Fixed minor issues. (#1257)

* Fixed minor issues.

* Whoops. Forgot to commit these.

* CMake update.

* One more time.

11 files changed, 13 insertions, 16 deletions

diff --git a/MANIFEST b/MANIFEST
index bfb062e..ecf69a3 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -280,6 +280,9 @@
 ./doxygen/img/FF-IH_FileObject.gif
 ./doxygen/img/FileFormatSpecChunkDiagram.jpg
 ./doxygen/img/HDFG-logo.png
+./doxygen/img/IOFlow.gif
+./doxygen/img/IOFlow2.gif
+./doxygen/img/IOFlow3.gif
 ./doxygen/img/PaletteExample1.gif
 ./doxygen/img/Palettes.fm.anc.gif
 ./doxygen/img/ftv2node.png
diff --git a/configure.ac b/configure.ac
index e5cc5df..b3b7fe5 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1198,7 +1198,7 @@ if test "X$HDF5_DOXYGEN" = "Xyes"; then
   DOXYGEN_HTML_HEADER='$(SRCDIR)/doxygen/hdf5_header.html'
   DOXYGEN_HTML_FOOTER='$(SRCDIR)/doxygen/hdf5_footer.html'
   DOXYGEN_HTML_EXTRA_STYLESHEET='$(SRCDIR)/doxygen/hdf5doxy.css'
-  DOXYGEN_HTML_EXTRA_FILES='$(SRCDIR)/doxygen/hdf5_navtree_hacks.js $(SRCDIR)/doxygen/img/ftv2node.png $(SRCDIR)/doxygen/img/ftv2pnode.png'
+  DOXYGEN_HTML_EXTRA_FILES='$(SRCDIR)/doxygen/hdf5_navtree_hacks.js $(SRCDIR)/doxygen/img/FF-IH_FileGroup.gif $(SRCDIR)/doxygen/img/FF-IH_FileObject.gif $(SRCDIR)/doxygen/img/FileFormatSpecChunkDiagram.jpg $(SRCDIR)/doxygen/img/ftv2node.png $(SRCDIR)/doxygen/img/ftv2pnode.png $(SRCDIR)/doxygen/img/HDFG-logo.png $(SRCDIR)/doxygen/img/IOFlow2.gif $(SRCDIR)/doxygen/img/IOFlow3.gif $(SRCDIR)/doxygen/img/IOFlow.gif $(SRCDIR)/doxygen/img/PaletteExample1.gif $(SRCDIR)/doxygen/img/Palettes.fm.anc.gif'
   DOXYGEN_TAG_FILE=hdf5.tag
   DOXYGEN_SERVER_BASED_SEARCH=NO
   DOXYGEN_EXTERNAL_SEARCH=NO
diff --git a/doxygen/CMakeLists.txt b/doxygen/CMakeLists.txt
index 36ce590..ca36ef1 100644
--- a/doxygen/CMakeLists.txt
+++ b/doxygen/CMakeLists.txt
@@ -21,7 +21,7 @@ if (DOXYGEN_FOUND)
   set (DOXYGEN_HTML_HEADER ${HDF5_DOXYGEN_DIR}/hdf5_header.html)
   set (DOXYGEN_HTML_FOOTER ${HDF5_DOXYGEN_DIR}/hdf5_footer.html)
   set (DOXYGEN_HTML_EXTRA_STYLESHEET ${HDF5_DOXYGEN_DIR}/hdf5doxy.css)
-  set (DOXYGEN_HTML_EXTRA_FILES "${HDF5_DOXYGEN_DIR}/hdf5_navtree_hacks.js ${HDF5_DOXYGEN_DIR}/img/ftv2node.png ${HDF5_DOXYGEN_DIR}/img/ftv2pnode.png")
+  set (DOXYGEN_HTML_EXTRA_FILES "${HDF5_DOXYGEN_DIR}/hdf5_navtree_hacks.js ${HDF5_DOXYGEN_DIR}/img/FF-IH_FileGroup.gif ${HDF5_DOXYGEN_DIR}/img/FF-IH_FileObject.gif ${HDF5_DOXYGEN_DIR}/img/FileFormatSpecChunkDiagram.jpg ${HDF5_DOXYGEN_DIR}/img/ftv2node.png ${HDF5_DOXYGEN_DIR}/img/ftv2pnode.png ${HDF5_DOXYGEN_DIR}/img/HDFG-logo.png ${HDF5_DOXYGEN_DIR}/img/IOFlow2.gif ${HDF5_DOXYGEN_DIR}/img/IOFlow3.gif ${HDF5_DOXYGEN_DIR}/img/IOFlow.gif ${HDF5_DOXYGEN_DIR}/img/PaletteExample1.gif ${HDF5_DOXYGEN_DIR}/img/Palettes.fm.anc.gif")
   set (DOXYGEN_TAG_FILE ${HDF5_BINARY_DIR}/hdf5.tag)
   set (DOXYGEN_SERVER_BASED_SEARCH NO)
   set (DOXYGEN_EXTERNAL_SEARCH NO)
diff --git a/doxygen/dox/ReferenceManual.dox b/doxygen/dox/ReferenceManual.dox
index cc0f99b..53f64a7 100644
--- a/doxygen/dox/ReferenceManual.dox
+++ b/doxygen/dox/ReferenceManual.dox
@@ -15,7 +15,6 @@ The functions provided by the HDF5 C-API are grouped into the following
 \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)"
@@ -23,14 +22,11 @@ The functions provided by the HDF5 C-API are grouped into the following
 \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;vertical-align: top;">
-\li Functions with \ref ASYNC "asynchronous variants"
 \li \ref api-compat-macros
 \li <a href="./deprecated.html">Deprecated functions</a>
 \li High-level Extensions
@@ -43,8 +39,8 @@ The functions provided by the HDF5 C-API are grouped into the following
     </ul>
 </td></tr>
 <tr><td colspan="3" style="border: none;">
-\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
+\ref H5 \ref H5A \ref H5D \ref H5E \ref H5F \ref H5G \ref H5I \ref H5L
+\ref H5O \ref H5P \ref H5PL \ref H5R \ref H5S \ref H5T \ref H5Z
 </td></tr>
 </table>
 
