In the BGL package we get a warning like:
```
/home/cgal-testsuite/cgal_doc_build/CGAL-5.4-Ic-33/doc/BGL/PackageDescription.txt:29: warning: ignoring \dot command because HAVE_DOT is not set
```
The BGL package uses the `\dot` and has now to use the setting `HAVE_DOT=YES` to see the dot image.
Till now this went OK as the `\dot` command didn't look at the setting of the `HAVE_DOT` setting in the Doxyfile, though by the issue https://github.com/doxygen/doxygen/issues/7273 and the pull request https://github.com/doxygen/doxygen/pull/8663 it is now required that `HAVE_DOT` is set.
The idea of setting `HAVE_DOT` for the BGL project removed the warning (and shows the figure again) though has also as side effect that the inheritance graphs are shown. Until now CGAL shows for the inheritance just the text version.
Doxygen now has for the `CLASS_GRAPH` setting the possibility `TEXT` that does exactly what is required.
Due to the general setting of `HAVE_DOT` also the not needed `graph_legend` was generated and some `INCLUDE_GRAPH`s, by setting this to `NO ` these are no suppressed as well.
```
warning: Tag 'LATEX_SOURCE_CODE' at line 1971 of file '.../doc_dxy/BaseDoxyfile' has become obsolete.
To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
warning: Tag 'RTF_SOURCE_CODE' at line 2061 of file '.../doc_dxy/BaseDoxyfile' has become obsolete.
To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
warning: Tag 'DOCBOOK_PROGRAMLISTING' at line 2166 of file '.../BaseDoxyfile' has become obsolete.
To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
```
these tags have been declared obsolete (in the current master version), so they should be removed..
CGAL doesn't use the involved formats so this has no influence on the CGAL documentation processing.
In pull request #4644 a central MATHJAX_CODEFILE was introduced, but the snap rounding package was omitted, so this is corrected here.
For the MathJax V3 ( see #5707) this change is even mandatory (the current construct doesn't work).
Below the bottom blue block we see for the packages some extra white space. For the Manual page this white space is not present.
The reason is the placing of the "hack.js" code.
In the version 1.9.0 the setting `COLS_IN_ALPHA_INDEX` has been made obsolete and generates a warning during building.
As the default value is used it can also be removed (doxygen will automatically take the default value in the older versions).
For a better quality also the close image was converted to an svg image, so the png does not exists anymore. This has to be reflected in this file as well.
For a better quality also the close image was converted to an svg image, so the png does not exists anymore. This has to be reflected in this file as well.
Due to some subtle interactions between used doxygen commands and the defined `\cgalAdvancedEnd` incorrect HTML code is generated.
This was shown by `xmllint (and some options) as
```
parser error : Opening and ending tag mismatch: div line</td></tr>
```
With the `\noop` "trick" this can here be overcome.
The presented output though looked OK.
Laurent Rineau
Sébastien Loriot
Mael Rouxel-Labbé
albert-github
Dmitry Anisimov
Dmitry Anisimov
Maxime Gimeno