Ignore it, it was opened by mistake so I have closed it myself, Sorry.

apps/server/src/provider/CodexDeveloperInstructions.ts

@@ -195,6 +195,7 @@ ${browserToolInstructions(browserToolsAvailable)}
 export interface CodexRuntimeInfo {
   readonly model: string;
   readonly reasoningEffort: string;
+  readonly multiRepo?: boolean | undefined;
 }
 
 export function buildCodexDeveloperInstructions(

apps/server/src/provider/Layers/AntigravityAdapter.ts

@@ -192,6 +192,8 @@ interface TurnIntent {
 interface SessionContext {
   readonly threadId: ThreadId;
   readonly cwd: string;
+  /** The session spans several repository roots. */
+  readonly multiRepo: boolean;
   readonly nativeSessionId: string;
   readonly scope: Scope.Closeable;
   readonly runtime: Runtime;
@@ -865,6 +867,7 @@ export const makeAntigravityAdapter = Effect.fn("makeAntigravityAdapter")(functi
               context = {
                 threadId: input.threadId,
                 cwd,
+                multiRepo: (input.additionalRoots?.length ?? 0) > 0,
                 nativeSessionId: started.sessionId,
                 scope: sessionScope,
                 runtime,
@@ -1085,7 +1088,11 @@ export const makeAntigravityAdapter = Effect.fn("makeAntigravityAdapter")(functi
                   ...prompt,
                   {
                     type: "text",
-                    text: buildRuntimeInstructions({ harness: "Antigravity", model }),
+                    text: buildRuntimeInstructions({
+                      harness: "Antigravity",
+                      model,
+                      multiRepo: context.multiRepo,
+                    }),
                   },
                 ],
               },

apps/server/src/provider/Layers/ClaudeAdapter.test.ts

@@ -461,6 +461,29 @@ describe("ClaudeAdapterLive", () => {
     );
   });
 
+  it.effect("asks a multi-repo session for absolute file paths", () => {
+    const harness = makeHarness();
+    return Effect.gen(function* () {
+      const adapter = yield* ClaudeAdapter;
+      yield* adapter.startSession({
+        threadId: THREAD_ID,
+        provider: ProviderDriverKind.make("claudeAgent"),
+        cwd: "/workspace",
+        additionalRoots: ["/workspace/api", "/workspace/web"],
+        runtimeMode: "full-access",
+      });
+
+      assert.deepEqual(harness.getLastCreateQueryInput()?.options.systemPrompt, {
+        type: "preset",
+        preset: "claude_code",
+        append: buildRuntimeInstructions({ harness: "Claude Code", multiRepo: true }),
+      });
+    }).pipe(
+      Effect.provideService(Random.Random, makeDeterministicRandomService()),
+      Effect.provide(harness.layer),
+    );
+  });
+
   it.effect("derives auto permission mode from auto runtime policy without skip flag", () => {
     const harness = makeHarness();
     return Effect.gen(function* () {

apps/server/src/provider/Layers/ClaudeAdapter.ts

@@ -4925,7 +4925,10 @@ export const makeClaudeAdapter = Effect.fn("makeClaudeAdapter")(function* (
           type: "preset",
           preset: "claude_code",
           // Model and effort can change after this session-level prompt is set.
-          append: buildRuntimeInstructions({ harness: "Claude Code" }),
+          append: buildRuntimeInstructions({
+            harness: "Claude Code",
+            multiRepo: (input.additionalRoots?.length ?? 0) > 0,
+          }),
         },
         settingSources: [...CLAUDE_SETTING_SOURCES],
         // `ultracode` is a Claude Code setting, not an API effort level. It is

apps/server/src/provider/Layers/CodexSessionRuntime.test.ts

@@ -287,6 +287,24 @@ describe("buildTurnStartParams", () => {
     });
   });
 
+  it.effect("asks a multi-repo session for absolute file paths", () =>
+    Effect.gen(function* () {
+      const instructions = function* (multiRepo: boolean) {
+        const params = yield* buildTurnStartParams({
+          threadId: "provider-thread-1",
+          runtimeMode: "full-access",
+          prompt: "Go",
+          interactionMode: "default",
+          multiRepo,
+        });
+        return params.collaborationMode?.settings.developer_instructions ?? "";
+      };
+
+      NodeAssert.match(yield* instructions(true), /<multi_repo_workspace>/);
+      NodeAssert.doesNotMatch(yield* instructions(false), /<multi_repo_workspace>/);
+    }),
+  );
+
   it("reports the same fallback model and effort in settings and instructions", () => {
     const params = Effect.runSync(
       buildTurnStartParams({

