Fix errors in duplicate reaction checks

[speth]

Fix two problems identified in the duplicate reaction checks from a mechanism provided by @rwest .

In the first, we were comparing each reaction against the wrong reaction (i.e. not ones that we had identified as having the same set of species participating) causing a lot of unmarked duplicates to slip through.

In the second, reaction pairs like

OH* -> OH
OH* + CO2 -> OH + CO2

were mistakenly being flagged as duplicates.

[codecov]

Codecov Report

Merging #468 into master will decrease coverage by <.01%.
The diff coverage is 64.7%.

@@            Coverage Diff             @@
##           master     #468      +/-   ##
==========================================
- Coverage   58.33%   58.32%   -0.01%     
==========================================
  Files         386      386              
  Lines       42362    42364       +2     
  Branches     7260     7262       +2     
==========================================
- Hits        24712    24710       -2     
  Misses      15464    15464              
- Partials     2186     2190       +4

Impacted Files	Coverage Δ
src/kinetics/Kinetics.cpp	76.74% <64.7%> (-1.19%)	⬇️

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