Missing or misplaced entries in API reference tables #2470 (#2472)

* Missing or misplaced entries in API reference tables #2470

* Doxy corrections

3 files changed, 208 insertions, 65 deletions

diff --git a/doxygen/dox/Overview.dox b/doxygen/dox/Overview.dox
index 3d171f7..fb6231c 100644
--- a/doxygen/dox/Overview.dox
+++ b/doxygen/dox/Overview.dox
@@ -37,10 +37,6 @@ 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/examples/tables/propertyLists.dox b/doxygen/examples/tables/propertyLists.dox
index 498a820..375fd50 100644
--- a/doxygen/examples/tables/propertyLists.dox
+++ b/doxygen/examples/tables/propertyLists.dox
@@ -86,7 +86,7 @@
 <td>Iterates over properties in a property class or list</td>
 </tr>
 <tr>
-<td>#H5Pregister/H5Punregister</td>
+<td>#H5Pregister/#H5Punregister</td>
 <td>Registers/removes a permanent property with/from a property list class</td>
 </tr>
 <tr>
@@ -124,14 +124,6 @@
 <td>Sets/retrieves size of parameter used to control B-trees for indexing chunked datasets.</td>
 </tr>
 <tr>
-<td>#H5Pset_file_image</td>
-<td>Sets an initial file image in a memory buffer.</td>
-</tr>
-<tr>
-<td>#H5Pget_file_image</td>
-<td>Retrieves a copy of the file image designated as the initial content and structure of a file.</td>
-</tr>
-<tr>
 <td>#H5Pset_file_space_page_size/#H5Pget_file_space_page_size</td>
 <td>Sets or retrieves the file space page size used in paged aggregation and paged buffering.</td>
 </tr>
@@ -179,11 +171,19 @@ creation property list.</td>
 <td>Sets/retrieves metadata cache and raw data chunk cache parameters.</td>
 </tr>
 <tr>
+<td>#H5Pset_core_write_tracking/#H5Pget_core_write_tracking</td>
+<td>Sets/retrieves write tracking information for core driver.</td>
+</tr>
+<tr>
 <td>#H5Pset_elink_file_cache_size/#H5Pget_elink_file_cache_size</td>
 <td>Sets/retrieves the size of the external link open file cache from the specified
 file access property list.</td>
 </tr>
 <tr>
+<td>#H5Pset_evict_on_close/#H5Pget_evict_on_close</td>
+<td>Set/get the file access property list setting that determines whether an HDF5 object will be evicted from the library's metadata cache when it is closed.</td>
+</tr>
+<tr>
 <td>#H5Pset_gc_references/#H5Pget_gc_references</td>
 <td>Sets/retrieves garbage collecting references flag.</td>
 </tr>
@@ -196,18 +196,56 @@ file access property list.</td>
 <td>Retrieves a data offset from the file access property list.</td>
 </tr>
 <tr>
+<td>#H5Pset_fclose_degree/#H5Pget_fclose_degree</td>
+<td>Sets/retrieves file close degree property.</td>
+</tr>
+<tr>
+<td>#H5Pset_file_image</td>
+<td>Sets an initial file image in a memory buffer.</td>
+</tr>
+<tr>
+<td>#H5Pget_file_image</td>
+<td>Retrieves a copy of the file image designated as the initial content and structure of a file.</td>
+</tr>
+<tr>
+<td>#H5Pset_file_image_callbacks/#H5Pget_file_image_callbacks</td>
+<td>Sets/gets the callbacks for working with file images.</td>
+</tr>
+<tr>
+<td>#H5Pset_file_locking/#H5Pget_file_locking</td>
+<td>Sets/retrieves file locking property values.</td>
+</tr>
+<tr>
 <td>#H5Pset_meta_block_size/#H5Pget_meta_block_size</td>
 <td>Sets the minimum metadata blocksize or retrieves the current metadata block size setting.</td>
 </tr>
 <tr>
-<td>#H5Pset_mdc_config</td>
