JLinAlg v0.3.4

JLinAlg 0.3.4

High-core adaptive omics scheduling

• Automatic feature blocks are sized from both current JVM heap headroom and
  the requested thread count.
• When memory permits, each block queues at least two complete 256-feature
  chunks per scan worker, giving work stealing enough queued work to absorb
  uneven feature-fit times without leaving cores idle at block barriers.
• Under tighter memory, JLinAlg selects the largest complete worker wave that
  fits or safely caps worker capacity. An explicit --block-size remains
  authoritative.

Pedigree singleton handling

• Phenotype individuals absent from the pedigree file are retained as
  unrelated, noninbred singleton founders instead of stopping the analysis.
• Repeated observations with the same missing pedigree ID remain grouped in
  one singleton family. The console, log, and manifest report singleton
  families and observations.

CLI documentation and transform semantics

• Added a comprehensive CLI-only guide and copy-pasteable command-line examples
  to the model vignettes, including grouped REML, pedigrees, GRMs, GLMMs,
  genotype scans, Cox models, and specialized subcommands.
• Omics row transforms intentionally run after phenotype complete-case
  filtering, so winsor_mad and other row-statistic transforms use the final
  analysis sample set.

Release downloads: jlinalg-0.3.4.jar is the self-contained executable;
JLinAlg-0.3.4-library.jar is the thin library. Sources and Javadoc JARs and
SHA256SUMS.txt are also included.