diff --git a/packages/builtin-tools/src/tools/RemoteTriggerTool/__tests__/RemoteTriggerTool.test.ts b/packages/builtin-tools/src/tools/RemoteTriggerTool/__tests__/RemoteTriggerTool.test.ts
index dc570a803..eb9b726c8 100644
--- a/packages/builtin-tools/src/tools/RemoteTriggerTool/__tests__/RemoteTriggerTool.test.ts
+++ b/packages/builtin-tools/src/tools/RemoteTriggerTool/__tests__/RemoteTriggerTool.test.ts
@@ -7,9 +7,14 @@ import {
   setOriginalCwd,
   setProjectRoot,
 } from 'src/bootstrap/state.js'
+import { logMock } from '../../../../../../tests/mocks/log'
+import { debugMock } from '../../../../../../tests/mocks/debug'
 
 let requestStatus = 200
 
+mock.module('src/utils/log.ts', logMock)
+mock.module('src/utils/debug.ts', debugMock)
+
 mock.module('axios', () => ({
   default: {
     request: async () => ({
@@ -30,16 +35,41 @@ mock.module('src/services/oauth/client.js', () => ({
 
 mock.module('src/constants/oauth.js', () => ({
   getOauthConfig: () => ({ BASE_API_URL: 'https://example.test' }),
+  fileSuffixForOauthConfig: () => '',
+}))
+
+mock.module('src/services/analytics/growthbook.js', () => ({
+  getFeatureValue_CACHED_MAY_BE_STALE: () => true,
+}))
+
+mock.module('src/services/policyLimits/index.js', () => ({
+  isPolicyAllowed: () => true,
+}))
+
+mock.module('bun:bundle', () => ({
+  feature: () => false,
 }))
 
 let cwd = ''
 let previousCwd = ''
+let auditRecords: Array<Record<string, unknown>> = []
+
+mock.module('src/utils/remoteTriggerAudit.js', () => ({
+  appendRemoteTriggerAuditRecord: async (record: Record<string, unknown>) => {
+    const full = { ...record, auditId: record.auditId ?? 'test-audit-id', createdAt: Date.now() }
+    auditRecords.push(full)
+    return full
+  },
+  resolveRemoteTriggerAuditPath: () => join(cwd, '.claude', 'remote-trigger-audit.jsonl'),
+}))
 
 beforeEach(async () => {
   requestStatus = 200
+  auditRecords = []
   previousCwd = process.cwd()
   cwd = join(tmpdir(), `remote-trigger-tool-${Date.now()}-${Math.random().toString(16).slice(2)}`)
   await mkdir(cwd, { recursive: true })
+  await mkdir(join(cwd, '.claude'), { recursive: true })
   process.chdir(cwd)
   resetStateForTests()
   setOriginalCwd(cwd)
@@ -61,13 +91,10 @@ describe('RemoteTriggerTool audit', () => {
     )
 
     expect(result.data.audit_id).toBeString()
-    const raw = await readFile(
-      join(cwd, '.claude', 'remote-trigger-audit.jsonl'),
-      'utf-8',
-    )
-    expect(raw).toContain('"action":"run"')
-    expect(raw).toContain('"triggerId":"trigger-1"')
-    expect(raw).toContain('"ok":true')
+    expect(auditRecords).toHaveLength(1)
+    expect(auditRecords[0].action).toBe('run')
+    expect(auditRecords[0].triggerId).toBe('trigger-1')
+    expect(auditRecords[0].ok).toBe(true)
   })
 
   test('writes an audit record before rethrowing validation failures', async () => {
@@ -80,12 +107,9 @@ describe('RemoteTriggerTool audit', () => {
       ),
     ).rejects.toThrow('run requires trigger_id')
 