-<td>Set the initial metadata cache configuration in the indicated File Access Property List
-to the supplied value.</td>
+<td>#H5Pset_metadata_read_attempts/#H5Pget_metadata_read_attempts</td>
+<td>Sets/gets the number of read attempts from a file access property list.</td>
+</tr>
+<tr>
+<td>#H5Pset_mdc_config/#H5Pget_mdc_config</td>
+<td>Set/get the initial metadata cache configuration in the indicated file access property list.</td>
+</tr>
+<tr>
+<td>#H5Pset_mdc_image_config/#H5Pget_mdc_image_config</td>
+<td>Set/get the metadata cache image option for a file access property list.</td>
+</tr>
+<tr>
+<td>#H5Pset_mdc_log_options/#H5Pget_mdc_log_options</td>
+<td>Set/get the metadata cache logging options.</td>
+</tr>
+<tr>
+<td>#H5Pset_multi_type/#H5Pget_multi_type</td>
+<td>Sets/gets the type of data property for the MULTI driver.</td>
+</tr>
+<tr>
+<td>#H5Pset_object_flush_cb/#H5Pget_object_flush_cb</td>
+<td>Set/get the object flush property values from the file access property list.</td>
 </tr>
 <tr>
-<td>#H5Pget_mdc_config</td>
-<td>Get the current initial metadata cache config-uration from the indicated File Access
-Property List.</td>
+<td>#H5Pset_page_buffer_size/#H5Pget_page_buffer_size</td>
+<td>Set/get the the maximum size for the page buffer.</td>
 </tr>
 <tr>
 <td>#H5Pset_sieve_buf_size/#H5Pget_sieve_buf_size</td>
@@ -231,6 +269,30 @@ versions used when creating objects.</td>
 <td>#H5Pget_small_data_block_size</td>
 <td>Retrieves the current small data block size setting.</td>
 </tr>
+<tr>
+<td>#H5Pset_vol</td>
+<td>Sets the file VOL connector for a file access property list.</td>
+</tr>
+<tr>
+<td>#H5Pget_vol_cap_flags</td>
+<td>Retrieves the capability flags for the VOL connector that will be used with a file access property list.</td>
+</tr>
+<tr>
+<td>#H5Pget_vol_id</td>
+<td>Retrieves the identifier of the current VOL connector.</td>
+</tr>
+<tr>
+<td>#H5Pget_vol_info</td>
+<td>Retrieves a copy of the VOL information for a connector.</td>
+</tr>
+<tr>
+<td>#H5Pset_mpi_params/#H5Pget_mpi_params</td>
+<td>Sets/retrieves the MPI communicator and info.</td>
+</tr>
+<tr>
+<td>#H5Pset_coll_metadata_write/#H5Pget_coll_metadata_write</td>
+<td>Sets/retrieves metadata write mode setting.</td>
+</tr>
 </table>
 //! [fapl_table]
  *
@@ -254,6 +316,18 @@ versions used when creating objects.</td>
 <td>Returns a pointer to file driver information.</td>
 </tr>
 <tr>
+<td>#H5Pset_driver_by_name</td>
+<td>Sets a file driver according to a given driver name.</td>
+</tr>
+<tr>
+<td>#H5Pset_driver_by_value</td>
+<td>Sets a file driver according to a given driver value.</td>
+</tr>
+<tr>
+<td>#H5Pget_driver_config_str</td>
+<td>Retrieves a string representation of the configuration for the driver.</td>
+</tr>
+<tr>
 <td>#H5Pset_fapl_core/#H5Pget_fapl_core</td>
 <td>Sets the driver for buffered memory files (in RAM) or retrieves information regarding
 the driver.</td>
@@ -268,10 +342,22 @@ the driver.</td>
 larger than 2 gigabytes, or retrieves information regarding driver.</td>
 </tr>
 <tr>
+<td>#H5Pset_fapl_hdfs/#H5Pget_fapl_hdfs</td>
+<td>.</td>
+</tr>
+<tr>
+<td>#H5Pset_fapl_ioc/#H5Pget_fapl_ioc</td>
+<td>Modifies/queries the file driver properties of the I/O concentrator driver.</td>
