Update doxygen Chemical Kinetics/Numerics Documentation

[ischoegl]

Changes proposed in this pull request

Restructure/consolidate/correct/update doxygen documentation for the following:

• Chemical Kinetics objects
• Numerical utilities
• Global Data
• Exception Handling

The main objective is to generate an adequate browsable structure for the Modules tab; the underlying docstrings are largely unchanged.

In addition, the mainfile is switched to Markdown (supported since doxygen 1.8.3 - released in 2012).

Partially addresses #1535

Closes #1516

Checklist

• The pull request includes a clear description of this code change
• Commit messages have short titles and reference relevant issues
• Build passes (scons build & scons test) and unit tests address code coverage
• Style & formatting of contributed code follows contributing guidelines
• The pull request is ready for review

[codecov]

Codecov Report

Merging #1534 (3b64999) into main (f89efe8) will increase coverage by 0.00%.
The diff coverage is 100.00%.

@@           Coverage Diff           @@
##             main    #1534   +/-   ##
=======================================
  Coverage   70.50%   70.50%           
=======================================
  Files         376      376           
  Lines       59075    59081    +6     
  Branches    21219    21222    +3     
=======================================
+ Hits        41649    41657    +8     
+ Misses      14348    14344    -4     
- Partials     3078     3080    +2     

Impacted Files	Coverage Δ
include/cantera/base/Array.h	82.75% <ø> (ø)
include/cantera/base/ExternalLogger.h	39.13% <ø> (ø)
include/cantera/base/NoExitLogger.h	0.00% <ø> (ø)
include/cantera/base/Solution.h	87.50% <ø> (ø)
include/cantera/base/ctexceptions.h	60.86% <ø> (ø)
include/cantera/base/global.h	81.81% <ø> (ø)
include/cantera/base/logger.h	78.57% <ø> (ø)
include/cantera/base/utilities.h	96.66% <ø> (ø)
include/cantera/equil/ChemEquil.h	100.00% <ø> (ø)
include/cantera/equil/MultiPhase.h	100.00% <ø> (ø)
... and 34 more

... and 3 files with indirect coverage changes

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[ischoegl]

@speth ... I am stopping here. I think that navigating the "C++ Modules" structure has become a bit easier and I also started to fill in some gaps. I have made no attempts to update sections on integrators, phases, oneD and zeroD, or some of the ungrouped Cantera capabilities.

The PR targets the structure and should help locating information based on a handful of topics. Revising of actual docstrings goes beyond the scope of the PR.

[speth]

Thanks for working on this, @ischoegl. I think the new landing page is a much friendlier alternative to the essentially blank page that's there now. I have only a few minor suggestions.

[ischoegl]

Thanks, @speth! I believe it's all addressed. I replaced some old group labels with a more standardized xyzGroup (only where you had comments).

[speth]

Thanks, @ischoegl, this looks good to me.