more doxygen warning fixes

docs/Doxyfile.in

@@ -2037,7 +2037,7 @@ SKIP_FUNCTION_MACROS   = YES
 
 # TAGFILES               = html/guide.tag=./html_guide "html/tutorial.tag = ./html_tutorial"
 #TAGFILES = ../../NUG/html/nug.tag=../../../NUG/html
-TAGFILES = ../../NUG/html/nug.tag=https://docs.unidata.ucar.edu/nug
+#TAGFILES = ../../NUG/html/nug.tag=https://docs.unidata.ucar.edu/nug
 
 # When a file name is specified after GENERATE_TAGFILE, doxygen will create a
 # tag file that is based on the input files it reads. See section "Linking to

docs/FAQ.md

@@ -67,7 +67,7 @@ that is part of the netCDF software distribution. It is a command line
 tool that provides a text representation of a netCDF file's data, just its
 metadata, or just the data for specified
 variables, depending on what arguments you use. For more information,
-see the \ref ncdump_guide documentation.
+see the [ncdump User's Guide](https://docs.unidata.ucar.edu/nug/current/netcdf_utilities_guide.html#ncdump_guide) documentation.
 
 Another good tool for conversion of netCDF data to text is the ["ncks" program](http://nco.sourceforge.net/nco.html#ncks-netCDF-Kitchen-Sink) that's one of the utility programs in the [NCO (NetCDF Operators)](software.html#NCO) package. Similar capabilities are available using programs from the [CDO (Climate Data Operators)](software.html#CDO) software, commands from [NCL (NCAR Command Language)](software.html#NCL), or various other packages such as [ANAX](http://science.arm.gov/~cflynn/ARM_Tested_Tools/), cdf2asc, and NOESYS, all "third party" netCDF utilities developed and supported by other organizations. You can find more information about these third-party packages on the [Software for Manipulating or Displaying NetCDF Data](software.html) page.
 
@@ -322,7 +322,7 @@ We test releases on the following operating systems with various compilers:
 -   Solaris
 -   Windows (some versions, see below)
 
