v0.7.0

Added

• Cross-level staleness guard. A level refuses to re-run in place when a later level built from it
  is already in the run directory — re-running would leave that downstream output silently mismatched.
  This covers both the pipeline chain (re-running genomes would orphan the sequences under it) and
  DrivenBy conditioning (re-running a traits run that a genomes rate was conditioned on orphans
  that genomes, and the sequences beneath it — the dependency is recorded in a small conditioned_on
  marker). --force re-runs anyway and removes the now-stale downstream, so a run's levels can never
  quietly disagree. The forward pipeline is unaffected (each level is run once); applies to the default
  grouped layout — --flat commingles the levels and is left to the user. (#243)
• Onboarding nudges. After a level runs, a one-line pointer names the output file(s) worth looking
  at — a species run names both its complete and its extant tree — so a newcomer can find what they
  made. It says only what was written and where, never what to do next (a run is not one road);
  suppressed by --quiet. The top-level --help now leads with the levels and the plain quickstart,
  with the DrivenBy / joint coupling note moved below them. (#244)

Fixed

• A non-nucleotide sequences run no longer leaves an empty sequences/genomes/ directory behind (the
  assembled-genome FASTAs are a nucleotide-run output). (#244)
• The sequences run log now records the substitution model's effective parameters (e.g. kappa 2.0,
  frequencies [0.25, 0.25, 0.25, 0.25]) instead of the bare None args, so a run reproduces from its
  log alone, without the reader having to know each model's defaults. (#244)