1.14.0: Brings the following changesets over from develop: (#2330)

* Brings the following changesets over from develop:

b9244a85d9f1cc5e9bbec61ca73c0cbd9c4cf249 Align arg types of H5D_chunk_iter_op_t with H5Dget_chunk_info (#2074)
70cf2c390bc2eef8e57f8fa023341011e2d02d9d Removed idioms and misc. text clean-up (#2320)
8102fa8c972bdc0d8fd8f3dae604e070893150d6 Only document Fortran functions (#2319)
784061b15e176b9919c19a220ce278a9f4cddf0e moved onion VFD to FAPL group (#2321)
6b6bcdead66f0456ac0528683faac6a8e48b6565 Hdffv 11052 (#2315)
10c693a04ff0c4a5219879d7f8900157dcbece66 Update hdf5_header.html
0cb58080875070db09b5ecae92482519d58872bc Hdffv 11052 (#2303)
a1c81eda203addced514ef655f7a9079f3f0bb04 added doc. warning for H5Literate_async return value (#2295)
502b32b0f22a4bcf6333c85c256db34162c2764a Updated H5ES documenation (#2293)
a9036005c3916e6fda0296026323f00d043300f8 Fix for HDFFV-11052: h5debug fails on a corrupted file (h5_nrefs_POC)… (#2291)

* Brings the following changes over from develop:

c1e44d32e616518e0626bdfe042bed0052846fef Fix doxygen warnings and remove javadocs (#2324)
149b8e9769887c5b23400b526dc10463f88f2c3e Disable hl tools by default (#2313)

12 files changed, 63 insertions, 50 deletions

diff --git a/src/H5Amodule.h b/src/H5Amodule.h
index 7f88a22..4823d0d 100644
--- a/src/H5Amodule.h
+++ b/src/H5Amodule.h
@@ -363,7 +363,7 @@
  * will be ignored by HDF5.
  *
  * The use of ASCII or UTF-8 characters is determined by the character encoding property. See
- * #H5Pset_char_encoding in the \ref RM.
+ * #H5Pset_char_encoding in the \ref RM.
  *
  * <h4>No Special I/O or Storage</h4>
  *
diff --git a/src/H5D.c b/src/H5D.c
index d921356..006f4a9 100644
--- a/src/H5D.c
+++ b/src/H5D.c
@@ -2515,18 +2515,18 @@ done:
  *
  *        typedef int (*H5D_chunk_iter_op_t)(
  *            const hsize_t *offset,
- *            uint32_t filter_mask,
+ *            unsigned filter_mask,
  *            haddr_t addr,
- *            uint32_t nbytes,
+ *            hsize_t size,
  *            void *op_data);
  *
  *      H5D_chunk_iter_op_t parameters:
- *          hsize_t *offset;        IN/OUT: Array of starting logical coordinates of chunk.
- *          uint32_t filter_mask;   IN: Filter mask of chunk.
- *          haddr_t addr;           IN: Offset in file of chunk data.
- *          uint32_t nbytes;        IN: Size in number of bytes of chunk data in file.
- *          void *op_data;          IN/OUT: Pointer to any user-defined data
- *                                  associated with the operation.
+ *          hsize_t *offset;        IN/OUT: Logical position of the chunk’s first element in units of dataset
+ *                                          elements
+ *          unsigned filter_mask;   IN: Bitmask indicating the filters used when the chunk was written haddr_t
+ *          addr;                   IN: Chunk address in the file
+ *          hsize_t;                IN: Chunk size in bytes, 0 if the chunk does not exist
+ *          void *op_data;          IN/OUT: Pointer to any user-defined data associated with the operation.
  *
  *      The return values from an operator are:
  *          Zero (H5_ITER_CONT) causes the iterator to continue, returning zero when all
diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c
index 40f8359..830560d 100644
--- a/src/H5Dchunk.c
+++ b/src/H5Dchunk.c
@@ -8278,8 +8278,8 @@ H5D__chunk_iter_cb(const H5D_chunk_rec_t *chunk_rec, void *udata)
     FUNC_ENTER_PACKAGE_NOERR
 
