF5 object, its
+      owner or attributee, and used to represent application domain-specific
+      metadata of the object. Intuitively, the set of an object's attributes can
+      be thought of as its key-value pair collection. Attribute names (keys) can
+      be arbitrary Unicode strings, but must be unique per object, i.e., an
+      object can have at most one attribute with a given name.</P>
+    <P>A scalar attribute is an attribute backed by a singleton array
+    variable. A null attribute is attribute backed by an empty array
+    variable.</P>
+</DD>
+</DL>
+
+\section GLS_B B
+
+<DL>
+  <DT>Bitfield datatype</DT>
+  <DD>A family of HDF5 datatypes whose elements are fixed-width bit fields.</DD>
+</DL>
+
+\section GLS_C C
+
+<DL>
+  <DT>Chunked layout</DT>
+  <DD>
+    <P>A dataset storage layout where the dataset elements are partitioned into
+      fixed-size multidimensional chunks or tiles. Chunked layout is mandatory
+      for datasets with one or more dimensions of indefinite (infinite) extent
+      or where compression or other filters are applied to the dataset elements.</P>
+    <P>Chunked layout may improve I/O performance for certain access patterns.</P>
+</DD>
+</DL>
+
+<DL>
+  <DT>Committed datatype</DT>
+  <DD>An immutable kind of HDF5 object that is used to store an HDF5 datatype
+  definition, which can be referenced by multiple array variables. When linked
+  to an HDF5 group, a committed datatype can be located by an HDF5 path name,
+  and is sometimes called a named datatype.</DD>
+</DL>
+
+<DL>
+  <DT>Compact layout</DT>
+  <DD></DD>
+</DL>
+
+<DL>
+  <DT>Compound datatype</DT>
+  <DD>
+    <P>A family of HDF5 datatypes whose elements are records with named fields
+    of other HDF5 datatypes. Currently, on ASCII field names are supported.</P>
+    <P>Similar to a <CODE>struct</CODE> in C or a <CODE>COMMON</CODE> block in
+    Fortran.</P>
+</DD>
+</DL>
+
+<DL>
+  <DT>Contiguous layout</DT>
+  <DD>A dataset storage layout where the dataset elements are physically stored
+  in an HDF5 file as a contiguous block of bytes.</DD>
+</DL>
+
+\section GLS_D D
+
+<DL>
+  <DT>Dataset</DT>
+  <DD>
+    <P>A kind of HDF5 object, a linked array variable. which can be located in
+      an HDF5 file through a path name. Datasets are commonly used to store
+      "heavy-weight" problem-sized data.</P>
+    <P>The HDF5 library offers a lot of features aimed at optimized dataset
+      access and storage, including compression and partial I/O.</P>
+</DD>
+</DL>
+
+<DL>
+  <DT>Dataspace</DT>
+  <DD>The shape of an array variable. With the exception of degenerate cases
+  (empty set, singleton), this is a rectilinear lattice or grid of a certain
+  rank (dimensionality) and extent.</DD>
+</DL>
+
+<DL>
+  <DT>Datatype</DT>
+  <DD>
+    <P>An HDF5 datatype consists of an abstract data type (a set of elements)
+    and a bit-level representation of these elements in storage such as an HDF5
+    file or memory.</P>
+    <P>The HDF5 library comes with a large set of predefined datatypes and
+    offers mechanisms for creating user-defined datatypes.</P>
+    <P>The ten major families or classes of HDF5 datatypes are:</P>
+    <UL>
+      <LI>Integer datatypes</LI>
+      <LI>Floating-point number datatypes</LI>
+      <LI>String datatypes</LI>
+      <LI>Bitfield datatypes</LI>
+      <LI>Opaque datatypes</LI>
+      <LI>Compound datatypes</LI>
+      <LI>Reference datatypes</LI>
+      <LI>Enumerated datatypes</LI>
+      <LI>Variable-length sequence datatypes</LI>
+      <LI>Array datatypes</LI>
+    </UL>
+</DD>
+</DL>
+
+\section GLS_E E
+
+<DL>
+  <DT>Enumeration datatype</DT>
+  <DD>A family of HDF5 datatypes whose elements represent named integer values
+  called members or enumerators. Currently, only ASCII names are supported.</DD>
+</DL>
+
+<DL>
+  <DT>External layout</DT>
+  <DD>A form of contiguous layout where a dataset's elements are physically
+  stored in unformatted binary files outside the HDF5 file.</DD>
+</DL>
+
+<DL>
+  <DT>External link</DT>
+  <DD>An HDF5 link whose destination is specified as a pair of an HDF5 file name
+and an HDF5 path name in that file.</DD>
