Make chat work directory per-run instead of global

The work directory was stored in a single shared config file, so setting
it in one chat changed it for every chat and new chats inherited a stale
value. Store it as run-scoped metadata: captured on the start event at
creation and updatable mid-chat via an appended workdir-changed event.
The runtime reads the per-run value from AgentState, and the chat input
reads/writes it against the run (pending chats pass it into runs:create).

apps/x/packages/core/src/agents/runtime.ts

@@ -36,19 +36,6 @@ import { getRaw as getInlineTaskAgentRaw } from "../knowledge/inline_task_agent.
 import { getRaw as getAgentNotesAgentRaw } from "../knowledge/agent_notes_agent.js";
 
 const AGENT_NOTES_DIR = path.join(WorkDir, 'knowledge', 'Agent Notes');
-const WORKDIR_CONFIG_FILE = path.join(WorkDir, 'config', 'workdir.json');
-
-function loadUserWorkDir(): string | null {
-    try {
-        if (!fs.existsSync(WORKDIR_CONFIG_FILE)) return null;
-        const raw = fs.readFileSync(WORKDIR_CONFIG_FILE, 'utf-8');
-        const parsed = JSON.parse(raw) as { path?: unknown };
-        const value = typeof parsed.path === 'string' ? parsed.path.trim() : '';
-        return value || null;
-    } catch {
-        return null;
-    }
-}
 
 function loadAgentNotesContext(): string | null {
     const sections: string[] = [];
@@ -673,6 +660,7 @@ export class AgentState {
     runProvider: string | null = null;
     runUseCase: UseCase | null = null;
     runSubUseCase: string | null = null;
+    workingDirectory: string | null = null;
     messages: z.infer<typeof MessageList> = [];
     lastAssistantMsg: z.infer<typeof AssistantMessage> | null = null;
     subflowStates: Record<string, AgentState> = {};
@@ -790,6 +778,10 @@ export class AgentState {
                 this.runProvider = event.provider;
                 this.runUseCase = event.useCase ?? null;
                 this.runSubUseCase = event.subUseCase ?? null;
+                this.workingDirectory = event.workingDirectory ?? null;
+                break;
+            case "workdir-changed":
+                this.workingDirectory = event.workingDirectory ?? null;
                 break;
             case "spawn-subflow":
                 // Seed the subflow state with its agent so downstream loadAgent works.
@@ -1122,7 +1114,7 @@ export async function* streamAgent({
             if (agentNotesContext) {
                 instructionsWithDateTime += `\n\n${agentNotesContext}`;
             }
-            const userWorkDir = loadUserWorkDir();
+            const userWorkDir = state.workingDirectory;
             if (userWorkDir) {
                 loopLogger.log('injecting user work directory', userWorkDir);
                 instructionsWithDateTime += `\n\n# User Work Directory

apps/x/packages/core/src/runs/repo.ts

@@ -5,7 +5,7 @@ import path from "path";
 import fsp from "fs/promises";
 import fs from "fs";
 import readline from "readline";
-import { Run, RunEvent, StartEvent, ListRunsResponse, MessageEvent, UseCase } from "@x/shared/dist/runs.js";
+import { Run, RunEvent, StartEvent, ListRunsResponse, MessageEvent, UseCase, WorkdirChangedEvent } from "@x/shared/dist/runs.js";
 import { getDefaultModelAndProvider } from "../models/defaults.js";
 
 /**
@@ -37,6 +37,7 @@ export type CreateRunRepoOptions = {
     provider: string;
     useCase: z.infer<typeof UseCase>;
     subUseCase?: string;
+    workingDirectory?: string;
 };
 
 function runLogPath(runId: string): string {
@@ -206,6 +207,7 @@ export class FSRunsRepo implements IRunsRepo {
             provider: options.provider,
             useCase: options.useCase,
             ...(options.subUseCase ? { subUseCase: options.subUseCase } : {}),
+            ...(options.workingDirectory ? { workingDirectory: options.workingDirectory } : {}),
             subflow: [],
             ts,
         };
@@ -218,6 +220,7 @@ export class FSRunsRepo implements IRunsRepo {
             provider: options.provider,
             useCase: options.useCase,
             ...(options.subUseCase ? { subUseCase: options.subUseCase } : {}),
+            ...(options.workingDirectory ? { workingDirectory: options.workingDirectory } : {}),
             log: [start],
         };
     }
@@ -244,6 +247,14 @@ export class FSRunsRepo implements IRunsRepo {
         };
         const events: z.infer<typeof RunEvent>[] = [start, ...rawEvents.slice(1) as z.infer<typeof RunEvent>[]];
         const title = this.extractTitle(events);
+        // The current work directory is the start event's value, overridden by the
+        // most recent workdir-changed event (append-only log — last write wins).
+        let workingDirectory: string | undefined = start.workingDirectory || undefined;
+        for (const event of events) {
+            if (event.type === 'workdir-changed') {
+                workingDirectory = (event as z.infer<typeof WorkdirChangedEvent>).workingDirectory || undefined;
+            }
+        }
         return {
             id,
             title,
@@ -253,6 +264,7 @@ export class FSRunsRepo implements IRunsRepo {
             provider: start.provider,
             ...(start.useCase ? { useCase: start.useCase } : {}),
             ...(start.subUseCase ? { subUseCase: start.subUseCase } : {}),
+            ...(workingDirectory ? { workingDirectory } : {}),
             log: events,
         };
     }