     /* Check for callback failure and pass along return value */
-    if ((ret_value = (data->op)(offset, chunk_rec->filter_mask, chunk_rec->chunk_addr, chunk_rec->nbytes,
-                                data->op_data)) < 0)
+    if ((ret_value = (data->op)(offset, (unsigned)chunk_rec->filter_mask, chunk_rec->chunk_addr,
+                                (hsize_t)chunk_rec->nbytes, data->op_data)) < 0)
         HERROR(H5E_DATASET, H5E_CANTNEXT, "iteration operator failed");
 
     FUNC_LEAVE_NOAPI(ret_value)
diff --git a/src/H5Dpublic.h b/src/H5Dpublic.h
index ac76bc8..f7d208d 100644
--- a/src/H5Dpublic.h
+++ b/src/H5Dpublic.h
@@ -238,7 +238,7 @@ typedef herr_t (*H5D_gather_func_t)(const void *dst_buf, size_t dst_buf_bytes_us
  *          \li A negative (#H5_ITER_ERROR) causes the iterator to immediately
  *              return that value, indicating failure.
  */
-typedef int (*H5D_chunk_iter_op_t)(const hsize_t *offset, uint32_t filter_mask, haddr_t addr, uint32_t size,
+typedef int (*H5D_chunk_iter_op_t)(const hsize_t *offset, unsigned filter_mask, haddr_t addr, hsize_t size,
                                    void *op_data);
 //! <!-- [H5D_chunk_iter_op_t_snip] -->
 
diff --git a/src/H5ESpublic.h b/src/H5ESpublic.h
index 3d46e82..ecfd08f 100644
--- a/src/H5ESpublic.h
+++ b/src/H5ESpublic.h
@@ -189,7 +189,7 @@ H5_DLL herr_t H5ESwait(hid_t es_id, uint64_t timeout, size_t *num_in_progress, h
  * \param[out] err_occurred Status indicating if error is present in the event set
  * \returns \herr_t
  *
- * \details H5ESget_count() attempts to cancel operations in an event set specified
+ * \details H5EScancel() attempts to cancel operations in an event set specified
  *          by \p es_id. H5ES_NONE is a valid value for \p es_id, but functions as a no-op.
  *
  * \since 1.13.0
@@ -217,14 +217,14 @@ H5_DLL herr_t H5ESget_count(hid_t es_id, size_t *count);
 /**
  * \ingroup H5ES
  *
- * \brief Retrieves the next operation counter to be assigned in an event set
+ * \brief Retrieves the accumulative operation counter for an event set
  *
  * \es_id
- * \param[out] counter The next counter value to be assigned to an event
+ * \param[out] counter The accumulative counter value for an event set
  * \returns \herr_t
  *
- * \details H5ESget_op_counter() retrieves the \p counter that will be assigned
- *          to the next operation inserted into the event set \p es_id.
+ * \details H5ESget_op_counter() retrieves the current accumulative count of
+ *          event set operations since the event set creation of \p es_id.
  *
  * \note This is designed for wrapper libraries mainly, to use as a mechanism
  *       for matching operations inserted into the event set with possible
diff --git a/src/H5FDonion.h b/src/H5FDonion.h
index 63c2d77..0e605d0 100644
--- a/src/H5FDonion.h
+++ b/src/H5FDonion.h
@@ -142,11 +142,11 @@ H5_DLL hid_t H5FD_onion_init(void);
 
 /**
  * --------------------------------------------------------------------------
- * \ingroup H5P
+ * \ingroup FAPL
  *
  * \brief get the onion info from the file access property list
  *
- * \param[in] fapl_id The ID of the file access property list
+ * \fapl_id
  * \param[out] fa_out The pointer to the structure H5FD_onion_fapl_info_t
  *
  * \return \herr_t
@@ -159,11 +159,11 @@ H5_DLL herr_t H5Pget_fapl_onion(hid_t fapl_id, H5FD_onion_fapl_info_t *fa_out);
 