-The [NetCDF Installation and Porting Guide](@ref getting_and_building_netcdf) explains how to build netCDF from source on various platforms. Often, it's as easy as running
+The [NetCDF Installation and Porting Guide](https://docs.unidata.ucar.edu/nug/current/getting_and_building_netcdf.html) explains how to build netCDF from source on various platforms. Often, it's as easy as running
 
 ~~~~ {.boldcode}
   ./configure
@@ -483,7 +483,7 @@ How do I build and install netCDF for a specific development environment? {#How-
 You have to build and install the netCDF C library first, before you build and install other language libraries that depend on it, such as Fortran, C++, or Python netCDF libraries. The netCDF Java library is mostly independent of the netCDF C library, unless you need to write netCDF-4 files from Java, in which case you will also need an installed netCDF C library.
 
 For more details, see
-[NetCDF Installation and Porting Guide](@ref getting_and_building_netcdf).
+[NetCDF Installation and Porting Guide](https://docs.unidata.ucar.edu/nug/current/getting_and_building_netcdf.html).
 
 
 ----------

docs/nczarr.md

@@ -190,7 +190,7 @@ be a prefix of any other key.
 There several other concepts of note.
 1. __Dataset__ - a dataset is the complete tree contained by the key defining
 the root of the dataset.
-Technically, the root of the tree is the key <dataset>/.zgroup, where .zgroup can be considered the _superblock_ of the dataset.
+Technically, the root of the tree is the key \<dataset\>/.zgroup, where .zgroup can be considered the _superblock_ of the dataset.
 2. __Object__ - equivalent of the S3 object; Each object has a unique key
 and "contains" data in the form of an arbitrary sequence of 8-bit bytes.
 

docs/tutorial.dox

@@ -68,7 +68,7 @@ The utility ncdump can be used to show the contents of netCDF
 files. By default, ncdump shows the CDL description of the file. This
 CDL description can be fed into ncgen to create the data file.
 
-See also: \ref ncdump_guide
+See also: [The ncdump User's Guide](https://docs.unidata.ucar.edu/nug/current/netcdf_utilities_guide.html#ncdump_guide)
 
 \subsection netcdf_utilities_ncgen ncgen
 
@@ -76,15 +76,15 @@ The ncgen utility can take an ASCII input file, in CDL format, and
 generate a binary netCDF file. It is the opposite of ncdump.
 
 See also:
-- \ref guide_ncgen
-- \ref guide_ncgen3
+- [ncgen](https://docs.unidata.ucar.edu/nug/current/netcdf_utilities_guide.html#guide_ncgen)
+- [ncgen3](https://docs.unidata.ucar.edu/nug/current/netcdf_utilities_guide.html#guide_ncgen3)
 
 \subsection netcdf_utilities_nccopy nccopy
 
 The nccopy utility can copy a netCDF file, changing binary format,
 chunk sizes, compression, and other storage settings.
 
-See also: \ref guide_nccopy
+See also: [nccopy](https://docs.unidata.ucar.edu/nug/current/netcdf_utilities_guide.html#guide_nccopy)
 
 \section external_netcdf_tools Tools for Manipulating NetCDF Files
 
@@ -262,8 +262,9 @@ opaque types.
 </ul>
 
 These features may only be used when working with a netCDF-4/HDF5
-file. Files created in classic formats cannot support
-groups or user-defined types (see \ref netcdf_format).
+file. Files created in classic formats cannot support groups or
+user-defined types (see [NetCDF File
+Formats](https://docs.unidata.ucar.edu/nug/current/netcdf_introduction.html#netcdf_format)).
 
 <p>\image html nc4-model.png
 
@@ -455,7 +456,8 @@ of netCDF-4.
 - \ref example_simple_xy_nc4
 
 The examples are built and run with the “make check” command. (See
-\ref building).
+[Building
+netCDF-C](https://docs.unidata.ucar.edu/nug/current/getting_and_building_netcdf.html#building)).
 
 The corresponding examples in each language create identical netCDF
 data files. For example, the C program sfc_pres_temp_wr.c produces the
@@ -812,11 +814,13 @@ with nc_get_vara()/nc_put_vara().
 
 \page parallel_io Parallel I/O with NetCDF-4
 
-NetCDF-4 provides parallel file access to both classic and netCDF-4/HDF5 files.
-The parallel I/O to netCDF-4 files is achieved through the HDF5 library while
-the parallel I/O to classic files is through PnetCDF. A few functions have been
-added to the netCDF C API to handle parallel I/O. You must build netCDF-4
-properly to take advantage of parallel features (see \ref build_parallel).
+NetCDF-4 provides parallel file access to both classic and
+netCDF-4/HDF5 files.  The parallel I/O to netCDF-4 files is achieved
+through the HDF5 library while the parallel I/O to classic files is
+through PnetCDF. A few functions have been added to the netCDF C API
+to handle parallel I/O. You must build netCDF-4 properly to take
+advantage of parallel features (see [Building with Parallel I/O
+Support](https://docs.unidata.ucar.edu/nug/current/getting_and_building_netcdf.html#build_parallel)).
 
 The nc_open_par() and nc_create_par() functions are used to
 create/open a netCDF file with parallel access.

libdispatch/dattinq.c

@@ -30,8 +30,9 @@ Research/Unidata. See \ref copyright file for more info.  */
  * @param name Pointer to the location for the returned attribute \ref
  * object_name. \ref ignored_if_null.
  *
- * @param xtypep Pointer to location for returned attribute \ref
- * data_type. \ref ignored_if_null.
+ * @param xtypep Pointer to location for returned attribute [data
+ * type](https://docs.unidata.ucar.edu/nug/current/md_types.html#data_type). \ref
+ * ignored_if_null.
  *
  * @param lenp Pointer to location for returned number of values
  * currently stored in the attribute. For attributes of type
@@ -318,8 +319,8 @@ nc_inq_natts(int ncid, int *nattsp)
  *
  * @param name Attribute \ref object_name.
  *
- * @param xtypep Pointer to location for returned attribute \ref
- * data_type.
+ * @param xtypep Pointer to location for returned attribute [data
+ * type](https://docs.unidata.ucar.edu/nug/current/md_types.html#data_type).
  *
  * @section nc_inq_atttype_example Example
  *