Refactor/io and initial state

[xiaoxuan-yu]

This pull request introduces a new modular and robust initial state builder for the simulation core, improves restart output handling, and updates documentation for clarity. The most significant changes are the addition of the InitialStateBuilder class, a refactor of the HDF5 restart output interface, and documentation improvements.

Core Simulation Initialization

• Introduced the InitialStateBuilder class (initial_state.h, initial_state.cpp), which modularizes and enforces the correct order of simulation initialization steps, making the process more robust and maintainable. This builder covers loading the base state, initializing dynamics, building constraints and velocities, restoring protocol state, building coordinate derivatives, distributing state, and finalizing the run range. [1] [2]
• Added necessary includes to support the new builder and related IO functionality (MD_core.h).

Restart Output Refactor

• Refactored the HDF5 restart file export interface in trajectory_output to take a single RestartOutputState struct, simplifying the function signature and improving maintainability. Added validation for coordinate dimensions and improved error handling. [1] [2]

Documentation Updates

• Updated both Chinese and English README.md files to guide users to the new getting started and input file reference documents, improving onboarding and usability. [1] [2]

Build and Versioning

• Added a new GitHub Actions workflow (windows-installer-version.yml) to automate version checks and installer metadata validation for Windows builds.
• Cleaned up the version string in control.cpp by removing the codename from the SPONGE_VERSION macro.

Minor Fixes

• Removed a blocking getchar() call after an error message in generalized_Born.cpp to prevent unnecessary pauses on error exit.

[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 2026-09-16T05:57:11.833365Z	7c7101f	Manual request

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[yuhaosimba]

@codex There are still many header files included directly in main.cpp. Would it be better to consolidate them into main.h?

Also, please continue with the review.

[chatgpt-codex-connector]

Codex Review: Didn't find any major issues. Already looking forward to the next diff.

Reviewed commit: 7c7101f91a

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