docs: record E01 closed, open E12 for D3, and unblock E02/E03

[TheAmericanMaker]

E01 is merged at b868fd9; #399 is closed. This updates the two documents a new session reads first so they match the board.

• README / plan status. E01 is closed rather than "acceptance pending"; E02 ([E02] Persist isolated changes and immutable attempts #400) and E03 ([E03] Bind records to stable input and candidate snapshots #401) are eligible now, in parallel, sharing only the core/index.ts barrel edit. E09 stays on maintainer hold.
• D3 is now E12 ([E12] Establish and attest storage protection continuity (D3) #418), not E02. The spike left the protection-continuity mechanism as "an E02 investigation with an operator attestation at its root" — that would have dropped an unresolved security-design question on whoever picked up the store. E12 carries it independently; E02 ships reading protection from host configuration and reporting it faithfully, including as unknown.
• The standing consequence is written down. Until E12 lands, every acceptance classifies cooperative and VERIFIED_ACCEPTANCE_INTEGRATIONS stays empty. Downstream issues surface that; none may add a default, fallback, or trusted path that makes verified reachable without the mechanism.
• Two lessons E01 paid for, now binding on downstream issues: a trust rule that lives in a helper nothing calls is not a rule, and a degradation must lower trust rather than raise it. Both shipped as real bypasses in E01 and were caught in review.

Docs only — no code, no contract change. 973/973 tests pass.