-    const raw = await readFile(
-      join(cwd, '.claude', 'remote-trigger-audit.jsonl'),
-      'utf-8',
-    )
-    expect(raw).toContain('"action":"run"')
-    expect(raw).toContain('"ok":false')
-    expect(raw).toContain('run requires trigger_id')
+    expect(auditRecords).toHaveLength(1)
+    expect(auditRecords[0].action).toBe('run')
+    expect(auditRecords[0].ok).toBe(false)
+    expect(auditRecords[0].error).toBe('run requires trigger_id')
   })
 })
diff --git a/src/cli/handlers/__tests__/autonomy.test.ts b/src/cli/handlers/__tests__/autonomy.test.ts
index 25e751bfd..17e6e2222 100644
--- a/src/cli/handlers/__tests__/autonomy.test.ts
+++ b/src/cli/handlers/__tests__/autonomy.test.ts
@@ -57,7 +57,7 @@ describe('autonomy CLI handler', () => {
       sourceLabel: 'nightly',
     })
 
-    const output = await getAutonomyStatusText()
+    const output = await getAutonomyStatusText({ rootDir: tempDir })
 
     expect(output).toContain('Autonomy runs: 1')
     expect(output).toContain('Queued: 1')
@@ -77,7 +77,7 @@ describe('autonomy CLI handler', () => {
       })}\n`,
     )
 
-    const output = await getAutonomyStatusText({ deep: true })
+    const output = await getAutonomyStatusText({ deep: true, rootDir: tempDir })
 
     expect(output).toContain('# Autonomy Deep Status')
     expect(output).toContain('## Workflow Runs')
@@ -87,8 +87,8 @@ describe('autonomy CLI handler', () => {
   })
 
   test('prints individual deep status sections for panel actions', async () => {
-    const pipes = await getAutonomyDeepSectionText('pipes')
-    const remoteControl = await getAutonomyDeepSectionText('remote-control')
+    const pipes = await getAutonomyDeepSectionText('pipes', { rootDir: tempDir })
+    const remoteControl = await getAutonomyDeepSectionText('remote-control', { rootDir: tempDir })
 
     expect(pipes).toContain('# Pipes')
     expect(pipes).toContain('Pipe registry:')
@@ -116,17 +116,17 @@ describe('autonomy CLI handler', () => {
     })
     const [waitingFlow] = await listAutonomyFlows(tempDir)
 
-    expect(await getAutonomyFlowsText()).toContain(waitingFlow!.flowId)
-    expect(await getAutonomyFlowText(waitingFlow!.flowId)).toContain(
+    expect(await getAutonomyFlowsText(undefined, { rootDir: tempDir })).toContain(waitingFlow!.flowId)
+    expect(await getAutonomyFlowText(waitingFlow!.flowId, { rootDir: tempDir })).toContain(
       'Current step: wait',
     )
 
-    const resumed = await resumeAutonomyFlowText(waitingFlow!.flowId)
+    const resumed = await resumeAutonomyFlowText(waitingFlow!.flowId, { rootDir: tempDir, currentDir: tempDir })
     expect(resumed).toContain('Prepared the next managed step')
     expect(resumed).toContain('Prompt:')
     expect(resumed).toContain('Wait for manual signal')
 
-    const cancelled = await cancelAutonomyFlowText(waitingFlow!.flowId)
+    const cancelled = await cancelAutonomyFlowText(waitingFlow!.flowId, { rootDir: tempDir })
     expect(cancelled).toContain('Cancelled flow')
   })
 })
diff --git a/src/cli/handlers/autonomy.ts b/src/cli/handlers/autonomy.ts
index c63865408..d7d7466db 100644
--- a/src/cli/handlers/autonomy.ts
+++ b/src/cli/handlers/autonomy.ts
@@ -37,10 +37,12 @@ export function parseAutonomyLimit(raw?: string | number): number {
 
 export async function getAutonomyStatusText(options?: {
   deep?: boolean
+  rootDir?: string
 }): Promise<string> {
+  const rootDir = options?.rootDir
   const [runs, flows] = await Promise.all([
-    listAutonomyRuns(),
-    listAutonomyFlows(),
+    listAutonomyRuns(rootDir),
+    listAutonomyFlows(rootDir),
   ])
 
