diff --git a/src/cli/handlers/worktree.ts b/src/cli/handlers/worktree.ts
index 4775353df..3f24cfdd3 100644
--- a/src/cli/handlers/worktree.ts
+++ b/src/cli/handlers/worktree.ts
@@ -46,7 +46,8 @@ export const WORKTREE_HANDLERS: Record<string, CommandHandler> = {
       name: getRequiredStringFlag(flags, 'name'),
       baseBranch: getOptionalStringFlag(flags, 'base-branch'),
       linkedIssue: getOptionalNumberFlag(flags, 'issue'),
-      comment: getOptionalStringFlag(flags, 'comment')
+      comment: getOptionalStringFlag(flags, 'comment'),
+      runHooks: flags.get('run-hooks') === true
     })
     printResult(result, json, formatWorktreeShow)
   },
@@ -62,7 +63,8 @@ export const WORKTREE_HANDLERS: Record<string, CommandHandler> = {
   'worktree rm': async ({ flags, client, cwd, json }) => {
     const result = await client.call<{ removed: boolean }>('worktree.rm', {
       worktree: await getRequiredWorktreeSelector(flags, 'worktree', cwd, client),
-      force: flags.get('force') === true
+      force: flags.get('force') === true,
+      runHooks: flags.get('run-hooks') === true
     })
     printResult(result, json, (value) => `removed: ${value.removed}`)
   }
diff --git a/src/cli/help.ts b/src/cli/help.ts
index 864d5e526..2e8f6ddb9 100644
--- a/src/cli/help.ts
+++ b/src/cli/help.ts
@@ -115,11 +115,11 @@ Common Commands:
   orca open [--json]
   orca status [--json]
   orca worktree list [--repo <selector>] [--limit <n>] [--json]
-  orca worktree create --repo <selector> --name <name> [--base-branch <ref>] [--issue <number>] [--comment <text>] [--json]
+  orca worktree create --repo <selector> --name <name> [--base-branch <ref>] [--issue <number>] [--comment <text>] [--run-hooks] [--json]
   orca worktree show --worktree <selector> [--json]
   orca worktree current [--json]
   orca worktree set --worktree <selector> [--display-name <name>] [--issue <number|null>] [--comment <text>] [--json]
-  orca worktree rm --worktree <selector> [--force] [--json]
+  orca worktree rm --worktree <selector> [--force] [--run-hooks] [--json]
   orca worktree ps [--limit <n>] [--json]
   orca terminal list [--worktree <selector>] [--limit <n>] [--json]
   orca terminal show [--terminal <handle>] [--json]
diff --git a/src/cli/specs/core.ts b/src/cli/specs/core.ts
index 95f8f66f0..ca40b6bd8 100644
--- a/src/cli/specs/core.ts
+++ b/src/cli/specs/core.ts
@@ -72,9 +72,12 @@ export const CORE_COMMAND_SPECS: CommandSpec[] = [
     path: ['worktree', 'create'],
     summary: 'Create a new Orca-managed worktree',
     usage:
-      'orca worktree create --repo <selector> --name <name> [--base-branch <ref>] [--issue <number>] [--comment <text>] [--json]',
-    allowedFlags: [...GLOBAL_FLAGS, 'repo', 'name', 'base-branch', 'issue', 'comment'],
-    notes: ['By default this matches the Orca UI flow and activates the new worktree in the app.']
+      'orca worktree create --repo <selector> --name <name> [--base-branch <ref>] [--issue <number>] [--comment <text>] [--run-hooks] [--json]',
+    allowedFlags: [...GLOBAL_FLAGS, 'repo', 'name', 'base-branch', 'issue', 'comment', 'run-hooks'],
+    notes: [
+      'By default this matches the Orca UI flow and activates the new worktree in the app.',
+      'Repo-defined orca.yaml hooks are skipped unless --run-hooks is passed.'
+    ]
   },
   {
     path: ['worktree', 'set'],
@@ -86,8 +89,9 @@ export const CORE_COMMAND_SPECS: CommandSpec[] = [
   {
     path: ['worktree', 'rm'],
     summary: 'Remove a worktree from Orca and git',
-    usage: 'orca worktree rm --worktree <selector> [--force] [--json]',
-    allowedFlags: [...GLOBAL_FLAGS, 'worktree', 'force']
+    usage: 'orca worktree rm --worktree <selector> [--force] [--run-hooks] [--json]',
+    allowedFlags: [...GLOBAL_FLAGS, 'worktree', 'force', 'run-hooks'],
+    notes: ['Repo-defined orca.yaml archive hooks are skipped unless --run-hooks is passed.']
   },
   {
     path: ['worktree', 'ps'],
diff --git a/src/main/ipc/worktrees.test.ts b/src/main/ipc/worktrees.test.ts
index f02e8c756..0bbba1a6a 100644
--- a/src/main/ipc/worktrees.test.ts
+++ b/src/main/ipc/worktrees.test.ts
@@ -524,6 +524,55 @@ describe('registerWorktreeHandlers', () => {
     })
   })
 