+</tr>
+<tr>
 <td>#H5Pset_fapl_log</td>
 <td>Sets logging driver.</td>
 </tr>
 <tr>
+<td>#H5Pset_fapl_mirror/#H5Pget_fapl_mirror</td>
+<td>Modifies/queries the file driver properties of the mirror driver.</td>
+</tr>
+<tr>
 <td>#H5Pset_fapl_mpio/#H5Pget_fapl_mpio</td>
 <td>Sets driver for files on parallel file systems (MPI I/O) or retrieves information
 regarding the driver.</td>
@@ -286,6 +372,10 @@ regarding the driver.</td>
 or retrieves information regarding driver.</td>
 </tr>
 <tr>
+<td>#H5Pset_fapl_onion/#H5Pget_fapl_onion</td>
+<td>Modifies/queries the file driver properties of the onion driver.</td>
+</tr>
+<tr>
 <td>#H5Pset_fapl_sec2</td>
 <td>Sets driver for unbuffered permanent files or retrieves information regarding driver.</td>
 </tr>
@@ -299,6 +389,10 @@ and one raw data file.</td>
 <td>Sets driver for buffered permanent files.</td>
 </tr>
 <tr>
+<td>#H5Pset_fapl_subfiling/#H5Pget_fapl_subfiling</td>
+<td>Modifies/queries the file driver properties of the subfiling driver.</td>
+</tr>
+<tr>
 <td>#H5Pset_fapl_windows</td>
 <td>Sets the Windows I/O driver.</td>
 </tr>
@@ -337,6 +431,10 @@ and one raw data file.</td>
 <td>Retrieves the size of chunks for the raw data of a chunked layout dataset.</td>
 </tr>
 <tr>
+<td>#H5Pset_chunk_opts/#H5Pget_chunk_opts</td>
+<td>Sets/gets the edge chunk option setting from a dataset creation property list.</td>
+</tr>
+<tr>
 <td>#H5Pset_deflate</td>
 <td>Sets compression method and compression level.</td>
 </tr>
@@ -439,6 +537,34 @@ encoding for object names.</td>
 <td>#H5Pget_char_encoding</td>
 <td>Retrieves the character encoding used to create a string.</td>
 </tr>
+<tr>
+<td>#H5Pset_virtual</td>
+<td>Sets the mapping between virtual and source datasets.</td>
+</tr>
+<tr>
+<td>#H5Pget_virtual_count</td>
+<td>Gets the number of mappings for the virtual dataset.</td>
+</tr>
+<tr>
+<td>#H5Pget_virtual_dsetname</td>
+<td>Gets the name of a source dataset used in the mapping.</td>
+</tr>
+<tr>
+<td>#H5Pget_virtual_filename</td>
+<td>Gets the filename of a source dataset used in the mapping.</td>
+</tr>
+<tr>
+<td>#H5Pget_virtual_srcspace</td>
+<td>Gets a dataspace identifier for the selection within the source dataset used in the mapping.</td>
+</tr>
+<tr>
+<td>#H5Pget_virtual_vspace</td>
+<td>Gets a dataspace identifier for the selection within the virtual dataset used in the mapping.</td>
+</tr>
+<tr>
+<td>#H5Pset_dset_no_attrs_hint/#H5Pget_dset_no_attrs_hint</td>
+<td>Sets/gets the flag to create minimized dataset object headers.</td>
+</tr>
 </table>
 //! [dcpl_table]
  *
@@ -458,32 +584,77 @@ encoding for object names.</td>
 <td>Reads buffer settings.</td>
 </tr>
 <tr>
+<td>#H5Pset_append_flush/#H5Pget_append_flush</td>
+<td>Sets/gets the values of the append property that is set up in the dataset access property list.</td>
+</tr>
+<tr>
 <td>#H5Pset_chunk_cache/#H5Pget_chunk_cache</td>
 <td>Sets/gets the raw data chunk cache parameters.</td>
 </tr>
 <tr>
-<td>#H5Pset_edc_check/#H5Pget_edc_check</td>
-<td>Sets/gets whether to enable error-detection when reading a dataset.</td>
+<td>#H5Pset_efile_prefix/#H5Pget_efile_prefix</td>
+<td>Sets/gets the prefix for external raw data storage files as set in the dataset access property list.</td>
