More Sphinx / Doxygen updates

[speth]

Changes proposed in this pull request

• Use 'warning' admonition in Sphinx docs so these will be formatted similar to 'deprecated' admonitions now that we're using the PyData Sphinx theme.
• Add BibTeX entries for more references
• Remove references to obsolete member of VPStandardStateTP
• Fix Contributor Covenant link in README.rst
• Expand trees in Doxygen by default -- saves having to expand the "Cantera" namespace every time you go to the class / namespace list
• Adjust ordering of Doxygen pages to move auxiliary pages towards the bottom, and emphasize "class" documentation over the "namespace" documentation
• Make transport properties a top-level group in Doxygen, and move Phase and ThermoPhase into base thermoprops group

If applicable, provide an example illustrating new features this pull request is introducing

Member function with warning and versionadded directives:

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Default view of the "Classes" page:

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Checklist

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

[codecov[bot]]

Codecov Report

Merging #1590 (8e364b8) into main (43fca53) will increase coverage by 0.00%. The diff coverage is n/a.

@@           Coverage Diff           @@
##             main    #1590   +/-   ##
=======================================
  Coverage   70.60%   70.61%           
=======================================
  Files         379      379           
  Lines       59153    59153           
  Branches    21252    21252           
=======================================
+ Hits        41766    41768    +2     
+ Misses      14313    14311    -2     
  Partials     3074     3074           

Files Changed	Coverage Δ
include/cantera/oneD/IonFlow.h	73.33% <ø> (ø)
include/cantera/thermo/HMWSoln.h	40.00% <ø> (ø)
include/cantera/thermo/MixtureFugacityTP.h	33.33% <ø> (ø)
include/cantera/thermo/MolalityVPSSTP.h	80.00% <ø> (ø)
include/cantera/thermo/PDSS_HKFT.h	100.00% <ø> (ø)
include/cantera/thermo/Phase.h	78.57% <ø> (ø)
include/cantera/thermo/ThermoPhase.h	47.16% <ø> (ø)
include/cantera/thermo/VPStandardStateTP.h	100.00% <ø> (ø)
include/cantera/transport/Transport.h	17.43% <ø> (ø)
interfaces/cython/cantera/kinetics.pyx	91.81% <ø> (+0.43%)	:arrow_up:
... and 3 more

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[speth]

Thanks for catching those inconsistencies, @ischoegl. This should be good to go now.