Harden scientific parsing and release workflows

[D-sudoasd]

Summary

• fail closed on ambiguous or partially recognized composition and CIF element inputs
• preserve cross-platform elasticity index matching, nested manifests, and atomic publication behavior
• harden GUI failure classification, Windows launchers, quick export, and Materials Project guidance
• add release dependency preflight plus clean-wheel and installed-entrypoint verification
• refresh English and Chinese README content, scientific contracts, release guidance, issue templates, and CI coverage

Validation

• 403 passed, 1 skipped, 4 intentional warnings in the final local non-GUI suite
• 10 passed for focused GUI startup and Tcl/Tk error-classification tests
• Ruff, compileall, documentation checks, git diff checks, and pip check passed
• final-source wheel and sdist passed Twine checks
• isolated wheel install passed metadata 0.4.0, pip check, demo, verify, 45/45 benchmark checks, and quick-export bundle verification
• independent release-hardening code review: APPROVE / PASS

Environment and release boundary

The local Python 3.12 Tcl/Tk resource installation is damaged, so real local GUI construction is not claimed as passing. Ubuntu/Xvfb remains the dedicated real GUI construction and interaction check. macOS runs the complete suite. The GitHub-hosted Windows Python 3.13 runtime also lacked Tcl/Tk resource files, so Windows CI runs the complete core/CLI suite plus non-window GUI startup classification; it does not claim real Windows GUI construction.

The final clean-package run explicitly skipped the already completed test suite, so it correctly produced no full release acceptance receipt. This PR does not create a version tag or GitHub release; version 0.4.0 remains Unreleased pending the documented release decision.