diff --git a/doxygen/dox/Specifications.dox b/doxygen/dox/Specifications.dox
index 4ae48d0..bd7e849 100644
--- a/doxygen/dox/Specifications.dox
+++ b/doxygen/dox/Specifications.dox
@@ -3,7 +3,6 @@
 \section DDL
 
 \li \ref DDLBNF110 "DDL in BNF through HDF5 1.10"
-\li \ref DDLBNF112 "DDL in BNF for HDF5 1.12 and above"
 
 \section File Format
 
diff --git a/doxygen/img/IOFlow.gif b/doxygen/img/IOFlow.gif
new file mode 100644
index 0000000..3e79030
--- /dev/null
+++ b/doxygen/img/IOFlow.gif
diff --git a/doxygen/img/IOFlow2.gif b/doxygen/img/IOFlow2.gif
new file mode 100644
index 0000000..c75ca79
--- /dev/null
+++ b/doxygen/img/IOFlow2.gif
diff --git a/doxygen/img/IOFlow3.gif b/doxygen/img/IOFlow3.gif
new file mode 100644
index 0000000..316cd1e
--- /dev/null
+++ b/doxygen/img/IOFlow3.gif
diff --git a/src/H5Lpublic.h b/src/H5Lpublic.h
index be0d065..82f5f16 100644
--- a/src/H5Lpublic.h
+++ b/src/H5Lpublic.h
@@ -1248,7 +1248,7 @@ H5_DLL herr_t H5Lcreate_ud(hid_t link_loc_id, const char *link_name, H5L_type_t
  *          Remaining \c struct members are optional and may be passed as NULL.
  *
  *          The link class passed in \c class_id must be in the user-definable
- *          range between #H5L_TYPE_UD_MIN and #H5L_TYPE_UD_MAX
+ *          range between #H5L_TYPE_UD_MIN and #H5L_TYPE_MAX
  *          (see the table below) and will override
  *          any existing link class with that identifier.
  *
@@ -1294,7 +1294,7 @@ H5_DLL herr_t H5Lcreate_ud(hid_t link_loc_id, const char *link_name, H5L_type_t
  *            <tr>
  *              <td>255</td>
  *              <td>Maximum user-defined value</td>
- *              <td>#H5L_TYPE_UD_MAX</td>
+ *              <td>#H5L_TYPE_MAX</td>
  *            </tr>
  *            <tr>
  *              <td>255</td>
@@ -1349,7 +1349,6 @@ H5_DLL herr_t H5Lcreate_ud(hid_t link_loc_id, const char *link_name, H5L_type_t
  *            \li #H5L_TYPE_MAX is the maximum allowed value for a link type
  *                identifier.
  *            \li #H5L_TYPE_UD_MIN equals #H5L_TYPE_EXTERNAL.
- *            \li #H5L_TYPE_UD_MAX equals #H5L_TYPE_MAX.
  *            \li #H5L_TYPE_ERROR indicates that an error has occurred.
  *
  * \note \Bold{Registration with The HDF Group:}\n
diff --git a/src/H5Opublic.h b/src/H5Opublic.h
index 769df60..001ee31 100644
--- a/src/H5Opublic.h
+++ b/src/H5Opublic.h
@@ -1516,9 +1516,9 @@ H5_DLL herr_t H5Ovisit_by_name(hid_t loc_id, const char *obj_name, H5_index_t id
  *          retrieves the metadata describing that object in \p oinfo ,
  *          defined as a \c struct of type H5O_info1_t :
  *
- *          \snippet this H5O_info1_t_snip
+ *          \snippet this H5O_info_t_snip
  *
- *          Note the following about H5O_info1_t :
+ *          Note the following about H5O_info_t :
  *          - Of the four time fields (\c atime, \c mtime, \c ctime, and \c btime)
  *            only \c ctime has been implemented.
  *          - The \c atime value is the last time the object was read or written.
@@ -1642,7 +1642,7 @@ H5_DLL herr_t H5Oget_info_by_name1(hid_t loc_id, const char *name, H5O_info_t *o
  *
  *          \p oinfo, in which the object information is returned, is a \c struct of
  *          type H5O_info1_t .
- *          \snippet this H5O_info1_t_snip
+ *          \snippet this H5O_info_t_snip
  *
  *          The link access property list, \c lapl_id, is not currently used;
  *          it should be passed in as #H5P_DEFAULT.
diff --git a/src/H5Rpublic.h b/src/H5Rpublic.h
index 9682bf2..a21f5a0 100644
--- a/src/H5Rpublic.h
+++ b/src/H5Rpublic.h
@@ -201,7 +201,7 @@ H5_DLL hid_t H5Rget_region(hid_t dataset, H5R_type_t ref_type, const void *ref);
  * \param[in] id The dataset containing the reference object or the group
  *            containing that dataset
  * \param[in] ref_type Type of reference to query
- * \param[in] ref Reference to query
+ * \param[in] _ref Reference to query
  * \param[out] obj_type Type of referenced object
  *
  * \return \herr_t