+</DL>
+
+\section GLS_F F
+
+<DL>
+  <DT>Field</DT>
+  <DD>See compound datatype.</DD>
+</DL>
+
+<DL>
+  <DT>File</DT>
+  <DD>
+    <OL>
+      <LI>A byte stream (in a storage context such as a file system or in
+      memory) formatted according to the HDF5 File Format Specification.</LI>
+      <LI>A (logical) container for HDF5 objects.</LI>
+    </OL>
+  </DD>
+</DL>
+
+<DL>
+  <DT>File format</DT>
+  <DD></DD>
+</DL>
+
+<DL>
+  <DT>Fill value</DT>
+  <DD></DD>
+</DL>
+
+<DL>
+  <DT>Filter</DT>
+  <DD></DD>
+</DL>
+
+\section GLS_G G
+
+<DL>
+  <DT>Group</DT>
+  <DD>
+    <P>A kind of HDF5 object that stores a collection of HDF5 links. Each HDF5
+    file contains at least one group, it's root group.</P>
+    <P>Among the destinations of an HDF5 group's links may be other HDF5 groups
+    (including the group itself!). This ability is sometimes referred to as the
+    closure property of groups. It is the basis for creating hierarchical or
+    more general graph-like structures.</P>
+</DD>
+</DL>
+
+\section GLS_H H
+
+<DL>
+  <DT>Hard link</DT>
+  <DD>An HDF5 link whose destination is specified (internally) as the address of
+  an HDF5 object in the same HDF5 file.</DD>
+</DL>
+
+<DL>
+  <DT>Hierarchy</DT>
+  <DD>See group.</DD>
+</DL>
+
+<DL>
+  <DT>Hyperslab</DT>
+  <DD>
+    <P>A regular multidimensional pattern described by four vectors whose length
+    equals the rank of the pattern.</P>
+    <OL>
+      <LI><CODE>start</CODE> - the offset where the first block of the hyperslab begins</LI>
+      <LI><CODE>stride</CODE> - the offset between pattern blocks</LI>
+      <LI><CODE>count</CODE> - the number of blocks</LI>
+      <LI><CODE>block</CODE> - the extent of an individual pattern block</LI>
+    </OL>
+    <P>For example, the black squares on a (two-dimensional) chessboard with
+      origin at <CODE>(0,0)</CODE> can be represented as the union of two
+      hyperslabs representing the even <CODE>(0,2,4,6)</CODE> and
+      odd <CODE>(1,3,5,7)</CODE> rows, respectively.</P>
+    <IMG SRC="https://upload.wikimedia.org/wikipedia/commons/thumb/d/d7/Chessboard480.svg/176px-Chessboard480.svg.png"/>
+    <P>The hyperslab parameters for the even rows are: <CODE>start (0,0)</CODE>,
+      <CODE>stride (2,2)</CODE>, <CODE>count (4,4)</CODE>, <CODE>block
+        (1,1)</CODE>. Likewise the parameters for the odd rows are: <CODE>start
+        (1,1)</CODE>, <CODE>stride (2,2)</CODE>, <CODE>count
+        (4,4)</CODE>, <CODE>block (1,1)</CODE>.</P>
+</DD>
+</DL>
+
+\section GLS_I I
+
+<DL>
+  <DT>Identifier</DT>
+  <DD>An opaque, transient handle used by the HDF5 library to manipulate
+  in-memory representations of HDF5 items.</DD>
+</DL>
+
+\section GLS_L L
+
+<DL>
+  <DT>Library</DT>
+  <DD></DD>
+</DL>
+
+<DL>
+  <DT>Link</DT>
+  <DD>
+    <P>A named, uni-directional association between a source and a
+    destination. In HDF5, the source is always the HDF5 group that hosts the
+    link in its link collection.</P>
+    <P>There are several ways to specify a link's destination:</P>
+    <UL>
+      <LI>The address of an HDF5 object in the same HDF5 file; so-called hard
+      link.</LI>
+      <LI>A path name in the same or a different file; so-called soft or
+      external link.</LI>
+      <LI>User-defined</LI>
+    </UL>
+    <P>A link name can be any Unicode string that does not contain slashes
+      (<CODE>"/"</CODE>) or consists of a single dot character
+      (<CODE>"."</CODE>). A link name must be unique in a group's link
+      collection.</P>
+  </DD>
+</DL>
+
+\section GLS_M M
+
+<DL>
+  <DT>Metadata</DT>
+  <DD>Data that in a given context has a descriptive or documentation function
+  for other data. Typically, the metadata is small compared to the data it
+  describes.</DD>
+</DL>
+
+<DL>
+  <DT>Member</DT>
+  <DD>
+    <P>A link destination is sometimes referred to as a member of the link's
+    source (group). This way of speaking invites confusion: A destination (e.g.,
+    object) can be the destination of multiple links in the same (!) or
+    different groups. It would then be a "member" of a given group with
+    multiplicity greater than one and be a member of multiple groups.</P>