apps/x/packages/core/src/runs/runs.ts

@@ -1,7 +1,7 @@
 import z from "zod";
 import container from "../di/container.js";
 import { IMessageQueue, UserMessageContentType, VoiceOutputMode, MiddlePaneContext } from "../application/lib/message-queue.js";
-import { AskHumanResponseEvent, ToolPermissionRequestEvent, ToolPermissionResponseEvent, CreateRunOptions, Run, ListRunsResponse, ToolPermissionAuthorizePayload, AskHumanResponsePayload } from "@x/shared/dist/runs.js";
+import { AskHumanResponseEvent, ToolPermissionRequestEvent, ToolPermissionResponseEvent, CreateRunOptions, Run, ListRunsResponse, ToolPermissionAuthorizePayload, AskHumanResponsePayload, WorkdirChangedEvent } from "@x/shared/dist/runs.js";
 import { IRunsRepo } from "./repo.js";
 import { IAgentRuntime } from "../agents/runtime.js";
 import { IBus } from "../application/lib/bus.js";
@@ -34,11 +34,23 @@ export async function createRun(opts: z.infer<typeof CreateRunOptions>): Promise
         provider,
         useCase,
         ...(opts.subUseCase ? { subUseCase: opts.subUseCase } : {}),
+        ...(opts.workingDirectory ? { workingDirectory: opts.workingDirectory } : {}),
     });
     await bus.publish(run.log[0]);
     return run;
 }
 
+export async function setWorkdir(runId: string, workingDirectory: string | null): Promise<void> {
+    const repo = container.resolve<IRunsRepo>('runsRepo');
+    const event: z.infer<typeof WorkdirChangedEvent> = {
+        runId,
+        type: "workdir-changed",
+        subflow: [],
+        ...(workingDirectory ? { workingDirectory } : {}),
+    };
+    await repo.appendEvents(runId, [event]);
+}
+
 export async function createMessage(runId: string, message: UserMessageContentType, voiceInput?: boolean, voiceOutput?: VoiceOutputMode, searchEnabled?: boolean, middlePaneContext?: MiddlePaneContext): Promise<string> {
     const queue = container.resolve<IMessageQueue>('messageQueue');
     const id = await queue.enqueue(runId, message, voiceInput, voiceOutput, searchEnabled, middlePaneContext);

apps/x/packages/shared/src/ipc.ts

@@ -234,6 +234,15 @@ const ipcSchemas = {
     }),
     res: Run,
   },
+  'runs:setWorkdir': {
+    req: z.object({
+      runId: z.string(),
+      workingDirectory: z.string().nullable(),
+    }),
+    res: z.object({
+      success: z.literal(true),
+    }),
+  },
   'runs:list': {
     req: z.object({
       cursor: z.string().optional(),

apps/x/packages/shared/src/runs.ts

@@ -31,6 +31,9 @@ export const StartEvent = BaseRunEvent.extend({
         "knowledge_sync",
     ]).optional(),
     subUseCase: z.string().optional(),
+    // Per-run work directory chosen at creation. Optional: a run may have none,
+    // and it can be changed later via WorkdirChangedEvent.
+    workingDirectory: z.string().optional(),
 });
 
 export const SpawnSubFlowEvent = BaseRunEvent.extend({
@@ -105,6 +108,12 @@ export const RunStoppedEvent = BaseRunEvent.extend({
     reason: z.enum(["user-requested", "force-stopped"]).optional(),
 });
 
+export const WorkdirChangedEvent = BaseRunEvent.extend({
+    type: z.literal("workdir-changed"),
+    // Absent/empty means the work directory was cleared.
+    workingDirectory: z.string().optional(),
+});
+
 export const RunEvent = z.union([
     RunProcessingStartEvent,
     RunProcessingEndEvent,
@@ -121,6 +130,7 @@ export const RunEvent = z.union([
     ToolPermissionResponseEvent,
     RunErrorEvent,
     RunStoppedEvent,
+    WorkdirChangedEvent,
 ]);
 
 export const ToolPermissionAuthorizePayload = ToolPermissionResponseEvent.pick({
@@ -153,6 +163,7 @@ export const Run = z.object({
     provider: z.string(),
     useCase: UseCase.optional(),
     subUseCase: z.string().optional(),
+    workingDirectory: z.string().optional(),
     log: z.array(RunEvent),
 });
 
@@ -172,4 +183,5 @@ export const CreateRunOptions = z.object({
     provider: z.string().optional(),
     useCase: UseCase.optional(),
     subUseCase: z.string().optional(),
+    workingDirectory: z.string().optional(),
 });