Close document, recovery, and precomplex correctness gaps

[dhsohn]

Motivation

I reviewed the document lifecycle, Calculation Plan handoff, and test gate for
failure modes that could silently lose edits, revive stale reviewed geometry, or
leave tests undiscovered. The same review found that a release tag could publish
without proving its version, main-branch ancestry, and CI result.

Changes

• Treat symlink, hard-link, case-sensitive-volume, and already-open document
  identities consistently, and refuse unsafe Save As replacements.
• Bind crash-recovery sessions to process creation identity while preserving the
  version-1 manifest and retaining unreadable recovery data fail-closed.
• Centralize reviewed-precomplex freshness validation, bind it to environment,
  electronic annotations, and stereo direction, and block stale Graph Patch or
  pack-step publication.
• Build one indexed component inventory for document inspection.
• Discover nested tests recursively, validate and cap concurrency, isolate each
  test file, and keep failure logs collision-free.
• Verify release tags against the package version, main ancestry, and the exact
  successful main push CI run before distribution builds begin.
• Update the English and Korean architecture/CLI documentation and changelog.

Verification

• make check — Ruff, formatting, mypy, and all 303 test files passed.
• Release-preflight unit tests cover version mismatch, non-main commits,
  annotated tags, missing credentials, malformed CI responses, and failed CI.
• The preflight was also exercised against the published v0.5.1 tag and its
  successful main CI run.
• GUI document/session probes and RDKit-backed reviewed-precomplex tests passed
  in the focused review runs.

[chatgpt-codex-connector]

Codex Review Summary

This comment shows the latest Codex review activity on this pull request.

Review	Status	Commit	Review trigger
📝 Code Review	✅ Completed 2026-08-30T11:46:35.637239Z	999e002	PR opened

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