Enhance clustering outputs with structured artifacts

[LeeLupton]

Summary

• add existence checks and logging for clustering inputs and outputs
• emit cluster assignments and aggregated results as structured JSON/CSV artifacts
• support configurable output roots and optional per-cluster directories with summaries
• fix cluster result export typing to satisfy static checks
• document Windows setup and command usage in the README
• improve missing-file error messaging and Windows sample commands

Testing

• make lint

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Codex Task