+  it('runs the archive hook on remove when skipArchive is not set', async () => {
+    listWorktreesMock.mockResolvedValue([])
+    removeWorktreeMock.mockResolvedValue(undefined)
+    getEffectiveHooksMock.mockReturnValue({
+      scripts: {
+        archive: 'echo archived'
+      }
+    })
+    runHookMock.mockResolvedValue({ success: true, output: '' })
+
+    await handlers['worktrees:remove'](null, {
+      worktreeId: 'repo-1::/workspace/feature-wt'
+    })
+
+    expect(runHookMock).toHaveBeenCalledWith(
+      'archive',
+      '/workspace/feature-wt',
+      expect.objectContaining({ id: 'repo-1' })
+    )
+    expect(removeWorktreeMock).toHaveBeenCalledWith(
+      '/workspace/repo',
+      '/workspace/feature-wt',
+      false
+    )
+  })
+
+  it('skips the archive hook on remove when skipArchive is true', async () => {
+    listWorktreesMock.mockResolvedValue([])
+    removeWorktreeMock.mockResolvedValue(undefined)
+    getEffectiveHooksMock.mockReturnValue({
+      scripts: {
+        archive: 'echo archived'
+      }
+    })
+    runHookMock.mockResolvedValue({ success: true, output: '' })
+
+    await handlers['worktrees:remove'](null, {
+      worktreeId: 'repo-1::/workspace/feature-wt',
+      skipArchive: true
+    })
+
+    expect(runHookMock).not.toHaveBeenCalled()
+    expect(removeWorktreeMock).toHaveBeenCalledWith(
+      '/workspace/repo',
+      '/workspace/feature-wt',
+      false
+    )
+  })
+
   it('rejects ask-policy creates before mutating git state when setup decision is missing', async () => {
     getEffectiveHooksMock.mockReturnValue({
       scripts: {
diff --git a/src/main/ipc/worktrees.ts b/src/main/ipc/worktrees.ts
index fc2fba573..141b4c155 100644
--- a/src/main/ipc/worktrees.ts
+++ b/src/main/ipc/worktrees.ts
@@ -249,7 +249,7 @@ export function registerWorktreeHandlers(mainWindow: BrowserWindow, store: Store
 
   ipcMain.handle(
     'worktrees:remove',
-    async (_event, args: { worktreeId: string; force?: boolean }) => {
+    async (_event, args: { worktreeId: string; force?: boolean; skipArchive?: boolean }) => {
       const { repoId, worktreePath } = parseWorktreeId(args.worktreeId)
       const repo = store.getRepo(repoId)
       if (!repo) {
@@ -273,7 +273,7 @@ export function registerWorktreeHandlers(mainWindow: BrowserWindow, store: Store
 
