fix: prevent nested .fusion/.fusion dir from PluginStore path bug

PluginStore's constructor treats its rootDir arg as a project root and
internally appends `.fusion` before opening the SQLite DB. Several CLI
call sites were passing the already-resolved `.fusion` directory,
producing a doubled `.fusion/.fusion/fusion.db` that the dashboard
process kept recreating on every project load.

Pass the project root instead so the DB lands in the canonical
`.fusion/fusion.db` alongside the rest of the project's state.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

packages/core/src/index.ts

@@ -1,5 +1,5 @@
-export { COLUMNS, COLUMN_LABELS, COLUMN_DESCRIPTIONS, VALID_TRANSITIONS, DEFAULT_SETTINGS, DEFAULT_GLOBAL_SETTINGS, DEFAULT_PROJECT_SETTINGS, GLOBAL_SETTINGS_KEYS, PROJECT_SETTINGS_KEYS, isGlobalSettingsKey, isProjectSettingsKey, THINKING_LEVELS, THEME_MODES, COLOR_THEMES, WORKFLOW_STEP_TEMPLATES, AGENT_PERMISSIONS, agentToConfigSnapshot, diffConfigSnapshots, isEphemeralAgent, hasAgentIdentity, CheckoutConflictError, EXECUTION_MODES, DEFAULT_EXECUTION_MODE } from "./types.js";
-export type { Column, IssueInfo, IssueState, PrInfo, PrStatus, Task, TaskAttachment, TaskComment, TaskCommentInput, TaskDocument, TaskDocumentRevision, TaskDocumentCreateInput, TaskDocumentWithTask, TaskCreateInput, TaskDetail, InboxTask, AgentLogEntry, AgentLogType, AgentRole, BoardConfig, MergeDetails, MergeResult, Settings, GlobalSettings, ProjectSettings, SettingsScope, DaemonTokenSettings, TaskStep, StepStatus, TaskLogEntry, RunMutationContext, ActivityLogEntry, ActivityEventType, ThinkingLevel, ThemeMode, ColorTheme, ExecutionMode, PlanningQuestion, PlanningSummary, PlanningResponse, PlanningQuestionType, ArchivedTaskEntry, BatchStatusRequest, BatchStatusResponse, BatchStatusEntry, BatchStatusResult, ModelPreset, WorkflowStep, WorkflowStepMode, WorkflowStepPhase, WorkflowStepInput, WorkflowStepResult, WorkflowStepTemplate, Agent, OrgTreeNode, AgentState, AgentDetail, AgentCreateInput, AgentUpdateInput, AgentApiKey, AgentApiKeyCreateResult, AgentCapability, AgentPromptTemplate, AgentPromptsConfig, AgentPermission, TaskAssignSource, AgentAccessState, AgentHeartbeatConfig, AgentBudgetConfig, AgentBudgetStatus, InstructionsBundleConfig, MessageResponseMode, AgentHeartbeatEvent, AgentHeartbeatRun, BlockedStateSnapshot, HeartbeatInvocationSource, AgentTaskSession, AgentRating, AgentRatingSummary, AgentRatingInput, AgentConfigSnapshot, RevisionFieldDiff, AgentConfigRevision, AgentStats, ReflectionTrigger, ReflectionMetrics, AgentReflection, AgentPerformanceSummary, NtfyNotificationEvent, SteeringComment, ParticipantType, MessageType, Message, MessageCreateInput, MessageFilter, Mailbox, CheckoutLease, RunAuditDomain, RunAuditEvent, RunAuditEventInput, RunAuditEventFilter } from "./types.js";
+export { COLUMNS, COLUMN_LABELS, COLUMN_DESCRIPTIONS, VALID_TRANSITIONS, DEFAULT_SETTINGS, DEFAULT_GLOBAL_SETTINGS, DEFAULT_PROJECT_SETTINGS, GLOBAL_SETTINGS_KEYS, PROJECT_SETTINGS_KEYS, isGlobalSettingsKey, isProjectSettingsKey, THINKING_LEVELS, THEME_MODES, COLOR_THEMES, WORKFLOW_STEP_TEMPLATES, AGENT_PERMISSIONS, agentToConfigSnapshot, diffConfigSnapshots, isEphemeralAgent, hasAgentIdentity, CheckoutConflictError, EXECUTION_MODES, DEFAULT_EXECUTION_MODE, validateMessageMetadata } from "./types.js";
+export type { Column, IssueInfo, IssueState, PrInfo, PrStatus, Task, TaskAttachment, TaskComment, TaskCommentInput, TaskDocument, TaskDocumentRevision, TaskDocumentCreateInput, TaskDocumentWithTask, TaskCreateInput, TaskDetail, InboxTask, AgentLogEntry, AgentLogType, AgentRole, BoardConfig, MergeDetails, MergeResult, Settings, GlobalSettings, ProjectSettings, SettingsScope, DaemonTokenSettings, TaskStep, StepStatus, TaskLogEntry, RunMutationContext, ActivityLogEntry, ActivityEventType, ThinkingLevel, ThemeMode, ColorTheme, ExecutionMode, PlanningQuestion, PlanningSummary, PlanningResponse, PlanningQuestionType, ArchivedTaskEntry, BatchStatusRequest, BatchStatusResponse, BatchStatusEntry, BatchStatusResult, ModelPreset, WorkflowStep, WorkflowStepMode, WorkflowStepPhase, WorkflowStepInput, WorkflowStepResult, WorkflowStepTemplate, Agent, OrgTreeNode, AgentState, AgentDetail, AgentCreateInput, AgentUpdateInput, AgentApiKey, AgentApiKeyCreateResult, AgentCapability, AgentPromptTemplate, AgentPromptsConfig, AgentPermission, TaskAssignSource, AgentAccessState, AgentHeartbeatConfig, AgentBudgetConfig, AgentBudgetStatus, InstructionsBundleConfig, MessageResponseMode, AgentHeartbeatEvent, AgentHeartbeatRun, BlockedStateSnapshot, HeartbeatInvocationSource, AgentTaskSession, AgentRating, AgentRatingSummary, AgentRatingInput, AgentConfigSnapshot, RevisionFieldDiff, AgentConfigRevision, AgentStats, ReflectionTrigger, ReflectionMetrics, AgentReflection, AgentPerformanceSummary, NtfyNotificationEvent, SteeringComment, ParticipantType, MessageType, Message, MessageCreateInput, MessageFilter, MessageMetadata, MessageReplyReference, Mailbox, CheckoutLease, RunAuditDomain, RunAuditEvent, RunAuditEventInput, RunAuditEventFilter } from "./types.js";
 export { AGENT_VALID_TRANSITIONS } from "./types.js";
 export {
   BUILTIN_AGENT_PROMPTS,

