Summary

This PR implements improved order-independent hashing for directories and unordered collections, controlled by the NXF_PATCH_DIRECTORY_HASH environment variable.

Key Features

• Order-independent directory hashing: Directory traversal order no longer affects hash values
• Consistent unordered collection hashing: Sets and Bags produce consistent hashes regardless of internal ordering
• Backward compatible: Feature is disabled by default, enabled via NXF_PATCH_DIRECTORY_HASH=true
• Addresses edge cases: Fixes issue where directories with similar contents could have the same hash (relates to Add additional test for hasher #6198)

Technical Implementation

• Uses commutative byte addition for order independence in both directory and collection hashing
• Implements separate "patched" methods: hashDirSha256Patched() and hashUnorderedCollectionPatched()
• Maintains full backward compatibility - default behavior unchanged
• Added comprehensive tests covering both default and patched behaviors

Usage

To enable the patch:

export NXF_PATCH_DIRECTORY_HASH=true
nextflow run your-pipeline.nf

Test Coverage

• ✅ Original tests continue to pass (backward compatibility)
• ✅ New tests verify order independence for directories with same content but different creation order
• ✅ Tests verify different content yields different hashes (no false positives)
• ✅ Comprehensive SysEnv testing for environment variable control

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