fix: address release readiness issues

[yuhaosimba]

Summary

• correct virtual atom type 0 reflection to use z_v = 2h - z_source while preserving the existing input format
• parse standard SemVer release tags in the Windows installer and separate numeric file versions from display versions
• remove the blocking stdin read from the missing-GB-parameters error path
• align the getting-started TOML example and documentation entry points with current behavior
• remove the stale hard-coded release codename

Validation

• full dev-cpu SPONGE build
• SPONGE -v reports only the version sourced from pixi.toml
• all 44 configured CTest tests passed; 4 existing runtime tests were skipped by configuration
• all 10 noPBC virtual atom validation tests passed
• mdin schema example validation passed
• repository format-check passed
• git diff --check passed

Windows PowerShell and NSIS packaging will be validated by the Windows release CI job.

[yuhaosimba]

@codex review

[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 2026-09-12T03:08:24.758451Z	f3760de	Manual request

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[xiaoxuan-yu]

Please also update the version information in SPONGE/control.cpp for release. In particular, SPONGE_CODENAME is still set to 2026-04-01 April Fools' Day.

[chatgpt-codex-connector]

💡 Codex Review

Here are some automated review suggestions for this pull request.

Reviewed commit: f3760de182

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[chatgpt-codex-connector]

Update the direct Type 0 coordinate oracle

When the medium or production A/B suite runs normal_virtual_atoms_all_types, this corrected formula places fixture atom 6 at (4, 4, 3) because its source has z=1 and h=2. However, _focused_virtual_atom_coordinate_oracle() still hard-codes that atom as (4, 4, 7) at lines 17238–17240, and the input.topology.virtual_atoms path invokes that oracle at lines 13288–13293. Consequently, both otherwise-correct runtime branches now fail _assert_virtual_atom_oracle; update the direct oracle along with this rerun oracle.

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