#208 Fix: [for cherry-picking] Made nested baseline directory traversal dete

Fixed Findings

• Deduplicate baseline variants by directory precedence

Automated fix from agentic review of https://github.com/metaphorics/bamTiScript/pull/207

Summary by Sourcery

Deduplicate baseline variants according to deterministic directory precedence during filesystem resolution.

Bug Fixes:

• Make baseline directory traversal deterministic and prevent duplicate nested variants from creating ambiguous matches.

Enhancements:

• Preserve flat baseline files as authoritative while applying deterministic precedence to nested directories.

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Summary by cubic

Makes baseline directory traversal deterministic so duplicate nested variants no longer create ambiguous matches.

• Sorts nested directories during filesystem resolution.
• Deduplicates variant suffixes by keeping the first occurrence.
• Preserves flat baseline files as authoritative over nested copies.