packages/core/src/message-store.test.ts

@@ -80,6 +80,44 @@ describe("MessageStore", () => {
       expect(message.metadata).toEqual({ taskId: "FN-001", priority: "high" });
     });
 
+    it("persists reply link metadata through storage roundtrip", () => {
+      const original = store.sendMessage({
+        fromId: "user-1",
+        fromType: "user",
+        toId: "agent-1",
+        toType: "agent",
+        content: "Can you help?",
+        type: "user-to-agent",
+      });
+
+      const reply = store.sendMessage({
+        fromId: "agent-1",
+        fromType: "agent",
+        toId: "user-1",
+        toType: "user",
+        content: "Sure",
+        type: "agent-to-user",
+        metadata: { replyTo: { messageId: original.id } },
+      });
+
+      expect(reply.metadata).toEqual({ replyTo: { messageId: original.id } });
+      expect(store.getMessage(reply.id)?.metadata).toEqual({ replyTo: { messageId: original.id } });
+    });
+
+    it("rejects malformed reply metadata", () => {
+      expect(() => {
+        store.sendMessage({
+          fromId: "agent-1",
+          fromType: "agent",
+          toId: "user-1",
+          toType: "user",
+          content: "Bad metadata",
+          type: "agent-to-user",
+          metadata: { replyTo: { messageId: "" } },
+        });
+      }).toThrow("metadata.replyTo.messageId must be a non-empty string");
+    });
+
     it("returns null for non-existent message", () => {
       const result = store.getMessage("msg-nonexistent");
       expect(result).toBeNull();

packages/core/src/message-store.ts

@@ -14,14 +14,7 @@ import { EventEmitter } from "node:events";
 import { randomUUID } from "node:crypto";
 import type { Database } from "./db.js";
 import { fromJson, toJsonNullable } from "./db.js";
-import type {
-  Message,
-  MessageCreateInput,
-  MessageFilter,
-  MessageType,
-  Mailbox,
-  ParticipantType,
-} from "./types.js";
+import { validateMessageMetadata, type Message, type MessageCreateInput, type MessageFilter, type MessageType, type Mailbox, type ParticipantType } from "./types.js";
 