+    <P> It is the link that is a member of the group's link collection and not
+    the link destination.</P>
+  </DD>
+</DL>
+
+\section GLS_N N
+
+<DL>
+  <DT>Name</DT>
+  <DD>
+    <P>A Unicode string that depending on the item it names might be subject to
+    certain character restrictions, such as ASCII-encoded only. In HDF5, the
+    user might encounter the following names:</P>
+    <UL>
+      <LI>A link name</LI>
+      <LI>A path name</LI>
+      <LI>An attribute name</LI>
+      <LI>A field name (compound datatypes)</LI>
+      <LI>A constant name (enumeration datatypes)</LI>
+      <LI>A tag name (opaque datatypes)</LI>
+      <LI>A file name</LI>
+    </UL>
+  </DD>
+</DL>
+
+
+<DL>
+  <DT>Named datatype</DT>
+  <DD>See committed datatype.</DD>
+</DL>
+
+<DL>
+  <DT>Null dataspace</DT>
+  <DD>A shape which represents the empty set. Array variables with this shape
+  cannot store any values.</DD>
+</DL>
+
+\section GLS_O O
+
+<DL>
+  <DT>Object</DT>
+  <DD>An HDF5 group, dataset or named datatype; an HDF5 item that can be linked
+  to zero or more groups and decorated with zero or more HDF5 attributes.</DD>
+</DL>
+
+<DL>
+  <DT>Object reference</DT>
+  <DD>
+    <OL>
+      <LI>A datatype for representing references to objects in a file.</LI>
+      <LI>A value of the object reference datatype.</LI>
+    </OL>
+  </DD>
+</DL>
+
+<DL>
+  <DT>Opaque datatype</DT>
+  <DD>A family of HDF5 datatypes whose elements are byte sequences of a given
+  fixed length. An opaque datatype can be tagged with a sequence of up to 256
+  ASCII characters, e.g., MIME code.</DD>
+</DL>
+
+\section GLS_P P
+
+<DL>
+  <DT>Path name</DT>
+  <DD>A Unicode string that is the concatenation of link names separated by
+    slashes (<CODE>'/'</CODE>). In HDF5, path names are used to locate and refer
+    to HDF5 objects.</DD>
+</DL>
+
+<DL>
+  <DT>Plugin</DT>
+  <DD>An HDF5 library feature or capability that can be added dynamically at
+    application run time rather than library compilation time. Plugins are
+    usually implemented as shared libraries, and their discovery and loading
+    behavior can be controlled programmatically or through environment
+    variables.
+  </DD>
+</DL>
+
+<DL>
+  <DT>Point selection</DT>
+  <DD>A dataspace selection that consists of a set of points (coordinates) in
+  the same dataspace.</DD>
+</DL>
+
+<DL>
+  <DT>Property list</DT>
+  <DD>
+    <P>An HDF5 API construct, a means of customizing the behavior of the HDF5
+    library when creating, accessing or modifying HDF5 items.</P>
+    <P>While the default property settings are sufficient in many cases, certain
+    HDF5 features, such as compression, can be reasonably controlled only by the
+    user who has to provide the desired settings via property lists.</P>
+</DD>
+</DL>
+
+\section GLS_R R
+
+<DL>
+  <DT>Rank</DT>
+  <DD>The number of dimensions of a non-null dataspace.</DD>
+</DL>
+
+<DL>
+  <DT>Reference</DT>
+  <DD>
+    <OL>
+      <LI>An HDF5 object reference</LI>
+      <LI>An HDF5 dataset region reference</LI>
+    </OL>
+  </DD>
+</DL>
+
+<DL>
+  <DT>Reference datatype</DT>
+  <DD>
+    <OL>
+      <LI>An HDF5 datatype whose elements represent references to HDF5
+      objects.</LI>
+      <LI>An HDF5 datatype whose elements represent references to regions of an
+      HDF5 dataset.</LI>
+    </OL>
+  </DD>
+</DL>
+
+<DL>
+  <DT>Region reference</DT>
+  <DD>See dataset region reference.</DD>
+</DL>
+
+<DL>
+  <DT>Root group</DT>
+  <DD>
+    <P>An HDF5 group that is present in all HDF5 files and that acts as the
+    entry or base point for all other data stored in an HDF5 file.</P>
+    <P>The root group is "the mother of all objects" in an HDF5 file in the
+    sense that all objects (and their attributes) can be discovered,
+    beginning at the root group, by combinations of the following
+    operations:</P>
+    <UL>
+      <LI>Link traversal</LI>
+      <LI>De-referencing of object references</LI>
+    </UL>
+    <P>This discovery is portable and robust with respect to file-internal
+    storage reorganization.</P>
+</DD>
+</DL>
+
+\section GLS_S S
+
+<DL>