       // Run archive hook before removal
       const hooks = getEffectiveHooks(repo)
-      if (hooks?.scripts.archive) {
+      if (hooks?.scripts.archive && !args.skipArchive) {
         const result = await runHook('archive', worktreePath, repo)
         if (!result.success) {
           console.error(`[hooks] archive hook failed for ${worktreePath}:`, result.output)
diff --git a/src/main/runtime/orca-runtime.test.ts b/src/main/runtime/orca-runtime.test.ts
index 310a20c76..3a50b194e 100644
--- a/src/main/runtime/orca-runtime.test.ts
+++ b/src/main/runtime/orca-runtime.test.ts
@@ -1,7 +1,7 @@
 /* eslint-disable max-lines -- Why: runtime behavior is stateful and cross-cutting, so these tests stay in one file to preserve the end-to-end invariants around handles, waits, and graph sync. */
 import { afterEach, describe, expect, it, vi } from 'vitest'
 import type { WorktreeMeta } from '../../shared/types'
-import { addWorktree, listWorktrees } from '../git/worktree'
+import { addWorktree, listWorktrees, removeWorktree } from '../git/worktree'
 import { createSetupRunnerScript, getEffectiveHooks, runHook } from '../hooks'
 import { OrchestrationDb } from './orchestration/db'
 import { OrcaRuntimeService } from './orca-runtime'
@@ -9,6 +9,7 @@ import { OrcaRuntimeService } from './orca-runtime'
 const {
   MOCK_GIT_WORKTREES,
   addWorktreeMock,
+  removeWorktreeMock,
   computeWorktreePathMock,
   ensurePathWithinWorkspaceMock,
   invalidateAuthorizedRootsCacheMock
@@ -23,6 +24,7 @@ const {
     }
   ],
   addWorktreeMock: vi.fn(),
+  removeWorktreeMock: vi.fn(),
   computeWorktreePathMock: vi.fn(),
   ensurePathWithinWorkspaceMock: vi.fn(),
   invalidateAuthorizedRootsCacheMock: vi.fn()
@@ -30,7 +32,8 @@ const {
 
 vi.mock('../git/worktree', () => ({
   listWorktrees: vi.fn().mockResolvedValue(MOCK_GIT_WORKTREES),
-  addWorktree: addWorktreeMock
+  addWorktree: addWorktreeMock,
+  removeWorktree: removeWorktreeMock
 }))
 
 vi.mock('../hooks', () => ({
@@ -70,6 +73,7 @@ vi.mock('../git/repo', async (importOriginal) => {
 afterEach(() => {
   vi.mocked(listWorktrees).mockResolvedValue(MOCK_GIT_WORKTREES)
   vi.mocked(addWorktree).mockReset()
+  vi.mocked(removeWorktree).mockReset()
   vi.mocked(createSetupRunnerScript).mockReset()
   vi.mocked(getEffectiveHooks).mockReset()
   vi.mocked(runHook).mockReset()
@@ -899,7 +903,7 @@ describe('OrcaRuntimeService', () => {
     await expect(runtime.searchRepoRefs('id:repo-1', 'main', -5)).rejects.toThrow('invalid_limit')
   })
 
-  it('returns a setup launch payload for CLI-created worktrees when orca.yaml defines setup', async () => {
+  it('returns a setup launch payload for CLI-created worktrees when hooks are explicitly enabled', async () => {
     const runtime = new OrcaRuntimeService(store)
     const activateWorktree = vi.fn()
     runtime.setNotifier({
@@ -940,7 +944,8 @@ describe('OrcaRuntimeService', () => {
 
     const result = await runtime.createManagedWorktree({
       repoSelector: 'id:repo-1',
-      name: 'runtime-hook-test'
+      name: 'runtime-hook-test',
+      runHooks: true
     })
 
     expect(createSetupRunnerScript).toHaveBeenCalledWith(
@@ -973,6 +978,90 @@ describe('OrcaRuntimeService', () => {
     expect(activateWorktree).toHaveBeenCalledWith('repo-1', expect.any(String), result.setup)
   })
 
