Harden and tidy the analysis template

[Marius1311]

Review-driven pass over the template covering security, the GPU/CI story, the demo notebook, onboarding, and repo hygiene. All tests and pre-commit hooks pass; pixi.lock regenerated; notebooks are output-clean.

Changes

• GPU/CI environment split — the GPU stack (rapids-singlecell + CUDA JAX) now lives in a dedicated gpu pixi feature/environment. The default environment is CPU-only, so CI and CPU-only machines no longer resolve unusable CUDA wheels. CPU JAX is available by default on both platforms. Activate GPU explicitly with pixi install -e gpu (documented in the README).
• CI — pin pixi-version: v0.60.0 and use frozen: true in both workflows.
• Onboarding — add scripts/rename_package.py (+ pixi run rename) to rename the placeholder package/project in one shot; rewrite README Step 3 with a complete checklist. Add a documented .env.example and a secrets section.
• Source — _constants.py gains marker-based root detection and a DatasetPaths accessor (raw/processed/resources/results) with create(); plotting.qc_violin accepts str | Path for save and uses fig.tight_layout().
• Docs — fix the dataset README (add resources), the bug-report template leftover (tradeseq → session_info2), and the inverted PR-template comments.

Bug fixes

• rapids-singlecell extra rapids12 → rapids-cu12 — the old extra doesn't exist on current versions, so rapids installed without GPU libs and silently fell back to CPU.
• CellTypist input scale — the demo now rebuilds log1p(normalize_total(1e4)) from the raw counts layer instead of trusting adata.X, preventing silently wrong annotations if X is later scaled/subset.
• version("myanalysis") is now updated by the rename script (would otherwise raise PackageNotFoundError after renaming).

New

• scripts/rename_package.py — stdlib-only, runnable before pixi install.
• DatasetPaths accessor and FilePaths.dataset() helper.
• .env.example.

Notes for reviewers

• Action required: the previously-committed-locally .env held real OpenAI/Gemini/Anthropic keys — these should be rotated in their dashboards (the file is removed, not in git history).
• Removed vestigial .cruft.json references and a stray personal prompt file (there's no cookiecutter/cruft sync here — the new init script replaces that need).
• The demo notebook was renamed: demo_scRNA_workflow.ipynb → ML-2026-01-27_demo_scRNA_workflow.ipynb.

Related issues

N/A