Add comprehensive README.md documentation

[Copilot]

Adds project documentation covering usage, installation, and structure as requested.

Changes

• Installation: Core requirements (Python 3.8+, NumPy) and optional acceleration deps (pydivsufsort, numba, Cython)
• CLI usage: Full argument reference with examples
• Output formats: BED, VCF, TRF, STRfinder column specs
• Detection tiers: Tier 1 (1-9bp perfect), Tier 2 (≥10bp imperfect), Tier 3 (100bp+ long-read)
• Project structure: Directory layout with module descriptions; mentions results/ test sequences without detail per spec

Example usage from README

# Basic
python -m src.main genome.fa

# With options
python -m src.main genome.fa --min-period 2 --max-period 50 --tiers tier1 --format vcf -v

Original prompt

On /, Write a comprehensive README.md file for this project. All you need to detail is how to use this tool, and how this tool is structured (mention, but do not detail, the test seqs).

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