feat(FN-4018): isolate split merger temp workspaces with settings persisten

Merged FN-4014 to fix dual-scope GitHub tracking settings persistence and validation (mission vs task scope), scoped repo saves to the relevant section, and documented the dual defaults. Also landed FN-4018 to isolate split merger temp workspaces and add regression checks for split-suite test isolat

Fusion-Task-Id: FN-4018

packages/core/src/__tests__/settings-parity.test.ts

@@ -4,6 +4,7 @@ import {
   DEFAULT_PROJECT_SETTINGS,
   GLOBAL_SETTINGS_KEYS,
   PROJECT_SETTINGS_KEYS,
+  isGlobalOnlySettingsKey,
   isGlobalSettingsKey,
   isProjectSettingsKey,
 } from "../types.js";
@@ -95,6 +96,8 @@ describe("settings key parity", () => {
     expect(isGlobalSettingsKey("githubAuthToken")).toBe(false);
     expect(isProjectSettingsKey("githubTrackingDefaultRepo")).toBe(true);
     expect(isGlobalSettingsKey("githubTrackingDefaultRepo")).toBe(true);
+    expect(isGlobalOnlySettingsKey("githubTrackingDefaultRepo")).toBe(false);
+    expect(isGlobalOnlySettingsKey("themeMode")).toBe(true);
   });
 
   it("keeps remoteAccess scoped to global settings only", () => {

packages/core/src/__tests__/store-settings.test.ts

@@ -554,6 +554,33 @@ describe("TaskStore", () => {
   // ── Scope Separation Regression Tests (FN-1729) ───────────────────────────
 
   describe("scope separation regression", () => {
+    it("keeps dual-scope githubTrackingDefaultRepo in project scope while excluding global-only keys", async () => {
+      await harness.store().updateGlobalSettings({
+        githubTrackingDefaultRepo: "global/default",
+        themeMode: "light",
+      });
+
+      await harness.store().updateSettings({
+        githubTrackingDefaultRepo: "project/default",
+        themeMode: "dark",
+      });
+
+      const merged = await harness.store().getSettings();
+      const mergedFast = await harness.store().getSettingsFast();
+      const { global, project } = await harness.store().getSettingsByScope();
+      const scopedFast = await harness.store().getSettingsByScopeFast();
+
+      expect(merged.githubTrackingDefaultRepo).toBe("project/default");
+      expect(mergedFast.githubTrackingDefaultRepo).toBe("project/default");
+      expect(project.githubTrackingDefaultRepo).toBe("project/default");
+      expect(scopedFast.project.githubTrackingDefaultRepo).toBe("project/default");
+      expect(global.githubTrackingDefaultRepo).toBe("global/default");
+      expect(scopedFast.global.githubTrackingDefaultRepo).toBe("global/default");
+
+      expect((project as Record<string, unknown>).themeMode).toBeUndefined();
+      expect((scopedFast.project as Record<string, unknown>).themeMode).toBeUndefined();
+    });
+
     it("getSettingsByScope: global lane keys never appear in project scope", async () => {
       await harness.store().updateGlobalSettings({
         executionGlobalProvider: "anthropic",

packages/core/src/settings-schema.ts

@@ -346,3 +346,7 @@ export function isGlobalSettingsKey(key: string): key is keyof GlobalSettings {
 export function isProjectSettingsKey(key: string): key is keyof ProjectSettings {
   return (PROJECT_SETTINGS_KEYS as readonly string[]).includes(key);
 }
+
+export function isGlobalOnlySettingsKey(key: string): key is keyof GlobalSettings {
+  return isGlobalSettingsKey(key) && !isProjectSettingsKey(key);
+}