+  it('skips setup hooks for CLI-created worktrees by default', async () => {
+    const runtime = new OrcaRuntimeService(store)
+    const activateWorktree = vi.fn()
+    runtime.setNotifier({
+      worktreesChanged: vi.fn(),
+      reposChanged: vi.fn(),
+      activateWorktree,
+      createTerminal: vi.fn(),
+      splitTerminal: vi.fn(),
+      renameTerminal: vi.fn(),
+      focusTerminal: vi.fn(),
+      closeTerminal: vi.fn()
+    })
+    runtime.attachWindow(1)
+
+    computeWorktreePathMock.mockReturnValue('/tmp/workspaces/runtime-hook-skip')
+    ensurePathWithinWorkspaceMock.mockReturnValue('/tmp/workspaces/runtime-hook-skip')
+    vi.mocked(getEffectiveHooks).mockReturnValue({
+      scripts: {
+        setup: 'pnpm worktree:setup'
+      }
+    })
+    vi.mocked(listWorktrees).mockResolvedValueOnce([
+      {
+        path: '/tmp/workspaces/runtime-hook-skip',
+        head: 'def',
+        branch: 'runtime-hook-skip',
+        isBare: false,
+        isMainWorktree: false
+      }
+    ])
+
+    const result = await runtime.createManagedWorktree({
+      repoSelector: 'id:repo-1',
+      name: 'runtime-hook-skip'
+    })
+
+    expect(createSetupRunnerScript).not.toHaveBeenCalled()
+    expect(runHook).not.toHaveBeenCalled()
+    expect(result).toEqual({
+      worktree: expect.objectContaining({
+        repoId: 'repo-1',
+        path: '/tmp/workspaces/runtime-hook-skip',
+        branch: 'runtime-hook-skip'
+      })
+    })
+    expect(activateWorktree).toHaveBeenCalledWith('repo-1', expect.any(String), undefined)
+  })
+
+  it('skips archive hooks for CLI worktree removal by default', async () => {
+    const runtime = new OrcaRuntimeService(store)
+    vi.mocked(getEffectiveHooks).mockReturnValue({
+      scripts: {
+        archive: 'pnpm worktree:archive'
+      }
+    })
+    vi.mocked(removeWorktree).mockResolvedValue(undefined)
+
+    await runtime.removeManagedWorktree(TEST_WORKTREE_ID)
+
+    expect(runHook).not.toHaveBeenCalled()
+    expect(removeWorktree).toHaveBeenCalledWith(TEST_REPO_PATH, TEST_WORKTREE_PATH, false)
+  })
+
+  it('runs archive hooks for CLI worktree removal when hooks are explicitly enabled', async () => {
+    const runtime = new OrcaRuntimeService(store)
+    vi.mocked(getEffectiveHooks).mockReturnValue({
+      scripts: {
+        archive: 'pnpm worktree:archive'
+      }
+    })
+    vi.mocked(runHook).mockResolvedValue({ success: true, output: '' })
+    vi.mocked(removeWorktree).mockResolvedValue(undefined)
+
+    await runtime.removeManagedWorktree(TEST_WORKTREE_ID, false, true)
+
+    expect(runHook).toHaveBeenCalledWith(
+      'archive',
+      TEST_WORKTREE_PATH,
+      expect.objectContaining({ id: TEST_REPO_ID, path: TEST_REPO_PATH })
+    )
+    expect(removeWorktree).toHaveBeenCalledWith(TEST_REPO_PATH, TEST_WORKTREE_PATH, false)
+  })
+
   it('invalidates the filesystem-auth cache after CLI worktree creation', async () => {
     // Reproduces: CLI-created worktrees fail with "Access denied: unknown
     // repository or worktree path" because the filesystem-auth cache was
diff --git a/src/main/runtime/orca-runtime.ts b/src/main/runtime/orca-runtime.ts
index b221afcff..216f21e17 100644
--- a/src/main/runtime/orca-runtime.ts
+++ b/src/main/runtime/orca-runtime.ts
@@ -949,6 +949,7 @@ export class OrcaRuntimeService {
     baseBranch?: string
     linkedIssue?: number | null
     comment?: string
+    runHooks?: boolean
   }): Promise<CreateWorktreeResult> {
     if (!this.store) {
       throw new Error('runtime_unavailable')
@@ -1035,7 +1036,7 @@ export class OrcaRuntimeService {
 