apps/server/src/provider/Layers/CodexSessionRuntime.ts

@@ -590,6 +590,7 @@ function buildCodexCollaborationMode(input: {
   readonly model?: string;
   readonly effort?: EffectCodexSchema.V2TurnStartParams__ReasoningEffort;
   readonly browserToolsAvailable?: boolean | T3CodeToolAvailability;
+  readonly multiRepo?: boolean;
 }): EffectCodexSchema.V2TurnStartParams__CollaborationMode | undefined {
   if (input.interactionMode === undefined) {
     return undefined;
@@ -603,7 +604,7 @@ function buildCodexCollaborationMode(input: {
       reasoning_effort: reasoningEffort,
       developer_instructions: buildCodexDeveloperInstructions(
         input.interactionMode,
-        { model, reasoningEffort },
+        { model, reasoningEffort, multiRepo: input.multiRepo },
         input.browserToolsAvailable ?? true,
       ),
     },
@@ -628,6 +629,8 @@ export function buildTurnStartParams(input: {
   readonly interactionMode?: ProviderInteractionMode;
   /** Defaults to true so callers that predate the agent-access gate are unchanged. */
   readonly browserToolsAvailable?: boolean | T3CodeToolAvailability;
+  /** The session spans several repository roots. */
+  readonly multiRepo?: boolean;
 }): Effect.Effect<
   CodexTurnStartParamsWithCollaborationMode,
   CodexErrors.CodexAppServerProtocolParseError
@@ -649,6 +652,7 @@ export function buildTurnStartParams(input: {
     ...(input.model ? { model: input.model } : {}),
     ...(input.effort ? { effort: input.effort } : {}),
     browserToolsAvailable: input.browserToolsAvailable ?? true,
+    ...(input.multiRepo ? { multiRepo: true } : {}),
   });
 
   return decodeCodexTurnStartParamsWithCollaborationMode({
@@ -2552,6 +2556,7 @@ export const makeCodexSessionRuntime = (
               options.appServerArgs,
               options.mcpCapabilities,
             ),
+            multiRepo: (options.additionalRoots?.length ?? 0) > 0,
           });
           const rawResponse = yield* client.raw.request("turn/start", params);
           const response = yield* decodeV2TurnStartResponse(rawResponse).pipe(

apps/server/src/provider/Layers/CursorAdapter.ts

@@ -138,6 +138,8 @@ interface CursorSessionContext {
   session: ProviderSession;
   readonly scope: Scope.Closeable;
   readonly acp: AcpSessionRuntime.AcpSessionRuntime["Service"];
+  /** The session spans several repository roots. */
+  readonly multiRepo: boolean;
   notificationFiber: Fiber.Fiber<void, never> | undefined;
   readonly pendingApprovals: Map<ApprovalRequestId, PendingApproval>;
   readonly pendingUserInputs: Map<ApprovalRequestId, PendingUserInput>;
@@ -793,6 +795,7 @@ export function makeCursorAdapter(
             session,
             scope: sessionScope,
             acp,
+            multiRepo: (input.additionalRoots?.length ?? 0) > 0,
             notificationFiber: undefined,
             pendingApprovals,
             pendingUserInputs,
@@ -1097,7 +1100,11 @@ export function makeCursorAdapter(
                     ...promptParts,
                     {
                       type: "text",
-                      text: buildRuntimeInstructions({ harness: "Cursor", model: resolvedModel }),
+                      text: buildRuntimeInstructions({
+                        harness: "Cursor",
+                        model: resolvedModel,
+                        multiRepo: ctx.multiRepo,
+                      }),
                     },
                   ],
             })

apps/server/src/provider/Layers/GrokAdapter.ts

@@ -138,6 +138,8 @@ interface GrokSessionContext {
   session: ProviderSession;
   readonly scope: Scope.Closeable;
   readonly acp: AcpSessionRuntime.AcpSessionRuntime["Service"];
+  /** The session spans several repository roots. */
+  readonly multiRepo: boolean;
   notificationFiber: Fiber.Fiber<void, never> | undefined;
   readonly pendingApprovals: Map<ApprovalRequestId, PendingApproval>;
   readonly pendingUserInputs: Map<ApprovalRequestId, PendingUserInput>;
@@ -1291,6 +1293,7 @@ export function makeGrokAdapter(grokSettings: GrokSettings, options?: GrokAdapte
             session,
             scope: sessionScope,
             acp,
+            multiRepo: (input.additionalRoots?.length ?? 0) > 0,
             notificationFiber: undefined,
             pendingApprovals,
             pendingUserInputs,
@@ -1647,6 +1650,7 @@ export function makeGrokAdapter(grokSettings: GrokSettings, options?: GrokAdapte
                       harness: "Grok",
                       model: displayModel,
                       reasoningEffort: normalizeGrokReasoningEffort(requestedTurnReasoningEffort),
+                      multiRepo: ctx.multiRepo,
                     });
               for (let yieldAttempt = 0; yieldAttempt < 8; yieldAttempt += 1) {
                 yield* Effect.yieldNow;

