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/apps/main/src/ipc.ts

@@ -524,6 +524,10 @@ export function setupIpcHandlers() {
     'runs:fetch': async (_event, args) => {
       return runsCore.fetchRun(args.runId);
     },
+    'runs:setWorkdir': async (_event, args) => {
+      await runsCore.setWorkdir(args.runId, args.workingDirectory);
+      return { success: true as const };
+    },
     'runs:list': async (_event, args) => {
       return runsCore.listRuns(args.cursor);
     },

apps/x/apps/renderer/src/App.tsx

@@ -970,6 +970,7 @@ function App() {
   const newChatTabId = () => `chat-tab-${++chatTabIdCounterRef.current}`
   const chatDraftsRef = useRef(new Map<string, string>())
   const selectedModelByTabRef = useRef(new Map<string, { provider: string; model: string }>())
+  const pendingWorkDirByTabRef = useRef(new Map<string, string>())
   const chatScrollTopByTabRef = useRef(new Map<string, number>())
   const [toolOpenByTab, setToolOpenByTab] = useState<Record<string, Record<string, boolean>>>({})
   const [chatViewportAnchorByTab, setChatViewportAnchorByTab] = useState<Record<string, ChatViewportAnchorState>>({})
@@ -2354,10 +2355,13 @@ function App() {
       let newRunCreatedAt: string | null = null
       if (!currentRunId) {
         const selected = selectedModelByTabRef.current.get(submitTabId)
+        const pendingWorkDir = pendingWorkDirByTabRef.current.get(submitTabId)
         const run = await window.ipc.invoke('runs:create', {
           agentId,
           ...(selected ? { model: selected.model, provider: selected.provider } : {}),
+          ...(pendingWorkDir ? { workingDirectory: pendingWorkDir } : {}),
         })
+        pendingWorkDirByTabRef.current.delete(submitTabId)
         currentRunId = run.id
         newRunCreatedAt = run.createdAt
         setRunId(currentRunId)
@@ -2666,6 +2670,7 @@ function App() {
     })
     chatDraftsRef.current.delete(tabId)
     selectedModelByTabRef.current.delete(tabId)
+    pendingWorkDirByTabRef.current.delete(tabId)
     chatScrollTopByTabRef.current.delete(tabId)
     setToolOpenByTab((prev) => {
       if (!(tabId in prev)) return prev
@@ -5300,6 +5305,13 @@ function App() {
                                 selectedModelByTabRef.current.delete(tab.id)
                               }
                             }}
+                            onWorkDirChange={(dir) => {
+                              if (dir) {
+                                pendingWorkDirByTabRef.current.set(tab.id, dir)
+                              } else {
+                                pendingWorkDirByTabRef.current.delete(tab.id)
+                              }
+                            }}
                             isRecording={isActive && isRecording}
                             recordingText={isActive ? voice.interimText : undefined}
                             recordingState={isActive ? (voice.state === 'connecting' ? 'connecting' : 'listening') : undefined}
@@ -5360,6 +5372,13 @@ function App() {
                     selectedModelByTabRef.current.delete(tabId)
                   }
                 }}
+                onWorkDirChangeForTab={(tabId, dir) => {
+                  if (dir) {
+                    pendingWorkDirByTabRef.current.set(tabId, dir)
+                  } else {
+                    pendingWorkDirByTabRef.current.delete(tabId)
+                  }
+                }}
                 pendingAskHumanRequests={pendingAskHumanRequests}
                 allPermissionRequests={allPermissionRequests}
                 permissionResponses={permissionResponses}

apps/x/apps/renderer/src/components/chat-input-with-mentions.tsx

@@ -133,6 +133,9 @@ interface ChatInputInnerProps {
   onTtsModeChange?: (mode: 'summary' | 'full') => void
   /** Fired when the user picks a different model in the dropdown (only when no run exists yet). */
   onSelectedModelChange?: (model: SelectedModel | null) => void
+  /** Fired when the user sets/clears the work directory before a run exists, so the
+   * parent can pass it into runs:create. Once a run exists, changes go straight to the run. */
+  onWorkDirChange?: (dir: string | null) => void
 }
 
 function ChatInputInner({
@@ -159,6 +162,7 @@ function ChatInputInner({
   onToggleTts,
   onTtsModeChange,
   onSelectedModelChange,
+  onWorkDirChange,
 }: ChatInputInnerProps) {
   const controller = usePromptInputController()
   const message = controller.textInput.value
@@ -256,21 +260,22 @@ function ChatInputInner({
     return () => window.removeEventListener('models-config-changed', handler)
   }, [loadModelConfig])
 
