docs: clarify rarefaction handling in alpha and beta diversity calculations

[ilypopv]

📝 Summary

Updated the paper's diversity calculations section to correct the documentation of rarefaction behavior. Alpha diversity is now described as computed on raw (unrarefied) counts, while beta diversity is documented as applying rarefaction prior to distance matrix calculation.

🛠 Type of Change

• Documentation

🔍 Key Changes

• Updated the comparison table to note alpha diversity is computed on raw counts and beta diversity includes rarefaction
• Rewrote the Alpha Diversity bullet to remove the claim of a built-in rarefaction procedure subsampling reads beforehand
• Rewrote the Beta Diversity bullet to state that rarefaction is applied prior to distance matrix calculation to account for uneven sequencing depths

🧪 How Has This Been Tested?

• Manual review of the updated paper/paper.md text against the documented diversity computation behavior

[codecov]

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