Add BDEI and BDSS linear phylodynamic models

[Horopter]

Summary

• Adds yaml/bdei.yml and yaml/bdss.yml for two-deme linear birth-death processes used in PhyloDeep (Voznica et al.).
• Registers each model with minimal wiring only: new .cc/.R files plus small patches to init.c, simulate.R, and yaml.R.
• Does not bulk-regenerate existing models via add_model.R.
• Refactors initial conditions to fraction-based IVPs (pop, fn/fs or fe/fi) matching the mers.yml pattern.
• Renames transmission rates to lambda_* (lambda_ie in BDEI; lambda_nn, lambda_ns, lambda_sn, lambda_ss in BDSS).
• Sets YAML rate defaults to midpoints of the PhyloDeep training priors (Voznica supplementary / treesimulator conventions).
• Adds paper citations with URLs in each model's details block.

King et al. / Voznica alignment

• BDEI: demes exposed and infectious (King Fig. 1A genealogy restriction). Rates: mu (E→I), lambda_ie (I→E birth), psi (I removal), Stadler sampling p on infectious removal — matches treesimulator BirthDeathExposedInfectiousModel. Default rates imply $R_0 \approx 2.3$, $T_I = 3$, $T_E/T_I \approx 2.6$.
• BDSS: two fixed infective demes with donor-dependent transmission and shared removal/sampling; constraint $\lambda_{ss}/\lambda_{ns} = \lambda_{sn}/\lambda_{nn}$ per Voznica. Default rates imply $\lambda_n = 1$, $f = 0.125$, $X = 6.5$, $\mu = 1$. Distinct from King Fig. 1D (nonlinear behavioral SI2R).

Test plan

• Rscript tests/bdei.R
• Rscript tests/bdss.R
• Package installs and compiles with both models registered
• Fraction IVP scaling verified (pop + deme fractions → integer initial counts)

[codecov]

Codecov Report

❌ Patch coverage is 96.29630% with 6 lines in your changes missing coverage. Please review.
✅ Project coverage is 98.80%. Comparing base (e2aaf75) to head (e1832a5).

Additional details and impacted files

@@            Coverage Diff             @@
##           master       #6      +/-   ##
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- Coverage   98.91%   98.80%   -0.11%     
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  Files          71       75       +4     
  Lines        3764     3926     +162     
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+ Hits         3723     3879     +156     
- Misses         41       47       +6     

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[kingaa]

@Horopter : I'd like to harmonize the parameter names in the codes you've written with those used in the rest of the package. I've adjusted the names in the BDEI case: perhaps you can make the corresponding adjustments in the BDSS case?

[kingaa]

@Horopter : see my changes to your pull request. Can you make the corresponding changes for the BDSS model?