docs: Refactor usage docs into user-centric multi-page structure

[adamrtalbot]

Summary

Restructures the monolithic docs/usage.md (831 lines) into a Quick Start landing page with 6 focused subpages, organised by user intent rather than pipeline code structure.

Closes #1737

Changes

New structure

docs/
├── usage.md                              → Quick Start (minimal working example, signposts)
├── usage/
│   ├── samplesheet.md                    → Samplesheet format (examples-first)
│   ├── reference-genomes.md              → Genome configuration
│   ├── alignment-and-quantification.md   → Analysis strategy (decision tree)
│   ├── preprocessing.md                  → Trimming, rRNA removal, contamination
│   ├── advanced-features.md              → UMIs, prokaryotic, 3'DGE, GPU
│   ├── configuration.md                  → Nextflow profiles, resources, custom config
│   └── differential_expression_analysis/
│       ├── introduction.md               → Brief intro + prerequisites
│       ├── running-the-pipeline.md       → Run rnaseq for DE (replaces theory.md + rnaseq.md)
│       └── de-analysis-in-r.md           → Hands-on DESeq2 (replaces de_rstudio.md + interpretation.md)
├── output.md                             → UNCHANGED
└── README.md                             → Updated index

Key design principles

• Examples before definitions — every page opens with a working example
• Decision trees over lists — "Which aligner?" not "Here are 5 aligners"
• Progressive disclosure — Quick Start → common config → advanced → reference
• One concern per page — each page answers one user question

DE tutorial refactoring

• Consolidated from 5 pages to 3
• Removed Gitpod dependency (works with any R/RStudio setup)
• Removed iGenomes recommendation (aligned with main docs guidance)
• Updated to generic paths instead of /workspace/gitpod/...
• Preserved all R code and analysis steps

Writing style

Applied nf-core writing style throughout:

• British English
• Active voice, no gerunds in headings
• Removed all "please", "e.g.", "i.e.", "etc."
• Sentence case headings

Content verification

• All 35+ original sections mapped to new files (nothing lost)
• 33 internal cross-references verified
• output.md unchanged
• Net reduction: 1456 insertions, 1815 deletions

nf-core format compatibility

Additional pages in docs/usage/ are explicitly supported by nf-core guidelines:

"Additional pages (e.g. tutorials, FAQs) can be added and will be automatically rendered on the nf-core website pipeline page."

This pattern is already used by nf-core/sarek (docs/usage/variantcalling/), nf-core/taxprofiler (docs/usage/tutorials.md), and this pipeline's existing DE tutorial.

[github-actions]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

[adamrtalbot]

This should be migrated to a specific section away from the general usage docs.