Overhaul repo: clean up, add docs, modernize pipeline

README:
- Rewrite following papa2 style (badges, install, Python API, Nextflow usage)
- Remove screenshots, live demo link, R Shiny references

Documentation:
- Add mkdocs-material site (index, quickstart, API reference, pipeline guide)
- Add GitHub Pages auto-deploy workflow

Pipeline:
- Default to Python/papa2 for all steps (lang='python', dada_engine follows lang)
- Remove R fallback hack in dada_engine resolution
- Update conda envs to use bioconda papa2 and microscape packages
- Streamline R env to bioconda packages only

Cleanup:
- Delete nextflow/bin/py/ (ported to microscape/ package)
- Delete screenshots, TODO.md, BENCHMARKS.md

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: rec3141

.github/workflows/docs.yml

@@ -0,0 +1,31 @@
+name: Deploy docs
+
+on:
+  push:
+    branches: [main]
+    paths:
+      - 'docs/**'
+      - 'mkdocs.yml'
+      - 'microscape/**'
+
+permissions:
+  contents: write
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - name: Install mkdocs and dependencies
+        run: pip install mkdocs-material "mkdocstrings[python]"
+
+      - name: Install microscape
+        run: pip install -e .
+
+      - name: Deploy to GitHub Pages
+        run: mkdocs gh-deploy --force