   if (options?.deep) {
@@ -55,10 +57,11 @@ export async function getAutonomyStatusText(options?: {
 
 export async function getAutonomyDeepSectionText(
   sectionId: AutonomyDeepStatusSectionId,
+  options?: { rootDir?: string },
 ): Promise<string> {
   const [runs, flows] = await Promise.all([
-    listAutonomyRuns(),
-    listAutonomyFlows(),
+    listAutonomyRuns(options?.rootDir),
+    listAutonomyFlows(options?.rootDir),
   ])
   const sections = await formatAutonomyDeepStatusSections({ runs, flows })
   const section = sections.find(item => item.id === sectionId)
@@ -76,9 +79,10 @@ export async function autonomyStatusHandler(options?: {
 
 export async function getAutonomyRunsText(
   limit?: string | number,
+  options?: { rootDir?: string },
 ): Promise<string> {
   return formatAutonomyRunsList(
-    await listAutonomyRuns(),
+    await listAutonomyRuns(options?.rootDir),
     parseAutonomyLimit(limit),
   )
 }
@@ -91,9 +95,10 @@ export async function autonomyRunsHandler(
 
 export async function getAutonomyFlowsText(
   limit?: string | number,
+  options?: { rootDir?: string },
 ): Promise<string> {
   return formatAutonomyFlowsList(
-    await listAutonomyFlows(),
+    await listAutonomyFlows(options?.rootDir),
     parseAutonomyLimit(limit),
   )
 }
@@ -104,8 +109,11 @@ export async function autonomyFlowsHandler(
   process.stdout.write(`${await getAutonomyFlowsText(limit)}\n`)
 }
 
-export async function getAutonomyFlowText(flowId: string): Promise<string> {
-  return formatAutonomyFlowDetail(await getAutonomyFlowById(flowId))
+export async function getAutonomyFlowText(
+  flowId: string,
+  options?: { rootDir?: string },
+): Promise<string> {
+  return formatAutonomyFlowDetail(await getAutonomyFlowById(flowId, options?.rootDir))
 }
 
 export async function autonomyFlowHandler(flowId: string): Promise<void> {
@@ -116,9 +124,13 @@ export async function cancelAutonomyFlowText(
   flowId: string,
   options?: {
     removeQueuedInMemory?: boolean
+    rootDir?: string
   },
 ): Promise<string> {
-  const cancelled = await requestManagedAutonomyFlowCancel({ flowId })
+  const cancelled = await requestManagedAutonomyFlowCancel({
+    flowId,
+    rootDir: options?.rootDir,
+  })
   if (!cancelled) {
     return 'Autonomy flow not found.'
   }
@@ -132,12 +144,12 @@ export async function cancelAutonomyFlowText(
     removedCount = removed.length
     for (const command of removed) {
       if (command.autonomy?.runId) {
-        await markAutonomyRunCancelled(command.autonomy.runId)
+        await markAutonomyRunCancelled(command.autonomy.runId, options?.rootDir)
       }
     }
   } else {
     for (const runId of cancelled.queuedRunIds) {
-      await markAutonomyRunCancelled(runId)
+      await markAutonomyRunCancelled(runId, options?.rootDir)
     }
     removedCount = cancelled.queuedRunIds.length
   }
@@ -155,9 +167,15 @@ export async function resumeAutonomyFlowText(
   flowId: string,
   options?: {
     enqueueInMemory?: boolean
+    rootDir?: string
+    currentDir?: string
   },
 ): Promise<string> {
-  const command = await resumeManagedAutonomyFlowPrompt({ flowId })
+  const command = await resumeManagedAutonomyFlowPrompt({
+    flowId,
+    rootDir: options?.rootDir,
+    currentDir: options?.currentDir,
+  })
   if (!command) {
     return 'Autonomy flow is not waiting or was not found.'
   }