     let setup: CreateWorktreeResult['setup']
     const hooks = getEffectiveHooks(repo)
-    if (hooks?.scripts.setup) {
+    if (hooks?.scripts.setup && args.runHooks === true) {
       if (this.authoritativeWindowId !== null) {
         try {
           // Why: CLI-created worktrees must use the same runner-script path as the
@@ -1056,6 +1057,9 @@ export class OrcaRuntimeService {
           }
         })
       }
+    } else if (hooks?.scripts.setup) {
+      // Runtime RPC calls have no renderer trust prompt, so hooks require explicit CLI opt-in.
+      console.info(`[hooks] setup hook skipped for ${worktreePath}; pass --run-hooks to run it`)
     }
 
     this.notifier?.worktreesChanged(repo.id)
@@ -1101,7 +1105,11 @@ export class OrcaRuntimeService {
     return mergeWorktree(worktree.repoId, worktree.git, meta)
   }
 
-  async removeManagedWorktree(worktreeSelector: string, force = false): Promise<void> {
+  async removeManagedWorktree(
+    worktreeSelector: string,
+    force = false,
+    runHooks = false
+  ): Promise<void> {
     if (!this.store) {
       throw new Error('runtime_unavailable')
     }
@@ -1115,11 +1123,14 @@ export class OrcaRuntimeService {
     }
 
     const hooks = getEffectiveHooks(repo)
-    if (hooks?.scripts.archive) {
+    if (hooks?.scripts.archive && runHooks) {
       const result = await runHook('archive', worktree.path, repo)
       if (!result.success) {
         console.error(`[hooks] archive hook failed for ${worktree.path}:`, result.output)
       }
+    } else if (hooks?.scripts.archive) {
+      // Runtime RPC calls have no renderer trust prompt, so hooks require explicit CLI opt-in.
+      console.info(`[hooks] archive hook skipped for ${worktree.path}; pass --run-hooks to run it`)
     }
 
     try {
diff --git a/src/main/runtime/rpc/methods/worktree.ts b/src/main/runtime/rpc/methods/worktree.ts
index acc588d04..fafd86585 100644
--- a/src/main/runtime/rpc/methods/worktree.ts
+++ b/src/main/runtime/rpc/methods/worktree.ts
@@ -34,7 +34,8 @@ const WorktreeCreate = z.object({
     .pipe(z.string().min(1, 'Missing worktree name')),
   baseBranch: OptionalString,
   linkedIssue: TriStateLinkedIssue,
-  comment: OptionalString
+  comment: OptionalString,
+  runHooks: OptionalBoolean
 })
 
 const WorktreeSet = WorktreeSelector.extend({
@@ -44,7 +45,8 @@ const WorktreeSet = WorktreeSelector.extend({
 })
 
 const WorktreeRemove = WorktreeSelector.extend({
-  force: OptionalBoolean
+  force: OptionalBoolean,
+  runHooks: OptionalBoolean
 })
 
 export const WORKTREE_METHODS: RpcMethod[] = [
@@ -74,7 +76,8 @@ export const WORKTREE_METHODS: RpcMethod[] = [
         name: params.name,
         baseBranch: params.baseBranch,
         linkedIssue: params.linkedIssue,
-        comment: params.comment
+        comment: params.comment,
+        runHooks: params.runHooks === true
       })
   }),
   defineMethod({
@@ -92,7 +95,11 @@ export const WORKTREE_METHODS: RpcMethod[] = [
     name: 'worktree.rm',
     params: WorktreeRemove,
     handler: async (params, { runtime }) => {
-      await runtime.removeManagedWorktree(params.worktree, params.force === true)
+      await runtime.removeManagedWorktree(
+        params.worktree,
+        params.force === true,
+        params.runHooks === true
+      )
       return { removed: true }
     }
   })
diff --git a/src/preload/api-types.ts b/src/preload/api-types.ts
index f20d74a1c..828500265 100644
--- a/src/preload/api-types.ts
+++ b/src/preload/api-types.ts
@@ -342,7 +342,7 @@ export type PreloadApi = {
       headRefName?: string
       isCrossRepository?: boolean
     }) => Promise<{ baseBranch: string } | { error: string }>
-    remove: (args: { worktreeId: string; force?: boolean }) => Promise<void>
+    remove: (args: { worktreeId: string; force?: boolean; skipArchive?: boolean }) => Promise<void>
     updateMeta: (args: { worktreeId: string; updates: Partial<WorktreeMeta> }) => Promise<Worktree>
     persistSortOrder: (args: { orderedIds: string[] }) => Promise<void>
     onChanged: (callback: (data: { repoId: string }) => void) => () => void
diff --git a/src/preload/index.ts b/src/preload/index.ts
index f85c5f359..f621d5164 100644
--- a/src/preload/index.ts
+++ b/src/preload/index.ts
@@ -265,7 +265,7 @@ const api = {
     }): Promise<{ baseBranch: string } | { error: string }> =>
       ipcRenderer.invoke('worktrees:resolvePrBase', args),
 
