v0.4.0

Added

• analyses/ — a home for self-contained validation studies, each regenerating from fixed seeds:
  RED node-age validation (does Relative Evolutionary Divergence recover node ages under a
  realistic clock?) and the yeast inversion-rate study (inferring the genome inversion rate from
  synteny with the nucleotide genome model). (#227)
• zombi2.tree — one home for the Tree datatype and its toolkit, all free functions: with_stem,
  make_ultrametric, rescale, relative_evolutionary_divergence, red_scaled, distance
  (Robinson–Foulds / branch-score), and read_newick(assume_extant=). (#228)
• CLI: zombi2 tools tree (prune / round / stem / rescale / RED) and zombi2 tools treedist. (#228)
• The autocorrelated molecular clock (FromParent) at the sequence level, alongside the
  uncorrelated ByLineage. (#228)
• Release tooling: this CHANGELOG.md and scripts/release.sh.

Changed

• Tree, Node, read_newick, to_newick, prune moved from zombi2.species to zombi2.tree
  — import them from zombi2.tree now (zombi2.species keeps the simulator and Event). (#228)
• docs/design/MAP.md correctness pass: the quarantine now points at the sibling ZOMBI2_LEGACY/,
  the joint CLI is listed, sequences/traits are marked built, and stale signatures/sections fixed.
  (#228)

Fixed

• zombi2 tools treedist matches tips by label, not by parse-order node ids, so two external trees
  are compared by taxon rather than by structural position. (#228)