packages/core/src/store.ts

@@ -5,7 +5,7 @@ import { join } from "node:path";
 import { existsSync, watch, type FSWatcher } from "node:fs";
 import type { Task, TaskDetail, TaskCreateInput, TaskAttachment, AgentLogEntry, BoardConfig, Column, MergeResult, Settings, GlobalSettings, ProjectSettings, ActivityLogEntry, ActivityEventType, TaskDocument, TaskDocumentRevision, TaskDocumentCreateInput, TaskDocumentWithTask, InboxTask, TaskLogEntry, RunMutationContext, RunAuditEvent, RunAuditEventInput, RunAuditEventFilter, ArchivedTaskEntry, ArchiveAgentLogMode, TaskPriority, SourceType, WorkflowStepTemplate, Agent, AutostashOrphanRecord, TaskCommitAssociation, TaskCommitAssociationMatchSource, TaskCommitAssociationConfidence } from "./types.js";
 import { createActivityLogSnapshot, createRunAuditSnapshot, createTaskMetadataSnapshot, toTaskMetadataRecord, validateSnapshotEnvelope, type ActivityLogSnapshot, type RunAuditSnapshot, type TaskMetadataSnapshot } from "./shared-mesh-state.js";
-import { VALID_TRANSITIONS, DEFAULT_SETTINGS, isGlobalSettingsKey, WORKFLOW_STEP_TEMPLATES, validateDocumentKey } from "./types.js";
+import { VALID_TRANSITIONS, DEFAULT_SETTINGS, isGlobalOnlySettingsKey, WORKFLOW_STEP_TEMPLATES, validateDocumentKey } from "./types.js";
 import { normalizeTaskPriority } from "./task-priority.js";
 import { canAgentTakeImplementationTask } from "./agent-role-policy.js";
 import { GlobalSettingsStore } from "./global-settings.js";
@@ -1783,7 +1783,7 @@ export class TaskStore extends EventEmitter<TaskStoreEvents> {
     // Strip global-only keys from project-level settings so stale project-scoped
     // values don't override the correct global value during the spread merge.
     const projectSettings = Object.fromEntries(
-      Object.entries(config.settings ?? {}).filter(([key]) => !isGlobalSettingsKey(key)),
+      Object.entries(config.settings ?? {}).filter(([key]) => !isGlobalOnlySettingsKey(key)),
     );
     return canonicalizeSettings({
       ...DEFAULT_SETTINGS,
@@ -1818,7 +1818,7 @@ export class TaskStore extends EventEmitter<TaskStoreEvents> {
     // always done this; getSettingsFast() was missing the filter.
     const projectSettings: Partial<Settings> | undefined = raw
       ? (Object.fromEntries(
-          Object.entries(raw).filter(([key]) => !isGlobalSettingsKey(key)),
+          Object.entries(raw).filter(([key]) => !isGlobalOnlySettingsKey(key)),
         ) as Partial<Settings>)
       : undefined;
 
@@ -1846,7 +1846,7 @@ export class TaskStore extends EventEmitter<TaskStoreEvents> {
     const projectSettings: Partial<ProjectSettings> = {};
     if (config.settings) {
       for (const key of Object.keys(config.settings)) {
-        if (!isGlobalSettingsKey(key)) {
+        if (!isGlobalOnlySettingsKey(key)) {
           (projectSettings as Record<string, unknown>)[key] = (config.settings as Record<string, unknown>)[key];
         }
       }
@@ -1881,7 +1881,7 @@ export class TaskStore extends EventEmitter<TaskStoreEvents> {
     const projectScoped: Partial<ProjectSettings> = {};
     if (projectSettings) {
       for (const key of Object.keys(projectSettings)) {
-        if (!isGlobalSettingsKey(key)) {
+        if (!isGlobalOnlySettingsKey(key)) {
           (projectScoped as Record<string, unknown>)[key] = (projectSettings as Record<string, unknown>)[key];
         }
       }
@@ -1904,7 +1904,7 @@ export class TaskStore extends EventEmitter<TaskStoreEvents> {
     // Filter out global-only fields — they should go through updateGlobalSettings()
     const projectPatch: Partial<Settings> = {};
     for (const [key, value] of Object.entries(patch)) {
-      if (!isGlobalSettingsKey(key)) {
+      if (!isGlobalOnlySettingsKey(key)) {
         (projectPatch as Record<string, unknown>)[key] = value;
       }
     }

packages/core/src/types.ts

@@ -2469,6 +2469,7 @@ export {
   DEFAULT_SETTINGS,
   GLOBAL_SETTINGS_KEYS,
   PROJECT_SETTINGS_KEYS,
+  isGlobalOnlySettingsKey,
   isGlobalSettingsKey,
   isProjectSettingsKey,
 } from "./settings-schema.js";