FN-5741: persist merge-request handoff shadow contract

Introduce Phase 1 write-only persistence for merge-request handoff acceptance across core and engine paths.

- add persisted merge-request record types, schema/settings plumbing, and store write-path support
- update merger/executor/self-healing/run-audit flows to emit and consume the handoff-accepted shadow marker
- expand core/engine/roadmap tests and docs to cover the new merge-request shadow contract
- add a patch changeset for @runfusion/fusion for this bundled package update

Files changed:
 .changeset/fn-5741-merge-request-shadow.md         |   5 +
 AGENTS.md                                          |   1 +
 docs/architecture.md                               |   2 +
 docs/settings-reference.md                         |   1 +
 packages/core/src/__tests__/db-migrate.test.ts     |  12 +-
 packages/core/src/__tests__/db.test.ts             |  34 ++--
 packages/core/src/__tests__/goals-schema.test.ts   |   2 +-
 packages/core/src/__tests__/insight-store.test.ts  |  10 +-
 .../src/__tests__/merge-request-record.test.ts     |  97 +++++++++++
 packages/core/src/__tests__/mission-store.test.ts  |   2 +-
 packages/core/src/__tests__/run-audit.test.ts      |   2 +-
 packages/core/src/__tests__/secrets-schema.test.ts |   6 +-
 .../core/src/__tests__/settings-parity.test.ts     |   3 +
 .../core/src/__tests__/store-merge-queue.test.ts   |   2 +-
 packages/core/src/__tests__/task-documents.test.ts |   2 +-
 packages/core/src/db.ts                            |  49 +++++-
 packages/core/src/index.ts                         |   4 +-
 packages/core/src/settings-schema.ts               |  30 ++++
 packages/core/src/store.ts                         | 189 ++++++++++++++++++++-
 packages/core/src/types.ts                         |  37 ++++
 .../src/__tests__/merger-merge-lifecycle.test.ts   |  54 ++++++
 .../merge-request-shadow-handoff.test.ts           |  74 ++++++++
 packages/engine/src/executor.ts                    |  15 +-
 packages/engine/src/merger.ts                      |  37 ++++
 packages/engine/src/run-audit.ts                   |   1 +
 packages/engine/src/self-healing.ts                |  16 +-
 .../src/store/__tests__/roadmap-store.test.ts      |   4 +-
 27 files changed, 646 insertions(+), 45 deletions(-)

Fusion-Task-Id: FN-5741

Fusion-Task-Lineage: 3fec14c3-47ff-4f14-bc02-24021518c992

packages/core/src/settings-schema.ts

@@ -1,5 +1,9 @@
 import type { GlobalSettings, ProjectSettings, Settings } from "./types.js";
 
+export interface MergeRequestContractShadowSettingsSource {
+  mergeRequestContractShadowEnabled?: boolean;
+}
+
 type CompleteSettings<T> = { [K in keyof Required<T>]: Required<T>[K] | undefined };
 
 /**
@@ -18,6 +22,7 @@ export const DEFAULT_GLOBAL_SETTINGS = {
   defaultProvider: undefined,
   defaultModelId: undefined,
   testMode: undefined,
+  mergeRequestContractShadowEnabled: false,
   fallbackProvider: undefined,
   fallbackModelId: undefined,
   defaultThinkingLevel: undefined,
@@ -195,6 +200,7 @@ export const DEFAULT_PROJECT_SETTINGS = {
   overlapIgnorePaths: [],
   autoMerge: true,
   testMode: undefined,
+  mergeRequestContractShadowEnabled: false,
   mergeStrategy: "direct",
   directMergeCommitStrategy: "always-squash",
   mergeIntegrationWorktree: "reuse-task-worktree",
@@ -474,6 +480,30 @@ export function isGlobalOnlySettingsKey(key: string): key is keyof GlobalSetting
   return isGlobalSettingsKey(key) && !isProjectSettingsKey(key);
 }
 
+export function isMergeRequestContractShadowEnabled(
+  sources:
+    | {
+        project?: MergeRequestContractShadowSettingsSource;
+        global?: MergeRequestContractShadowSettingsSource;
+      }
+    | MergeRequestContractShadowSettingsSource
+    | undefined,
+): boolean {
+  if (!sources) return false;
+
+  const scoped = sources as {
+    project?: MergeRequestContractShadowSettingsSource;
+    global?: MergeRequestContractShadowSettingsSource;
+  };
+  if (typeof scoped.project !== "undefined" || typeof scoped.global !== "undefined") {
+    const projectValue = scoped.project?.mergeRequestContractShadowEnabled;
+    if (typeof projectValue === "boolean") return projectValue;
+    return scoped.global?.mergeRequestContractShadowEnabled === true;
+  }
+
+  return (sources as MergeRequestContractShadowSettingsSource).mergeRequestContractShadowEnabled === true;
+}
+
 export function resolvePersistAgentThinkingLog(
   settings: Partial<GlobalSettings> | undefined,
   opts: { ephemeral: boolean },