 /**
  * --------------------------------------------------------------------------
- * \ingroup H5P
+ * \ingroup FAPL
  *
  * \brief set the onion info for the file access property list
  *
- * \param[in] fapl_id The ID of the file access property list
+ * \fapl_id
  * \param[in] fa The pointer to the structure H5FD_onion_fapl_info_t
  *
  * \return \herr_t
diff --git a/src/H5Fint.c b/src/H5Fint.c
index 2c1b4b2..7ad35fc 100644
--- a/src/H5Fint.c
+++ b/src/H5Fint.c
@@ -1615,7 +1615,9 @@ H5F__dest(H5F_t *f, hbool_t flush)
     if (H5FO_top_dest(f) < 0)
         HDONE_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "problems closing file")
     f->shared = NULL;
-    f         = H5FL_FREE(H5F_t, f);
+
+    if (ret_value >= 0)
+        f = H5FL_FREE(H5F_t, f);
 
     FUNC_LEAVE_NOAPI(ret_value)
 } /* end H5F__dest() */
diff --git a/src/H5Gmodule.h b/src/H5Gmodule.h
index 4b58ee6..d4738f6 100644
--- a/src/H5Gmodule.h
+++ b/src/H5Gmodule.h
@@ -923,7 +923,7 @@
  *                containing thousands to millions of members. Links are stored in
  *                a fractal heap and indexed with an improved B-tree.
  *          \li The new implementation also enables the use of link names consisting of
- *              non-ASCII character sets (see H5Pset_char_encoding()) and is
+ *              non-ASCII character sets (see #H5Pset_char_encoding) and is
  *              required for all link types other than hard or soft links, e.g.,
  *              external and user-defined links (see the \ref H5L APIs).
  *
diff --git a/src/H5Lpublic.h b/src/H5Lpublic.h
index 6f6c638..d2d9e9d 100644
--- a/src/H5Lpublic.h
+++ b/src/H5Lpublic.h
@@ -729,7 +729,7 @@ H5_DLL herr_t H5Lexists_async(hid_t loc_id, const char *name, hbool_t *exists, h
  *          \p cset specifies the character set in which the link name is
  *          encoded. Valid values include the following:
  *          \csets
- *          This value is set with H5Pset_char_encoding().
+ *          This value is set with #H5Pset_char_encoding.
  *
  *          \c token is the location that a hard link points to, and
  *          \c val_size is the size of a soft link or user defined link value.
@@ -923,6 +923,11 @@ H5_DLL herr_t H5Literate2(hid_t grp_id, H5_index_t idx_type, H5_iter_order_t ord
 /**
  * --------------------------------------------------------------------------
  * \ingroup ASYNC
+ *
+ * \warning The returned value of the callback routine op will not be set
+ *          in the return value for H5Literate_async(), so the \p herr_t value
+ *          should not be used for determining the return state of the callback routine.
+ *
  * \async_variant_of{H5Literate}
  */
 #ifndef H5_DOXYGEN
@@ -1520,7 +1525,7 @@ typedef herr_t (*H5L_iterate1_t)(hid_t group, const char *name, const H5L_info1_
  *          \c cset specifies the character set in which the link name is
  *          encoded. Valid values include the following:
  *          \csets
- *          This value is set with H5Pset_char_encoding().
+ *          This value is set with #H5Pset_char_encoding.
  *
  *          \c address and \c val_size are returned for hard and symbolic
  *          links, respectively. Symbolic links include soft and external links
diff --git a/src/H5Tpublic.h b/src/H5Tpublic.h
index dcaffd8..16172a8 100644
--- a/src/H5Tpublic.h
+++ b/src/H5Tpublic.h
@@ -1035,7 +1035,7 @@ H5_DLLVAR hid_t H5T_NATIVE_UINT_FAST64_g;
  *          When creating a fixed-length string datatype, \p size will
  *          be the length of the string in bytes. The length of the
  *          string in characters will depend on i the encoding used; see
- *          H5Pset_char_encoding().
+ *          #H5Pset_char_encoding.
  *
  *          ENUMs created with this function have a signed native integer
  *          base datatype.  Use H5Tenum_create() if a different integer base
diff --git a/src/H5VLconnector_passthru.h b/src/H5VLconnector_passthru.h
index 68dd33a..d10bac4 100644
--- a/src/H5VLconnector_passthru.h
+++ b/src/H5VLconnector_passthru.h
@@ -71,7 +71,7 @@ H5_DLL herr_t H5VLcmp_connector_cls(int *cmp, hid_t connector_id1, hid_t connect
  *                 - #H5I_MAP
  *                 - #H5I_ATTR
  *
- * \return \hid_t
+ * \return \hid_t{VOL connector}
  *
  * \note This routine is mainly targeted toward wrapping objects for
  *       iteration routine callbacks (i.e. the callbacks from H5Aiterate*,
diff --git a/src/H5VLnative_file.c b/src/H5VLnative_file.c
index 907a12d..f2f0ea7 100644
--- a/src/H5VLnative_file.c
+++ b/src/H5VLnative_file.c
@@ -753,29 +753,35 @@ H5VL__native_file_close(void *file, hid_t H5_ATTR_UNUSED dxpl_id, void H5_ATTR_U
     FUNC_ENTER_PACKAGE
 