+  <DT>Scalar dataspace</DT>
+  <DD>A kind of HDF5 dataspace that has the shape of a singleton, i.e., a set
+  containing a single element. Array variables with this shape store exactly one
+  element.</DD>
+</DL>
+
+<DL>
+  <DT>Selection</DT>
+  <DD>
+    <OL>
+      <LI>A subset of points of an HDF5 dataspace. The subset might be a point
+        selection or a combination (union, intersection, etc.) of hyperslabs.</LI>
+      <LI>A subset of dataset elements associated with a dataspace selection as
+      described under 1.</LI>
+    </OL>
+  </DD>
+</DL>
+
+<DL>
+  <DT>Serialization</DT>
+  <DD>
+    <OL>
+      <LI>The flattening of an N-dimensional array into a 1-dimensional
+        array.</LI>
+      <LI>The encoding of a complex data item as a linear byte stream.</LI>
+    </OL>
+  </DD>
+</DL>
+
+<DL>
+  <DT>Soft link</DT>
+  <DD>A kind of HDF5 link in which the link destination is specified as an HDF5
+  path name. The path name may or may not refer to an actual object.</DD>
+</DL>
+
+<DL>
+  <DT>Storage layout</DT>
+  <DD>The storage arrangement for dataset elements, links in a group's link
+  collection, or attributes in an object's attribute collection.</DD>
+</DL>
+
+<DL>
+  <DT>String datatype</DT>
+  <DD></DD>
+</DL>
+
+<DL>
+  <DT>Super block</DT>
+  <DD>An HDF5 file format primitive; a block of data which contains information
+  required to access HDF5 files in a portable manner on multiple platforms. The
+  super block contains information such as version numbers, the size of offsets
+  and lengths, and the location of the root group.</DD>
+</DL>
+
+<DL>
+  <DT>SWMR</DT>
+  <DD>Single Writer Multiple Reader, a file access mode in which a single
+  process is permitted to write data to an HDF5 file while other processes are
+  permitted to read data from the same file without the need of inter-process
+  communication or synchronization.</DD>
+</DL>
+
+<DL>
+  <DT>Symbolic link</DT>
+  <DD>An external link or a soft link.</DD>
+</DL>
+
+\section GLS_U U
+
+<DL>
+  <DT>User block</DT>
+  <DD>An HDF5 file format primitive that allows one to set aside a fixed-size
+  (at least 512 bytes or any power of 2 thereafter) contiguous range of bytes at
+  the beginning of an HDF5 file for application purposes which will be
+  skipped/ignored by the HDF5 library.</DD>
+</DL>
+
+<DL>
+  <DT>UTF-8</DT>
+  <DD>
+    <P>A variable-length (1-4 bytes per code point) encoding of the Unicode set
+    of code points. This is the encoding supported by HDF5 to represent Unicode
+    strings.</P>
+    <P>The ASCII encoding is a proper subset of UTF-8.</P>
+</DD>
+</DL>
+
+\section GLS_V V
+
+<DL>
+  <DT>Variable-length (sequence) datatype</DT>
+  <DD>A family of HDF5 datatypes whose elements are variable-length sequences of
+  a given datatype.</DD>
+</DL>
+
+<DL>
+  <DT>Virtual Dataset (VDS)</DT>
+  <DD>An HDF5 dataset with virtual storage layout. A dataset whose elements are
+  partially or entirely stored physically in other datasets.</DD>
+</DL>
+
+<DL>
+  <DT>Virtual File Driver (VFD)</DT>
+  <DD></DD>
+</DL>
+
+
+<DL>
+  <DT>Virtual layout</DT>
+  <DD></DD>
+</DL>
+
+
+<DL>
+  <DT>Virtual Object Layer (VOL)</DT>
+  <DD></DD>
+</DL>
+
+*/
diff --git a/doxygen/dox/Overview.dox b/doxygen/dox/Overview.dox
index e9c52c2..040769c 100644
--- a/doxygen/dox/Overview.dox
+++ b/doxygen/dox/Overview.dox
@@ -1,9 +1,8 @@
 
 /** \mainpage notitle
 
-This is the documentation set for HDF5. You can
-<a href="hdf5-doc.tgz">download</a> it as a tgz archive for offline reading.
-This documentation includes specifications and documentation
+This is the documentation set for HDF5.
+It includes specifications and documentation
 of software and tools developed and maintained by
 <a href="https://www.hdfgroup.org/">The HDF Group</a>. It is impractical to document
 the entire HDF5 ecosystem in one place, and you should also consult the documentation
@@ -38,8 +37,8 @@ documents cover a mix of tasks, concepts, and reference, to help a specific
      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://hdfgroup.github.io/archive/hdf5doc/">here</a>.
+     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>.