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Deterministic runs
- Reproducible MCMC given same seed and thread count — Two Delphy runs with the same binary, seed, and thread count now produce byte-identical output (logs and trees). Reproducibility does not extend across platforms, compilers, or optimization levels due to floating-point reordering.
- Seed and thread count in log file headers — Every BEAST-format log and trees file now includes
# Seed:and# Parallelism:comment lines for reproducibility.