docs: add comprehensive MkDocs documentation website

[jayhesselberth]

Summary

• Add complete MkDocs documentation site with Material theme
• 21 documentation pages covering all aspects of the pipeline
• GitHub Actions workflow for automatic deployment to GitHub Pages

Documentation Structure

Section	Pages
Getting Started	Installation, Quick Start, First Analysis
User Guide	Configuration, Sample Files, Running Pipeline, Outputs
Workflow	Overview, Rules Reference, Scripts Reference, Demultiplexing
Cluster Setup	LSF, SLURM, GPU Configuration
Troubleshooting	Common Errors, FAQ, Debugging
Development	Architecture, Adding Rules, Contributing

Features

• Mermaid diagrams for workflow visualization
• Comprehensive rule-by-rule documentation (all 21 rules)
• Python scripts reference (8 scripts)
• WarpDemuX demultiplexing guide
• Dark/light mode toggle
• Search functionality
• Code copy buttons

Setup Required After Merge

1. Enable GitHub Pages in repository settings
2. Set source to "GitHub Actions"
3. Documentation will be available at https://rnabioco.github.io/aa-tRNA-seq-pipeline

Test plan

• Preview locally with mkdocs serve
• Verify all internal links work
• Check mermaid diagrams render
• Test search functionality
• Verify GitHub Actions workflow passes

🤖 Generated with Claude Code