[WIP] Documentation

[Copilot]

• Enhance N rich filter algorithm documentation
  • Document dynamic threshold computation in add_filter_nrich.py
  • Explain how threshold avoids poorly covered positions
  • Document the 0.05 hard threshold cap
• Document input parameters in usage.md
  • Add detailed descriptions for low_mappability_file
  • Add detailed descriptions for low_complexity_file
  • Add detailed descriptions for global_exons_file
  • Document parent_dna column and BAM merging capabilities
• Enhance output documentation in output.md
  • Add column descriptions for VCF output files
  • Add column descriptions for other output files
  • Document which outputs to use for downstream deepCSA analysis
  • Document which mutations are used for SigProfilerMatrixGenerator
  • Document which mutations are used for mutations per position plots
• Add resource management documentation
  • Document how sample count affects resource requirements
  • Add resource configuration examples for different scales
  • Document how to disable QCs with perform_qcs parameter
• Improve general documentation clarity and completeness

Fixes #37.

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