     /* This routine should only be called when a file ID's ref count drops to zero */
-    HDassert(H5F_ID_EXISTS(f));
-
-    /* Flush file if this is the last reference to this id and we have write
-     * intent, unless it will be flushed by the "shared" file being closed.
-     * This is only necessary to replicate previous behaviour, and could be
-     * disabled by an option/property to improve performance.
-     */
-    if ((H5F_NREFS(f) > 1) && (H5F_INTENT(f) & H5F_ACC_RDWR)) {
-        /* Get the file ID corresponding to the H5F_t struct */
-        if (H5I_find_id(f, H5I_FILE, &file_id) < 0 || H5I_INVALID_HID == file_id)
-            HGOTO_ERROR(H5E_ID, H5E_CANTGET, FAIL, "invalid ID")
-
-        /* Get the number of references outstanding for this file ID */
-        if ((nref = H5I_get_ref(file_id, FALSE)) < 0)
-            HGOTO_ERROR(H5E_ID, H5E_CANTGET, FAIL, "can't get ID ref count")
-        if (nref == 1)
-            if (H5F__flush(f) < 0)
-                HGOTO_ERROR(H5E_FILE, H5E_CANTFLUSH, FAIL, "unable to flush cache")
-    } /* end if */
-
-    /* Close the file */
-    if (H5F__close(f) < 0)
-        HGOTO_ERROR(H5E_FILE, H5E_CANTDEC, FAIL, "can't close file")
+    HDassert(f->shared == NULL || H5F_ID_EXISTS(f));
+
+    if (f->shared == NULL)
+        f = H5FL_FREE(H5F_t, f);
+
+    else {
+
+        /* Flush file if this is the last reference to this id and we have write
+         * intent, unless it will be flushed by the "shared" file being closed.
+         * This is only necessary to replicate previous behaviour, and could be
+         * disabled by an option/property to improve performance.
+         */
+        if ((H5F_NREFS(f) > 1) && (H5F_INTENT(f) & H5F_ACC_RDWR)) {
+            /* Get the file ID corresponding to the H5F_t struct */
+            if (H5I_find_id(f, H5I_FILE, &file_id) < 0 || H5I_INVALID_HID == file_id)
+                HGOTO_ERROR(H5E_ID, H5E_CANTGET, FAIL, "invalid ID")
+
+            /* Get the number of references outstanding for this file ID */
+            if ((nref = H5I_get_ref(file_id, FALSE)) < 0)
+                HGOTO_ERROR(H5E_ID, H5E_CANTGET, FAIL, "can't get ID ref count")
+            if (nref == 1)
+                if (H5F__flush(f) < 0)
+                    HGOTO_ERROR(H5E_FILE, H5E_CANTFLUSH, FAIL, "unable to flush cache")
+        } /* end if */
+
+        /* Close the file */
+        if (H5F__close(f) < 0)
+            HGOTO_ERROR(H5E_FILE, H5E_CANTDEC, FAIL, "can't close file")
+    }
 
 done:
     FUNC_LEAVE_NOAPI(ret_value)