apps/server/src/provider/Layers/OpenCodeAdapter.ts

@@ -341,6 +341,8 @@ interface OpenCodeSessionContext {
   readonly client: OpencodeClient;
   readonly server: OpenCodeServerConnection;
   readonly directory: string;
+  /** The session spans several repository roots. */
+  readonly multiRepo: boolean;
   openCodeSessionId: string;
   readonly relatedSessionIds: Set<string>;
   readonly resolvedRequestIds: Set<string>;
@@ -3007,6 +3009,7 @@ export function makeOpenCodeAdapter(
           client: started.client,
           server: started.server,
           directory,
+          multiRepo: (input.additionalRoots?.length ?? 0) > 0,
           openCodeSessionId: started.openCodeSession.id,
           relatedSessionIds: new Set([started.openCodeSession.id]),
           resolvedRequestIds: new Set(),
@@ -3283,6 +3286,7 @@ export function makeOpenCodeAdapter(
                     system: buildRuntimeInstructions({
                       harness: "OpenCode",
                       model: `${parsedModel.providerID}/${parsedModel.modelID}`,
+                      multiRepo: context.multiRepo,
                     }),
                     parts: [...(text ? [{ type: "text" as const, text }] : []), ...fileParts],
                   },

apps/server/src/provider/RuntimeInstructions.test.ts

@@ -25,4 +25,11 @@ describe("buildRuntimeInstructions", () => {
     expect(instructions).toContain("through the Cursor harness.");
     expect(instructions).not.toContain("reasoning effort");
   });
+
+  it("asks for absolute file paths only when the session spans several repos", () => {
+    expect(buildRuntimeInstructions({ harness: "Codex", multiRepo: true })).toContain(
+      "<multi_repo_workspace>",
+    );
+    expect(buildRuntimeInstructions({ harness: "Codex" })).not.toContain("<multi_repo_workspace>");
+  });
 });

apps/server/src/provider/RuntimeInstructions.ts

@@ -2,18 +2,24 @@ const PULL_REQUEST_LINKING_INSTRUCTIONS = `<pull_request_linking>
 When the t3-code MCP server exposes link_pull_request, you must use it to register every pull request you create or work on for this thread. Call link_pull_request with the full PR URL immediately after creating a PR or starting work on an existing PR. For a stack, call it for every layer, not just the current branch or the top PR. This applies when creating or updating PRs through gh, gh stack, another CLI, or the host API: those operations do not register the PRs with this thread. Linking an already-linked PR is safe. Before finishing PR work, call list_thread_pull_requests and link any PR from your work that is missing. Do not link unrelated PRs mentioned only as background. If a linking call fails, report that failure instead of claiming the PR is linked.
 </pull_request_linking>`;
 
+const MULTI_REPO_FILE_PATH_INSTRUCTIONS = `<multi_repo_workspace>
+This workspace contains more than one git repository. Tools such as git print paths relative to the repository they ran in, so the same relative path can refer to files in different repositories. When you mention a file or directory in your response, write its absolute path.
+</multi_repo_workspace>`;
+
 /** Shared runtime context; omit model and effort when the harness manages them dynamically. */
 export function buildRuntimeInstructions(runtime: {
   readonly harness: string;
   readonly model?: string | undefined;
   readonly reasoningEffort?: string | undefined;
+  /** True when the session spans more than one repository root. */
+  readonly multiRepo?: boolean | undefined;
 }): string {
   const harness = toSingleLine(runtime.harness);
   const model = toSingleLine(runtime.model ?? "");
   const effort = toSingleLine(runtime.reasoningEffort ?? "");
   const modelInfo = model && model !== "auto" && model !== "default" ? `, as ${model}` : "";
   const effortInfo = effort ? ` with ${effort} reasoning effort` : "";
-  return `<runtime_info>In case you're asked: you are running in T3 Code through the ${harness} harness${modelInfo}${effortInfo}. No need to mention this otherwise. You can embed images and videos in your response using Markdown with absolute file paths.</runtime_info>\n\n${PULL_REQUEST_LINKING_INSTRUCTIONS}`;
+  return `<runtime_info>In case you're asked: you are running in T3 Code through the ${harness} harness${modelInfo}${effortInfo}. No need to mention this otherwise. You can embed images and videos in your response using Markdown with absolute file paths.</runtime_info>\n\n${PULL_REQUEST_LINKING_INSTRUCTIONS}${runtime.multiRepo ? `\n\n${MULTI_REPO_FILE_PATH_INSTRUCTIONS}` : ""}`;
 }
 
 function toSingleLine(value: string): string {

apps/web/src/components/ChatMarkdown.tsx

@@ -2383,16 +2383,17 @@ function useChatMarkdownState({
     return metaByHref;
   }, [cwd, imageBaseDir, repoRootsKey, text]);
   const inlineCodeFileLinkMetaByText = useMemo(() => {
+    const roots = repoRootsKey ? repoRootsKey.split("\0") : undefined;
     const metaByText = new Map<string, MarkdownFileLinkMeta>();
     for (const span of extractInlineCodeSpans(text)) {
       if (metaByText.has(span)) continue;
-      const meta = resolveInlineCodeFileLinkMeta(span, cwd, imageBaseDir ?? cwd);
+      const meta = resolveInlineCodeFileLinkMeta(span, cwd, imageBaseDir ?? cwd, roots);
       if (meta) {
         metaByText.set(span, meta);
       }
     }
     return metaByText;
-  }, [cwd, imageBaseDir, text]);
+  }, [cwd, imageBaseDir, repoRootsKey, text]);
   const fileLinkParentSuffixByPath = useMemo(() => {
     const filePaths = [
       ...[...markdownFileLinkMetaByHref.values()].map((meta) => meta.filePath),