Pca

[quattro]

This PR addresses #50.

• Expand compute-pcs with sample and gene filtering, optional covariate alignment, and external library sizes.
• Separate normalization (library-size, tmm, or none) from transformation (log1p or none), defaulting to library-size normalization followed by log1p.
• Number PCs starting at 1, order them by explained variance, and save variance proportions for scree plots.
• Validate inputs and test TMM factors against edgeR reference cases.
• Reorganize CLI documentation into overview, mapping, and expression PCA pages; make the PCA guide example-driven.