-  // Load currently configured work directory
+  // The work directory is run-scoped. For an existing run, load it from the run.
-  const loadWorkDir = useCallback(async () => {
+  // For a new chat (no run yet) the chosen directory lives in local state until
-    try {
+  // the run is created, and is reported up via onWorkDirChange so it can be
-      const result = await window.ipc.invoke('workspace:readFile', { path: 'config/workdir.json' })
+  // passed into runs:create.
-      const parsed = JSON.parse(result.data)
-      const value = typeof parsed?.path === 'string' ? parsed.path.trim() : ''
-      setWorkDir(value || null)
-    } catch {
-      setWorkDir(null)
-    }
-  }, [])
-
   useEffect(() => {
-    loadWorkDir()
+    if (!runId) {
-  }, [isActive, loadWorkDir])
+      setWorkDir(null)
+      return
+    }
+    let cancelled = false
+    window.ipc.invoke('runs:fetch', { runId }).then((run) => {
+      if (cancelled) return
+      setWorkDir(run.workingDirectory ?? null)
+    }).catch(() => { /* legacy run or fetch failure — leave as-is */ })
+    return () => { cancelled = true }
+  }, [runId])
 
   const handleSetWorkDir = useCallback(async () => {
     try {
@@ -279,31 +284,33 @@ function ChatInputInner({
         defaultPath: workDir ?? undefined,
       })
       if (!chosen) return
-      await window.ipc.invoke('workspace:writeFile', {
+      if (runId) {
-        path: 'config/workdir.json',
+        await window.ipc.invoke('runs:setWorkdir', { runId, workingDirectory: chosen })
-        data: JSON.stringify({ path: chosen }, null, 2),
+      } else {
-      })
+        onWorkDirChange?.(chosen)
+      }
       setWorkDir(chosen)
       toast.success(`Work directory set: ${chosen}`)
     } catch (err) {
       console.error('Failed to set work directory', err)
       toast.error('Failed to set work directory')
     }
-  }, [workDir])
+  }, [workDir, runId, onWorkDirChange])
 
   const handleClearWorkDir = useCallback(async () => {
     try {
-      await window.ipc.invoke('workspace:writeFile', {
+      if (runId) {
-        path: 'config/workdir.json',
+        await window.ipc.invoke('runs:setWorkdir', { runId, workingDirectory: null })
-        data: JSON.stringify({}, null, 2),
+      } else {
-      })
+        onWorkDirChange?.(null)
+      }
       setWorkDir(null)
       toast.success('Work directory cleared')
     } catch (err) {
       console.error('Failed to clear work directory', err)
       toast.error('Failed to clear work directory')
     }
-  }, [])
+  }, [runId, onWorkDirChange])
 
   // Check search tool availability (exa or signed-in via gateway)
   useEffect(() => {
@@ -790,6 +797,7 @@ export interface ChatInputWithMentionsProps {
   onToggleTts?: () => void
   onTtsModeChange?: (mode: 'summary' | 'full') => void
   onSelectedModelChange?: (model: SelectedModel | null) => void
+  onWorkDirChange?: (dir: string | null) => void
 }
 
 export function ChatInputWithMentions({
@@ -819,6 +827,7 @@ export function ChatInputWithMentions({
   onToggleTts,
   onTtsModeChange,
   onSelectedModelChange,
+  onWorkDirChange,
 }: ChatInputWithMentionsProps) {
   return (
     <PromptInputProvider knowledgeFiles={knowledgeFiles} recentFiles={recentFiles} visibleFiles={visibleFiles}>
@@ -846,6 +855,7 @@ export function ChatInputWithMentions({
         onToggleTts={onToggleTts}
         onTtsModeChange={onTtsModeChange}
         onSelectedModelChange={onSelectedModelChange}
+        onWorkDirChange={onWorkDirChange}
       />
     </PromptInputProvider>
   )

apps/x/apps/renderer/src/components/chat-sidebar.tsx

@@ -195,6 +195,7 @@ interface ChatSidebarProps {
   getInitialDraft?: (tabId: string) => string | undefined
   onDraftChangeForTab?: (tabId: string, text: string) => void
   onSelectedModelChangeForTab?: (tabId: string, model: SelectedModel | null) => void
+  onWorkDirChangeForTab?: (tabId: string, dir: string | null) => void
   pendingAskHumanRequests?: ChatTabViewState['pendingAskHumanRequests']
   allPermissionRequests?: ChatTabViewState['allPermissionRequests']
   permissionResponses?: ChatTabViewState['permissionResponses']
@@ -250,6 +251,7 @@ export function ChatSidebar({
   getInitialDraft,
   onDraftChangeForTab,
   onSelectedModelChangeForTab,
+  onWorkDirChangeForTab,
   pendingAskHumanRequests = new Map(),
   allPermissionRequests = new Map(),
   permissionResponses = new Map(),
@@ -742,6 +744,7 @@ export function ChatSidebar({
                           initialDraft={getInitialDraft?.(tab.id)}
                           onDraftChange={onDraftChangeForTab ? (text) => onDraftChangeForTab(tab.id, text) : undefined}
                           onSelectedModelChange={onSelectedModelChangeForTab ? (m) => onSelectedModelChangeForTab(tab.id, m) : undefined}
+                          onWorkDirChange={onWorkDirChangeForTab ? (dir) => onWorkDirChangeForTab(tab.id, dir) : undefined}
                           isRecording={isActive && isRecording}
                           recordingText={isActive ? recordingText : undefined}
                           recordingState={isActive ? recordingState : undefined}

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(),
 });