fix(mothership): settle a sim_cli wait that outlasted --wait-timeout as done, not failed

apps/sim/lib/mothership/tools/handlers/sim-cli-bridge.test.ts

@@ -18,7 +18,8 @@ vi.mock('@/lib/execution/remote-sandbox/session-files', () => ({
   writeSessionSandboxFile: mockWrite,
   resolveSessionPath: (path: string) => (path.startsWith('/') ? path : `/home/user/${path}`),
 }))
-vi.mock('sim/embed', () => ({
+vi.mock('sim/embed', async (importOriginal) => ({
+  ...(await importOriginal<typeof import('sim/embed')>()),
   runEmbeddedCli: mockRunEmbeddedCli,
   createEmbeddedClient: vi.fn(),
 }))
@@ -202,4 +203,17 @@ describe('sim-cli handler executes the worker-built request', () => {
     expect(mockWrite).not.toHaveBeenCalled()
     expect(result.success).toBe(false)
   })
+
+  it('settles a wait that outlasted --wait-timeout as done, keeping its exit status for the worker', async () => {
+    const stderr = 'Run run-1 is still running after 240s and continues in the background.'
+    mockRunEmbeddedCli.mockResolvedValue({ exitCode: 4, stdout: '{"status":"running"}', stderr })
+    const result = await executeSimCli(
+      cli(['workflows', 'runs', 'wait', 'run-1', '--workflow', 'wf-1', '--wait-timeout', '240']),
+      context
+    )
+    expect(result).toEqual({
+      success: true,
+      output: { exitCode: 4, stdout: '{"status":"running"}', stderr },
+    })
+  })
 })

apps/sim/lib/mothership/tools/handlers/sim-cli.ts

@@ -1,5 +1,6 @@
 import { createLogger } from '@sim/logger'
 import { getErrorMessage } from '@sim/utils/errors'
+import { STILL_RUNNING_EXIT_CODE } from 'sim/embed'
 import { executeAgentCliRequest } from '@/lib/mothership/agent-cli'
 import { messageForCopilotApplicationError } from '@/lib/mothership/application/errors'
 import { AgentCliRequest } from '@/lib/mothership/generated/agent-cli'
@@ -15,6 +16,9 @@ const logger = createLogger('MothershipSimCli')
  * (`request`) beside the model's raw argv (`args`, kept for display and the log); only
  * the request is executed — this side never re-parses tokens. The worker folds
  * exitCode/stdout/stderr into the model window and applies its own output budget.
+ * A wait whose `--wait-timeout` elapsed with the work still going settles the call as
+ * done: the worker continues it in further calls, so the chat, the tool record and the
+ * tool metrics must not read it as a failure.
  */
 export async function executeSimCli(
   params: Record<string, unknown>,
@@ -63,12 +67,12 @@ export async function executeSimCli(
       sink: parsed.data.sink?.kind ?? 'none',
       stdoutBytes: result.stdout.length,
     })
+    if (result.exitCode === 0 || result.exitCode === STILL_RUNNING_EXIT_CODE)
+      return { success: true, output: result }
     return {
-      success: result.exitCode === 0,
+      success: false,
       output: result,
-      ...(result.exitCode === 0
-        ? {}
-        : { error: result.stderr.split('\n')[0] || `sim CLI exited with code ${result.exitCode}` }),
+      error: result.stderr.split('\n')[0] || `sim CLI exited with code ${result.exitCode}`,
     }
   } catch (error) {
     return {

packages/sim-cli/src/commands/protocol/workflow-run-wait.ts

@@ -6,6 +6,7 @@ import { hasProgressTerminal, styles } from '#sim-cli/output/presentation'
 import { CLI_CONTRACT } from '../../contract/commands'
 import type { CommandSpec } from '../../contract/types'
 import { setSoftExitCode } from '../../embed-context'
+import { STILL_RUNNING_EXIT_CODE } from '../../exit-codes'
 import { V2_OPERATIONS } from '../../generated/v2-api'
 import { SimApiError } from '../../http/client'
 import { apiCommand, type Connection } from '../../runtime/called-operations'
@@ -39,7 +40,7 @@ const WAIT_EXIT_CODES = {
   failed: 1,
   cancelled: 2,
   paused: 3,
-  timeout: 4,
+  timeout: STILL_RUNNING_EXIT_CODE,
 } as const
 
 type WaitOutcome = keyof typeof WAIT_EXIT_CODES

packages/sim-cli/src/commands/protocol/workspace-operation-wait.ts

@@ -1,6 +1,7 @@
 import { sleep } from '@sim/utils/helpers'
 import type { Command } from 'commander'
 import { CLI_CONTRACT } from '../../contract/commands'
+import { STILL_RUNNING_EXIT_CODE } from '../../exit-codes'
 import type { GetWorkspaceOperationResponse } from '../../generated/v2-api'
 import { SimApiError } from '../../http/client'
 import { apiCommand, type OperationClient } from '../../runtime/called-operations'
@@ -55,7 +56,7 @@ export function assertWorkspaceOperationOutcome(
   report: WorkspaceOperation,
   timedOut = false
 ): void {
-  const exitCode = timedOut ? 4 : EXIT_CODES[report.status]
+  const exitCode = timedOut ? STILL_RUNNING_EXIT_CODE : EXIT_CODES[report.status]
   if (!exitCode) return
   throw new SimApiError(
     timedOut

packages/sim-cli/src/embed.ts

@@ -34,6 +34,7 @@ import { buildProgram } from './program'
  */
 
 export type { EmbeddedCliIdentity, EmbeddedFileSnapshot } from './embed-context'
+export { STILL_RUNNING_EXIT_CODE } from './exit-codes'
 export type {
   ExportWorkflowResponse,
   ListFilesResponse,

packages/sim-cli/src/exit-codes.ts

@@ -0,0 +1,8 @@
+/**
+ * The exit status of a wait whose `--wait-timeout` elapsed while the work it watches
+ * keeps going: `workflows runs wait`, a synchronous `workflows run` that detached, and a
+ * workspace operation wait. The command did what it was asked and printed the record to
+ * continue from, so a host that runs the CLI for an agent treats it as a finished call,
+ * not a failed one; a script still branches on the non-zero status.
+ */
+export const STILL_RUNNING_EXIT_CODE = 4