Complete documentation, alpha artifact validation, and coordinated stable 2.0 release

[uermel]

Parent Epic: #85

Objective

Complete documentation, validate the published chimerax-copick alpha, and coordinate stable 2.0 only after all migrated package alphas pass together.

Prerequisite

• The installed published-alpha backend and ecosystem matrix is green on ChimeraX Daily 1.13 / Python 3.14.

Work

• Update README, Toolshed description, tutorial references, embedded user documentation, and changelog with:
  • Python 3.14 and ChimeraX Daily 1.13 requirements;
  • exact copick==2.0.0a1, copick-shared-ui==2.0.0a1, and ChimeraX-OME-Zarr==1.0.0a1 alpha installation instructions and checksum verification;
  • legacy OME-Zarr 0.4 / Zarr v2 readability;
  • OME-Zarr 0.5 / Zarr v3 new/rebuilt volume behavior;
  • metadata-defined pyramid levels;
  • layout-agnostic reader behavior;
  • verified backend status and optional SMB status; and
  • the GitHub-alpha versus stable-Toolshed distribution policy.
• Publish additional 2.0.0-alpha.N artifacts for fixes and update exact runbook selections deliberately.
• Require published validated alphas of copick, copick-utils, copick-torch, copick-shared-ui, and chimerax-copick before any coordinated stable promotion.
• Publish stable artifacts in dependency order: copick, then copick-utils/copick-shared-ui, then copick-torch/chimerax-copick.
• Replace chimerax-copick prerelease floors with stable floors: copick[all]>=2.0.0,<3, copick-shared-ui>=2.0.0,<3, and the first stable compatible ChimeraX-OME-Zarr 1.0 release.
• Synchronize v2.0 with current main, retain/reconcile both changelog histories, and rerun all source and installed-wheel gates.
• Merge with Release-As: 2.0.0, build the exact stable wheel, verify its metadata and checksum, and submit only that artifact to the public ChimeraX Toolshed.

Acceptance criteria

• Documentation distinguishes input compatibility from core writer defaults and gives reproducible alpha artifact install steps for the exact initial dependency stack.
• Every migrated package has a published alpha that passed its own matrix and the ecosystem integration gate.
• No package stable 2.0 is released early merely because its local implementation is complete.
• Stable chimerax-copick metadata contains no prerelease dependency floor and targets stable ChimeraX-OME-Zarr 1.0.
• The synchronized branch and exact stable wheel pass the full matrix.
• The Toolshed receives the tested stable wheel and not an alpha artifact.

Out of scope

• A public Toolshed alpha channel.

[uermel]

Documentation implementation is open in stacked PR #95. It covers the exact initial alpha stack, checksum-first GitHub wheel installation, GitHub-alpha versus stable-Toolshed policy, legacy v2 readability, v3 writes, and metadata/layout ownership. Release Please will generate the alpha changelog entry. Alpha publication, ecosystem validation, stable-floor replacement, and Toolshed submission remain pending.