docs: restart reference numbering per section

[jgoldfoot]

Problem

The whitepaper's reference list was left half-migrated across three different numbering schemes:

Section	Numbering
Primary Research	1-19
Agent Protocols	1-5 (restarts)
Rendering & Performance	10-13
Standards	14-18

The list originally ran as one continuous sequence split under headings, which is why Rendering & Performance began at 10 and Standards at 14. A later edit renumbered Agent Protocols to restart at 1 but did not update the two sections after it, so those two now continue a sequence that no longer exists.

This predates the 7/21 and 7/28 research scans (#143, #146).

Fix

Restart Rendering & Performance (1-4) and Standards (1-5) so every section is numbered independently, matching what Agent Protocols already does.

Why renumbering is safe

The body cites references by name and arXiv ID, never by number — grep -cE '\[[0-9]{1,2}\]' docs/whitepaper.md returns 0, and there are no "see reference N" constructions. The markers are purely ordinal, so nothing cross-references them.

The README needs no equivalent change; its reference section uses bullets, not numbers.

Verification

• npx prettier@3.9.6 --check clean repo-wide
• npm test — 122 passed, 7 suites
• Content unchanged; only list markers and their continuation indents