-    remove: (args: { worktreeId: string; force?: boolean }): Promise<void> =>
+    remove: (args: { worktreeId: string; force?: boolean; skipArchive?: boolean }): Promise<void> =>
       ipcRenderer.invoke('worktrees:remove', args),
 
     updateMeta: (args: {
diff --git a/src/renderer/src/components/sidebar/AddRepoSteps.tsx b/src/renderer/src/components/sidebar/AddRepoSteps.tsx
index 7e21f4e69..438ce8585 100644
--- a/src/renderer/src/components/sidebar/AddRepoSteps.tsx
+++ b/src/renderer/src/components/sidebar/AddRepoSteps.tsx
@@ -113,6 +113,9 @@ export function useRemoteRepo(
 
       const state = useAppStore.getState()
       const existingIdx = state.repos.findIndex((r) => r.id === repo.id)
+      if (existingIdx !== -1) {
+        state.clearOrcaHookTrustForRepo(repo.id)
+      }
       if (existingIdx === -1) {
         useAppStore.setState({ repos: [...state.repos, repo] })
       } else {
diff --git a/src/renderer/src/components/sidebar/OrcaYamlTrustDialog.tsx b/src/renderer/src/components/sidebar/OrcaYamlTrustDialog.tsx
new file mode 100644
index 000000000..1cbd7fefc
--- /dev/null
+++ b/src/renderer/src/components/sidebar/OrcaYamlTrustDialog.tsx
@@ -0,0 +1,107 @@
+import React, { useCallback } from 'react'
+import {
+  Dialog,
+  DialogContent,
+  DialogDescription,
+  DialogFooter,
+  DialogHeader,
+  DialogTitle
+} from '@/components/ui/dialog'
+import { Button } from '@/components/ui/button'
+import { useAppStore } from '@/store'
+import type { OrcaHookScriptKind } from '@/lib/orca-hook-trust'
+
+type ScriptKind = OrcaHookScriptKind
+
+const SCRIPT_KIND_LABEL: Record<ScriptKind, string> = {
+  setup: 'setup script',
+  archive: 'archive script',
+  issueCommand: 'issue command'
+}
+
+const SCRIPT_KIND_TRIGGER: Record<ScriptKind, string> = {
+  setup: 'when this workspace is created',
+  archive: 'when this workspace is removed',
+  issueCommand: 'when this workspace launches with a linked issue'
+}
+
+const OrcaYamlTrustDialog = React.memo(function OrcaYamlTrustDialog() {
+  const activeModal = useAppStore((s) => s.activeModal)
+  const modalData = useAppStore((s) => s.modalData)
+  const closeModal = useAppStore((s) => s.closeModal)
+  const markOrcaHookScriptConfirmed = useAppStore((s) => s.markOrcaHookScriptConfirmed)
+
+  const isOpen = activeModal === 'confirm-orca-yaml-hooks'
+
+  const repoId = typeof modalData.repoId === 'string' ? modalData.repoId : ''
+  const repoName = typeof modalData.repoName === 'string' ? modalData.repoName : 'this repository'
+  const scriptKind: ScriptKind =
+    modalData.scriptKind === 'archive'
+      ? 'archive'
+      : modalData.scriptKind === 'issueCommand'
+        ? 'issueCommand'
+        : 'setup'
+  const scriptContent = typeof modalData.scriptContent === 'string' ? modalData.scriptContent : ''
+  const contentHash = typeof modalData.contentHash === 'string' ? modalData.contentHash : ''
+  const onResolve =
+    typeof modalData.onResolve === 'function'
+      ? (modalData.onResolve as (decision: 'run' | 'skip') => void)
+      : null
+
+  const resolveAndClose = useCallback(
+    (decision: 'run' | 'skip') => {
+      if (decision === 'run' && repoId && contentHash) {
