fix: migrate the internal exec callers to timeoutSeconds

Removing `timeout` from the exec schema broke three real internal callers that
the earlier survey missed, plus two test files and the runtime's own reads.
`check-test-types` caught it; my local search had filtered `timeout:` matches to
lines mentioning "exec" and discarded these.

- src/auto-reply/reply/bash-command.ts
- src/auto-reply/reply/commands-diagnostics.ts
- src/auto-reply/reply/commands-export-trajectory.ts
  all passed `timeout: timeoutSec` and now pass `timeoutSeconds: timeoutSec`.
- bash-tools.exec-run.ts reads the field through the same typeof narrowing the
  third call site already used; `params` is loosely typed, so a raw read is
  `unknown`.
- Test fixtures updated. A vitest `waitFor({ timeout })` option in
  background-abort.test.ts is NOT an exec param and was left alone.

`run-tsgo.mjs -p test/tsconfig/tsconfig.core.test.json` now reports zero errors
in changed files; the 5 remaining `rejectSymlinks` errors are pre-existing on
main. 148 tests pass across the affected suites.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01XQojYRCUdXhcKFeu4QW5Gh

src/agents/bash-tools.exec-gateway-approval.e2e.test.ts

@@ -151,7 +151,7 @@ describe("gateway-hosted exec approvals", () => {
       const pending = await tool.execute("exec-approval-e2e", {
         command: "printf 'smoke\\n'",
         workdir: workspaceDir,
-        timeout: 5,
+        timeoutSeconds: 5,
       });
 
       expect(pending.details.status).toBe("approval-pending");

src/agents/bash-tools.exec-run.ts

@@ -421,7 +421,8 @@ export function createExecTool(
             strictInlineEval: defaults?.strictInlineEval,
             commandHighlighting: defaults?.commandHighlighting,
             trigger: defaults?.trigger,
-            timeoutSec: params.timeoutSeconds,
+            timeoutSec:
+              typeof params.timeoutSeconds === "number" ? params.timeoutSeconds : undefined,
             defaultTimeoutSec,
             approvalRunningNoticeMs,
             warnings,
@@ -444,7 +445,8 @@ export function createExecTool(
             pathPrepend: defaultPathPrepend,
             requestedEnv,
             pty: params.pty === true && !sandbox,
-            timeoutSec: params.timeoutSeconds,
+            timeoutSec:
+              typeof params.timeoutSeconds === "number" ? params.timeoutSeconds : undefined,
             defaultTimeoutSec,
             security,
             ask,

src/agents/bash-tools.exec.background-abort.test.ts

@@ -232,7 +232,7 @@ test("background exec still times out after tool signal abort", async () => {
     executeParams: {
       command: BACKGROUND_HOLD_CMD,
       background: true,
-      timeout: BACKGROUND_TIMEOUT_SEC,
+      timeoutSeconds: BACKGROUND_TIMEOUT_SEC,
     },
     abortAfterStart: true,
     expectedTimeoutSec: BACKGROUND_TIMEOUT_SEC,
@@ -261,7 +261,7 @@ test("background exec with timeout zero bypasses default timeout", async () => {
   const result = await tool.execute("toolcall", {
     command: BACKGROUND_HOLD_CMD,
     background: true,
-    timeout: 0,
+    timeoutSeconds: 0,
   });
   expect(result.details.status).toBe("running");
   const sessionId = (result.details as { sessionId: string }).sessionId;
@@ -279,7 +279,7 @@ test("yielded background exec still times out", async () => {
     executeParams: {
       command: BACKGROUND_HOLD_CMD,
       yieldMs: 5,
-      timeout: YIELDED_BACKGROUND_TIMEOUT_SEC,
+      timeoutSeconds: YIELDED_BACKGROUND_TIMEOUT_SEC,
     },
     expectedTimeoutSec: YIELDED_BACKGROUND_TIMEOUT_SEC,
   });

src/auto-reply/reply/bash-command.ts

@@ -369,7 +369,7 @@ export async function handleBashChatCommand(params: {
       command: commandText,
       background: shouldBackgroundImmediately,
       yieldMs: shouldBackgroundImmediately ? undefined : foregroundMs,
-      timeout: timeoutSec,
+      timeoutSeconds: timeoutSec,
       elevated: true,
     });
 

src/auto-reply/reply/commands-diagnostics.ts

@@ -313,7 +313,7 @@ async function requestGatewayDiagnosticsExportApproval(
       security: "allowlist",
       ask: "always",
       background: true,
-      timeout: timeoutSec,
+      timeoutSeconds: timeoutSec,
     });
     if (result.details?.status === "approval-pending") {
       return { status: "pending" };

src/auto-reply/reply/commands-export-trajectory.ts

@@ -203,7 +203,7 @@ async function requestTrajectoryExportApproval(
       security: "allowlist",
       ask: "always",
       background: true,
-      timeout: timeoutSec,
+      timeoutSeconds: timeoutSec,
     });
     return [
       `Trajectory bundle: requested \`${request.displayCommand}\` through exec approval. Approve once to create the bundle; do not use allow-all for trajectory exports.`,