 // ── Event Types ─────────────────────────────────────────────────────
 
@@ -112,7 +105,7 @@ export class MessageStore extends EventEmitter<MessageStoreEvents> {
       content: row.content,
       type: row.type as MessageType,
       read: row.read === 1,
-      metadata: fromJson<Record<string, unknown>>(row.metadata),
+      metadata: fromJson<Message["metadata"]>(row.metadata),
       createdAt: row.createdAt,
       updatedAt: row.updatedAt,
     };
@@ -126,6 +119,8 @@ export class MessageStore extends EventEmitter<MessageStoreEvents> {
    * @returns The created message
    */
   sendMessage(input: MessageCreateInput): Message {
+    validateMessageMetadata(input.metadata);
+
     const now = new Date().toISOString();
     const messageId = `msg-${randomUUID().slice(0, 8)}`;
 

packages/core/src/settings-schema.ts

@@ -29,6 +29,7 @@ export const DEFAULT_GLOBAL_SETTINGS = {
   favoriteModels: undefined,
   openrouterModelSync: true,
   modelOnboardingComplete: undefined,
+  useClaudeCli: undefined,
   // Global baseline lanes for per-role model selection
   executionGlobalProvider: undefined,
   executionGlobalModelId: undefined,

packages/core/src/types.ts

@@ -967,6 +967,17 @@ export interface GlobalSettings {
    *  false/undefined, the dashboard will auto-open the onboarding modal.
    *  Also set to true when the user explicitly dismisses onboarding. */
   modelOnboardingComplete?: boolean;
+  /** When true, route AI model calls through the locally-installed Claude CLI
+   *  via the `pi-claude-cli` pi extension (instead of the direct Anthropic
+   *  API). Enabling this also causes Fusion to symlink its skill into each
+   *  project's `.claude/skills/fusion/` on `fn init`, `fn project add`,
+   *  dashboard project creation, and server startup — so the skill is
+   *  available inside Claude Code sessions that pi spawns.
+   *
+   *  When left undefined, detection falls back to scanning the `packages`
+   *  array in the agent settings for `"npm:pi-claude-cli"` (legacy signal).
+   *  Setting this field explicitly (true/false) always wins. */
+  useClaudeCli?: boolean;
   /** Global baseline AI model provider for task execution (executor agent).
    *  This is the global lane that project-level `executionProvider` can override.
    *  Must be set together with `executionGlobalModelId`. Falls back to
@@ -2904,6 +2915,18 @@ export type ParticipantType = "agent" | "user" | "system";
 /** Message types/categories */
 export type MessageType = "agent-to-agent" | "agent-to-user" | "user-to-agent" | "system";
 
+/** Stable metadata contract for linking a reply to an earlier message. */
+export interface MessageReplyReference {
+  /** ID of the message this one is replying to. */
+  messageId: string;
+}
+
+/** Optional metadata attached to mailbox messages. */
+export interface MessageMetadata extends Record<string, unknown> {
+  /** Optional link to the original message when this message is a reply. */
+  replyTo?: MessageReplyReference;
+}
+
 /** Message record stored in the system */
 export interface Message {
   /** Unique identifier */
@@ -2923,7 +2946,7 @@ export interface Message {
   /** Whether the recipient has read this message */
   read: boolean;
   /** Optional extra data */
-  metadata?: Record<string, unknown>;
+  metadata?: MessageMetadata;
   /** ISO-8601 timestamp of creation */
   createdAt: string;
   /** ISO-8601 timestamp of last update */
@@ -2945,7 +2968,7 @@ export interface MessageCreateInput {
   /** Message category */
   type: MessageType;
   /** Optional extra data */
-  metadata?: Record<string, unknown>;
+  metadata?: MessageMetadata;
 }
 
 /** Filter options for querying messages */
@@ -2960,6 +2983,21 @@ export interface MessageFilter {
   offset?: number;
 }
 
+/** Validate mailbox metadata, including reply-link contract when present. */
+export function validateMessageMetadata(metadata: MessageMetadata | undefined): void {
+  if (!metadata || metadata.replyTo === undefined) {
+    return;
+  }
+
+  if (typeof metadata.replyTo !== "object" || metadata.replyTo === null || Array.isArray(metadata.replyTo)) {
+    throw new Error("metadata.replyTo must be an object");
+  }
+
+  if (typeof metadata.replyTo.messageId !== "string" || metadata.replyTo.messageId.trim().length === 0) {
+    throw new Error("metadata.replyTo.messageId must be a non-empty string");
+  }
+}
+
 /** Mailbox summary for a participant */
 export interface Mailbox {
   /** Owner identifier */