+        markOrcaHookScriptConfirmed(repoId, scriptKind, contentHash)
+      }
+      onResolve?.(decision)
+      closeModal()
+    },
+    [closeModal, contentHash, markOrcaHookScriptConfirmed, onResolve, repoId, scriptKind]
+  )
+
+  const handleOpenChange = useCallback(
+    (open: boolean) => {
+      if (!open) {
+        resolveAndClose('skip')
+      }
+    },
+    [resolveAndClose]
+  )
+
+  return (
+    <Dialog open={isOpen} onOpenChange={handleOpenChange}>
+      <DialogContent className="max-w-md sm:max-w-md" showCloseButton={false}>
+        <DialogHeader>
+          <DialogTitle className="text-sm">
+            Run {SCRIPT_KIND_LABEL[scriptKind]} from {repoName}?
+          </DialogTitle>
+          <DialogDescription className="text-xs">
+            This repository&apos;s <code>orca.yaml</code> defines a {SCRIPT_KIND_LABEL[scriptKind]}{' '}
+            that will execute on your machine {SCRIPT_KIND_TRIGGER[scriptKind]}. Only run it if you
+            trust the contents of this repository.
+          </DialogDescription>
+        </DialogHeader>
+
+        {scriptContent && (
+          <div className="rounded-md border border-border/70 bg-muted/35 px-3 py-2">
+            <div className="mb-1 text-[11px] font-medium uppercase tracking-wide text-muted-foreground">
+              {scriptKind} script
+            </div>
+            <pre className="max-h-48 overflow-auto whitespace-pre-wrap break-all font-mono text-xs text-foreground">
+              {scriptContent}
+            </pre>
+          </div>
+        )}
+
+        <DialogFooter>
+          <Button variant="outline" onClick={() => resolveAndClose('skip')}>
+            Don&apos;t run
+          </Button>
+          <Button onClick={() => resolveAndClose('run')}>Run hooks</Button>
+        </DialogFooter>
+      </DialogContent>
+    </Dialog>
+  )
+})
+
+export default OrcaYamlTrustDialog
diff --git a/src/renderer/src/components/sidebar/index.tsx b/src/renderer/src/components/sidebar/index.tsx
index e2ea1c5e5..d29ec8282 100644
--- a/src/renderer/src/components/sidebar/index.tsx
+++ b/src/renderer/src/components/sidebar/index.tsx
@@ -12,6 +12,7 @@ import DeleteWorktreeDialog from './DeleteWorktreeDialog'
 import NonGitFolderDialog from './NonGitFolderDialog'
 import RemoveFolderDialog from './RemoveFolderDialog'
 import AddRepoDialog from './AddRepoDialog'
+import OrcaYamlTrustDialog from './OrcaYamlTrustDialog'
 
 const MIN_WIDTH = 220
 const MAX_WIDTH = 500
@@ -70,6 +71,7 @@ function Sidebar(): React.JSX.Element {
       <NonGitFolderDialog />
       <RemoveFolderDialog />
       <AddRepoDialog />
+      <OrcaYamlTrustDialog />
     </TooltipProvider>
   )
 }
diff --git a/src/renderer/src/hooks/useComposerState.ts b/src/renderer/src/hooks/useComposerState.ts
index 35c6054a9..de8ebd2fb 100644
--- a/src/renderer/src/hooks/useComposerState.ts
+++ b/src/renderer/src/hooks/useComposerState.ts
@@ -34,6 +34,7 @@ import {
   type LinkedWorkItemSummary
 } from '@/lib/new-workspace'
 import { getSuggestedCreatureName } from '@/components/sidebar/worktree-name-suggestions'
+import { ensureHooksConfirmed } from '@/lib/ensure-hooks-confirmed'
 
