Reconstructed documentation proposal

[mdgrv]

Changelog

1. User guide — significant expansions:

• user_guide/ingestion.qmd: more detailed ingestion workflow guidance
• user_guide/processing.qmd: expanded processing documentation
• user_guide/downstream.qmd: downstream analysis content filled in
• user_guide/running_pipelines.qmd: additional detail on running pipelines

2. Contributing guides — updated for Viash 0.9.x syntax:

• contributing/creating_components.qmd: config examples migrated from old functionality:/platforms: to argument_groups:, engines:, runners:
• contributing/running_tests.qmd: major rewrite; added test structure layout, instructions for generating local test data
  (vs S3 download), workflow test pattern (test.nf)
• contributing/creating_pipelines.qmd: new full guide for creating Nextflow DSL2 workflows from scratch (was previously an empty stub)

3. Architecture page — simplified:

• fundamentals/architecture.qmd: large reduction, removed complex D2/Mermaid diagrams, replaced with a concise overview of where OpenPipelines fits in a single-cell project

4. Minor edits across: concepts.qmd, roadmap.qmd, faq.qmd, getting_started.qmd, project_structure.qmd, bug_reports.qmd, parameter_lists.qmd, .gitignore

Issue ticket number and link

Closes #120

Checklist before requesting a review

• I have performed a self-review of my code

• Check the correct box. Does this PR contain:

  • Breaking changes
  • New functionality
  • Major changes
  • Minor changes
  • Bug fixes

• Proposed changes are described in the CHANGELOG.md

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