Modernize coverage pipeline internals and tighten error handling

[telatin]

Summary

• guard coverage counter decrements, respect the configured minimum contig length threshold, and streamline option parsing with scoped enums and string views
• refactor the output writer to use std::optional, avoid pointer sentinels, and stop flushing on every line while preserving per-reference headers
• drop translation-unit wide namespace imports in the interval utilities and option parser, adopting modern includes and type aliases throughout

Testing

• not run

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https://chatgpt.com/codex/tasks/task_b_690bafbc98ac8330b8c9c9511d4c74a1