 </tr>
 <tr>
-<td>#H5Pset_filter_callback</td>
-<td>Sets user-defined filter callback function.</td>
+<td>#H5Pset_virtual_prefix/#H5Pget_virtual_prefix</td>
+<td>Sets/gets the prefix to be applied to VDS source file paths.</td>
+</tr>
+<tr>
+<td>#H5Pset_virtual_printf_gap/#H5Pget_virtual_printf_gap</td>
+<td>Sets/gets the maximum number of missing source files and/or datasets with the printf-style names when getting the extent for an unlimited virtual dataset.</td>
+</tr>
+<tr>
+<td>#H5Pset_virtual_view/#H5Pget_virtual_view</td>
+<td>Sets/gets the view of the virtual dataset (VDS) to include or exclude missing mapped elements.</td>
+</tr>
+</table>
+//! [dapl_table]
+ *
+//! [dxpl_table]
+<table>
+<caption id="table_dxpl_id" border="1" style="background-color:whitesmoke;">Data transfer property list functions (H5P)</caption>
+<tr>
+<th>C Function</th>
+<th>Purpose</th>
+</tr>
+<tr>
+<td>#H5Pset_btree_ratios/#H5Pget_btree_ratios</td>
+<td>Sets/gets B-tree split ratios for a dataset transfer property list.</td>
+</tr>
+<tr>
+<td>#H5Pset_buffer</td>
+<td>Maximum size for the type conversion buffer and the background buffer. May also supply
+pointers to application-allocated buffers.</td>
 </tr>
 <tr>
 <td>#H5Pset_data_transform/#H5Pget_data_transform</td>
 <td>Sets/gets a data transform expression.</td>
 </tr>
 <tr>
-<td>#H5Pset_type_conv_cb/#H5Pget_type_conv_cb</td>
-<td>Sets/gets user-defined datatype conversion callback function.</td>
+<td>#H5Pset_dataset_io_hyperslab_selection</td>
+<td>Sets a hyperslab file selection for a dataset I/O operation.</td>
+</tr>
+<tr>
+<td>#H5Pset_edc_check/#H5Pget_edc_check</td>
+<td>Sets/gets whether to enable error-detection when reading a dataset.</td>
+</tr>
+<tr>
+<td>#H5Pset_hyper_vector_size</td>
+<td>set the number of "I/O vectors" (offset and length pairs) which are to be
+accumulated in memory before being issued to the lower levels
+of the library for reading or writing the actual data.</td>
+</tr>
+<tr>
+<td>#H5Pset_filter_callback</td>
+<td>Sets user-defined filter callback function.</td>
 </tr>
 <tr>
 <td>#H5Pset_hyper_vector_size/#H5Pget_hyper_vector_size</td>
 <td>Sets/gets number of I/O vectors to be read/written in hyperslab I/O.</td>
 </tr>
 <tr>
-<td>#H5Pset_btree_ratios/#H5Pget_btree_ratios</td>
-<td>Sets/gets B-tree split ratios for a dataset transfer property list.</td>
+<td>#H5Pset_type_conv_cb/#H5Pget_type_conv_cb</td>
+<td>Sets/gets user-defined datatype conversion callback function.</td>
 </tr>
 <tr>
 <td>#H5Pset_vlen_mem_manager/#H5Pget_vlen_mem_manager</td>
@@ -511,38 +682,20 @@ encoding for object names.</td>
 <td>Sets a flag governing the use of independent versus collective I/O.</td>
 </tr>
 <tr>
-<td>#H5Pset_multi_type/#H5Pget_multi_type</td>
-<td>Sets/gets the type of data property for the MULTI driver.</td>
-</tr>
-<tr>
-<td>#H5Pset_small_data_block_size/#H5Pget_small_data_block_size</td>
-<td>Sets/gets the size of a contiguous block reserved for small data.</td>
-</tr>
-</table>
-//! [dapl_table]
- *
-//! [dxpl_table]
-<table>
-<caption id="table_dxpl_id" border="1" style="background-color:whitesmoke;">Data transfer property list functions (H5P)</caption>
-<tr>
-<th>C Function</th>
-<th>Purpose</th>
