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docs: merge duplicate paper sections and fix numbering#19

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nikstern wants to merge 1 commit intonerdsane:mainfrom
nikstern:docs/merge-paper-sections
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docs: merge duplicate paper sections and fix numbering#19
nikstern wants to merge 1 commit intonerdsane:mainfrom
nikstern:docs/merge-paper-sections

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@nikstern nikstern commented Mar 7, 2026

Summary

  • Merged two coexisting versions of the paper that had accumulated in PAPER.md into a single coherent document
  • Removed duplicate sections: Connection Handler stub, Connection-Level Transactions (shorter version), and the split Verification Pyramid / Verification Methodology
  • Consolidated pyramid diagram and per-layer methodology details into one unified Section 2
  • Renumbered all sections sequentially 1–6 with consistent subsection numbering throughout
  • Updated all cross-references and fixed an orphaned code fence on the pyramid diagram

Test plan

  • Read through the rendered markdown to verify section flow makes sense
  • Confirm no content was changed, only structure and numbering

🤖 Generated with Claude Code

- Merged two coexisting versions of the paper into one coherent structure
- Removed duplicate Connection-Level Transactions and Connection Handler sections
- Consolidated Verification Pyramid and Verification Methodology into single section
- Renumbered all sections sequentially (1-6) with consistent subsection numbering
- Updated all cross-references (Section 2.1, 2.3, 5.1)
- Fixed orphaned code fence on pyramid diagram
- Removed dangling lead-in sentence from deleted stub sections

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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