docs: prefer layers for single-cell count preservation

[Cmf (Cmfffff)]

Summary

• Clarify AnnData concatenation guidance around join='outer' for preserving the union of variables/features.
• Replace default .raw preservation recommendations with explicit adata.layers['counts'] = adata.X.copy() workflows.
• Align Scanpy workflow docs and analysis template with layers-first count preservation guidance.

Test Plan

• git diff --check HEAD~1 HEAD
• grep -R "adata\\.raw = adata\\|adata\\.raw = adata.copy()\\|use_raw=True\\|Always save raw counts\\|Raw data backup\\|Store raw" backend/cli/skills/biology/anndata backend/cli/skills/biology/scanpy || true
• grep -R "layers\\['counts'\\] = adata.X.copy()" backend/cli/skills/biology/anndata backend/cli/skills/biology/scanpy
• Bun validation/tests not run per maintainer instruction; changes are skill docs/template only.

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