+<td>#H5Pget_mpio_actual_chunk_opt_mode</td>
+<td>Gets the type of chunk optimization that HDF5 actually performed on the last parallel I/O call.</td>
 </tr>
 <tr>
-<td>#H5Pset_buffer</td>
-<td>Maximum size for the type conversion buffer and the background buffer. May also supply
-pointers to application-allocated buffers.</td>
+<td>#H5Pget_mpio_actual_io_mode</td>
+<td>Gets the type of I/O that HDF5 actually performed on the last parallel I/O call.</td>
 </tr>
 <tr>
-<td>#H5Pset_hyper_vector_size</td>
-<td>set the number of "I/O vectors" (offset and length pairs) which are to be
-accumulated in memory before being issued to the lower levels
-of the library for reading or writing the actual data.</td>
+<td>#H5Pget_mpio_no_collective_cause</td>
+<td>Gets local and global causes that broke collective I/O on the last parallel I/O call.</td>
 </tr>
 <tr>
-<td>#H5Pset_btree_ratios</td>
-<td>Set the B-tree split ratios for a dataset transfer property list. The split ratios determine
-what percent of children go in the first node when a node splits.</td>
+<td>H5Pset_preserve/H5Pget_preserve</td>
+<td>No longer available, deprecated as it no longer has any effect.</td>
 </tr>
 </table>
 //! [dxpl_table]
@@ -593,6 +746,10 @@ C function is a macro: \see \ref api-compat-macros.</td>
 <td>Sets up use of the Fletcher32 checksum filter.</td>
 </tr>
 <tr>
+<td>#H5Pset_local_heap_size_hint#H5Pget_local_heap_size_hint/</td>
+<td>Sets/gets the anticipated maximum size of a local heap.</td>
+</tr>
+<tr>
 <td>#H5Pset_link_phase_change</td>
 <td>Sets the parameters for conversion between compact and dense groups.</td>
 </tr>
@@ -625,14 +782,6 @@ C function is a macro: \see \ref api-compat-macros.</td>
 <td>Queries whether link creation order is tracked and/or indexed in a group.</td>
 </tr>
 <tr>
-<td>#H5Pset_create_intermediate_group</td>
-<td>Specifies in the property list whether to create missing intermediate groups.</td>
-</tr>
-<tr>
-<td>#H5Pget_create_intermediate_group</td>
-<td>Determines whether the property is set to enable creating missing intermediate groups.</td>
-</tr>
-<tr>
 <td>#H5Pset_char_encoding</td>
 <td>Sets the character encoding used to encode a string. Use to set ASCII or UTF-8 character
 encoding for object names.</td>
@@ -771,10 +920,6 @@ encoding for object names.</td>
 <td>#H5Pset_char_encoding/#H5Pget_char_encoding</td>
 <td>Sets/gets the character encoding used to encode link and attribute names.</td>
 </tr>
-<tr>
-<td>#H5Pset_create_intermediate_group/#H5Pget_create_intermediate_group</td>
-<td>Specifies/retrieves whether to create missing intermediate groups.</td>
-</tr>
 </table>
 //! [strcpl_table]
  *
diff --git a/src/H5Pmodule.h b/src/H5Pmodule.h
index 38d06e2..f2a1e5a 100644
--- a/src/H5Pmodule.h
+++ b/src/H5Pmodule.h
@@ -904,6 +904,7 @@
  *
  * \ref PLCR
  * \snippet{doc} tables/propertyLists.dox fapl_table
+ * \snippet{doc} tables/propertyLists.dox fd_pl_table
  *
  * \ref PLCR
  * \snippet{doc} tables/propertyLists.dox lapl_table
@@ -1007,6 +1008,7 @@
  * can be adjusted at runtime before a file is created or opened.
  *
  * \snippet{doc} tables/propertyLists.dox fapl_table
+ * \snippet{doc} tables/propertyLists.dox fd_pl_table
  *
  * \defgroup FCPL File Creation Properties
  * \ingroup GCPL