feat: add evolution controller and append-only ledger

[divo12]

Summary

• add typed, fsynced append-only evolution ledger with sequence-keyset paging, verified owner lock, corruption fail-closed replay, and idempotent event identities
• add resumable EvolutionController status/advance state machine coordinating hypothesis, candidate, evaluated receipt, gate decision, stops, and pre-PR5 AwaitingPublication barrier
• expose evolution_status and advance_evolution MCP tools and route the generated program through controller calls

Data flow and trust boundary

MCP -> EvolutionController -> typed policy/hypothesis/candidate/gate receipts -> FileEvolutionLedger in Git common control dir. No trace payloads or provider responses are persisted locally.

Verification

• PR3 resynced at c5e6a34
• 365 passed, 2 skipped; 94.74% coverage
• ruff, strict mypy, Radon, four skill validators, and plugin validation passed locally

Scope

Targets only stack/v2-03-gate-v2. No merge, deployment, System Book, harness/runtime/E2B/canary/live-adapter work, or uv.lock changes.

---

Summary by cubic

Adds a typed, fsynced append-only evolution ledger and resumable EvolutionController that replaces direct hypothesis recording and candidate execution with one-step evolution actions. The generated program now checks evolution_status, advances once per call, and stops before publication; trace payloads and provider responses remain unpersisted locally.

New Features

• Stores typed events in Git’s common control directory with keyset paging, verified owner locking, fail-closed replay, and idempotent identities.
• Binds receipts and gate decisions to accepted content identities so review decisions remain valid across rebases.
• Exposes evolution_status and advance_evolution through MCP and falls back to the persisted baseline commit when the active baseline is unavailable.

^{Written for commit 8fde9ef. Summary will update on new commits.}

[cubic-dev-ai]

All reported issues were addressed across 14 files

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[cubic-dev-ai]

All reported issues were addressed across 4 files (changes from recent commits).

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[cubic-dev-ai]

All reported issues were addressed across 10 files (changes from recent commits).

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[divo12]

Restack transparency note:

During the requested rebase onto stack/v2-03-gate-v2, the first guarded --force-with-lease attempt was intentionally rejected: it expected remote head 8cc0e1e4dd0d9cc06aee13e8de3b8d7c6c493255, but the remote branch had advanced to c719e050fbe4ca1be6c646eba437a11825c70f1d. After refreshing the remote state, the rebase was published with a guarded lease from exact old head c719e050fbe4ca1be6c646eba437a11825c70f1d to exact new head cd5e2316fa2fcedae6f76afa7b286768d63dd945. No unrelated remote work was overwritten; the lease protected against that case. No further force-pushes will be performed.

[cubic-dev-ai]

All reported issues were addressed across 4 files (changes from recent commits).

<sub>Tip: Review your code locally with the cubic CLI to iterate faster.

Re-trigger cubic</sub>

[cubic-dev-ai]

All reported issues were addressed across 2 files (changes from recent commits).

<sub>Tip: Review your code locally with the cubic CLI to iterate faster.

Re-trigger cubic</sub>