clean up Doxygen

Description

Describe the issue as clearly as possible. Issues are meant for bug reports and feature requests. The issue should contain enough information for a developer to put together a solution.

If this is a general question, please post to the forums.

Example

Here's the current errors.

mkdir -p doc/api
doxygen doxygen/doxygen.cfg
warning: Tag 'TCL_SUBST' at line 237 of file 'doxygen/doxygen.cfg' has become obsolete.
         To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
warning: Tag 'COLS_IN_ALPHA_INDEX' at line 1053 of file 'doxygen/doxygen.cfg' has become obsolete.
         To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
warning: Tag 'LATEX_SOURCE_CODE' at line 1758 of file 'doxygen/doxygen.cfg' 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 1840 of file 'doxygen/doxygen.cfg' has become obsolete.
         To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
warning: Tag 'CLASS_DIAGRAMS' at line 2132 of file 'doxygen/doxygen.cfg' has become obsolete.
         To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"

and so on for thousands of lines. So many that trying to post them all says

There was an error creating your Issue: body is too long (maximum is 65536 characters).

Expected Output

No errors

Current Version:

v4.3.1