refactor: reorganize src model layout

[leejet]

Summary

• Reorganize internal src files into core, runtime, conditioning, and model/* directories.

Related Issue / Discussion

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Additional Information

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Checklist

• I have read and confirmed this PR follows the contribution guidelines.

[wbruna]

@leejet , while we're at it: could we rename gits_noise.inl to gits_noise.h? We keep having to special-case the extension everywhere (CMakeLists.txt, formatting, synchronizing source trees, ...); and IMHO it's not a useful distinction for that single file, since we already have several other implementation-only .h and .hpp files.

[leejet]

That’s fine. I kept .inl only because the original contributor used the .inl file extension, and I didn’t change it.