v0.3.3

[0.3.3] - 2026-07-22

Fixed

• BoltzGen abort/resume robustness — hard-killing tt-bio gen mid-download no
  longer poisons the artifact cache or leaks .dl-* staging directories. A sweep
  on startup reaps orphaned staging dirs left by a killed fetch, and a download-path
  patch keeps partial downloads out of the cache so a resumed run picks up cleanly.
• BoltzGen design-spec-check perceived hang — tt-bio gen now reports progress
  during the design-spec check (the gap after mols.zip is cached where the CLI
  previously showed no output), so a genuinely slow conformer-generation step reads
  as activity instead of a frozen process. Print-only; parsed molecule data is
  bit-identical.

Changed

• Repo docs reorganization — internal engineering-journey notes moved out of the
  public repository into the private knowledge base, leaving the public docs focused
  on what a user needs to decide and use the package. Comment/docstring/doc-move
  only; no logic change.