Fix multidomain AutomaticMechanismAnalysis

[hwpang]

Bigger changes:

1. Append the global p vector (corresponding to multidomain) to each Simulation object in SystemSimulation, instead of the local p vector (corresponding to one domain). Append interfaces as well.
2. Uses the global p vector to calculate dSdt and the corresponding global indexes for species and reactions

[hwpang]

Previous push crashes single domain AMA. New push fixes it.

[hwpang]

Previous push crashes the test due to incorrect indexing. New push fixes it.

[hwpang]

New push fixes a bug related to the test for multidomain AMA

[codecov[bot]]

Codecov Report

Merging #183 (f462a06) into main (1dd0471) will increase coverage by 0.12%. The diff coverage is 62.16%.

@@            Coverage Diff             @@
##             main     #183      +/-   ##
==========================================
+ Coverage   52.28%   52.40%   +0.12%     
==========================================
  Files          29       29              
  Lines        5876     5883       +7     
==========================================
+ Hits         3072     3083      +11     
+ Misses       2804     2800       -4     

Impacted Files	Coverage Δ
src/TestReactors.jl	100.00% <ø> (ø)
src/TransitorySensitivities.jl	25.31% <21.42%> (ø)
src/Simulation.jl	31.55% <83.33%> (+0.59%)	:arrow_up:
src/AutomaticMechanismAnalysis.jl	88.97% <88.23%> (+0.09%)	:arrow_up:
src/Reactor.jl	75.78% <0.00%> (+0.87%)	:arrow_up:

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[hwpang]

Previous push encountered package version incompatibility problem after removing and reinstalling numpy, as well as installing nomkl. New push removed the related code.

[hwpang]

@mjohnson541 I have addressed all the comments.

[hwpang]

@mjohnson541 I have addressed all your comments & all tests have passed.