 export type UseComposerStateOptions = {
   initialRepoId?: string
@@ -979,12 +980,21 @@ export function useComposerState(options: UseComposerStateOptions): UseComposerS
     setCreateError(null)
     setCreating(true)
     try {
-      const result = await createWorktree(
-        repoId,
-        workspaceName,
-        baseBranch,
-        (resolvedSetupDecision ?? 'inherit') as SetupDecision
-      )
+      const setupTrustDecision = await ensureHooksConfirmed(useAppStore.getState(), repoId, 'setup')
+      const effectiveSetupDecision: SetupDecision =
+        setupTrustDecision === 'skip'
+          ? 'skip'
+          : ((resolvedSetupDecision ?? 'inherit') as SetupDecision)
+
+      let issueCommandTrustDecision: 'run' | 'skip' = 'run'
+      if (shouldRunIssueAutomation) {
+        issueCommandTrustDecision =
+          setupTrustDecision === 'skip'
+            ? 'skip'
+            : await ensureHooksConfirmed(useAppStore.getState(), repoId, 'issueCommand')
+      }
+
+      const result = await createWorktree(repoId, workspaceName, baseBranch, effectiveSetupDecision)
       const worktree = result.worktree
 
       await applyWorktreeMeta(worktree.id, {
@@ -993,14 +1003,15 @@ export function useComposerState(options: UseComposerStateOptions): UseComposerS
         ...(note.trim() ? { comment: note.trim() } : {})
       })
 
-      const issueCommand = shouldRunIssueAutomation
-        ? {
-            command: renderIssueCommandTemplate(issueCommandTemplate, {
-              issueNumber: parsedLinkedIssueNumber,
-              artifactUrl: linkedWorkItem?.url ?? null
-            })
-          }
-        : undefined
+      const issueCommand =
+        shouldRunIssueAutomation && issueCommandTrustDecision === 'run'
+          ? {
+              command: renderIssueCommandTemplate(issueCommandTemplate, {
+                issueNumber: parsedLinkedIssueNumber,
+                artifactUrl: linkedWorkItem?.url ?? null
+              })
+            }
+          : undefined
       const startupPlan = buildAgentStartupPlan({
         agent: tuiAgent,
         prompt: startupPrompt,
@@ -1087,11 +1098,17 @@ export function useComposerState(options: UseComposerStateOptions): UseComposerS
       setCreateError(null)
       setCreating(true)
       try {
+        const trustDecision = await ensureHooksConfirmed(useAppStore.getState(), repoId, 'setup')
+        const effectiveSetupDecision: SetupDecision =
+          trustDecision === 'skip'
+            ? 'skip'
+            : ((resolvedSetupDecision ?? 'inherit') as SetupDecision)
+
         const result = await createWorktree(
           repoId,
           workspaceName,
           baseBranch,
-          (resolvedSetupDecision ?? 'inherit') as SetupDecision
+          effectiveSetupDecision
         )
         const worktree = result.worktree
 
diff --git a/src/renderer/src/lib/ensure-hooks-confirmed.test.ts b/src/renderer/src/lib/ensure-hooks-confirmed.test.ts
new file mode 100644
index 000000000..3a185897e
--- /dev/null
+++ b/src/renderer/src/lib/ensure-hooks-confirmed.test.ts
@@ -0,0 +1,186 @@
+import { beforeEach, describe, expect, it, vi } from 'vitest'
+import type { AppState } from '@/store/types'
+import type { PersistedTrustedOrcaHooks } from '../../../shared/types'
+import { __resetTrustPromptChainForTests, ensureHooksConfirmed } from './ensure-hooks-confirmed'
+import { hashOrcaHookScript } from './orca-hook-trust'
+
+const hooksCheckMock = vi.fn()
+const readIssueCommandMock = vi.fn()
+
+;(globalThis as { window: unknown }).window = {
+  api: {
+    hooks: {
+      check: hooksCheckMock,
+      readIssueCommand: readIssueCommandMock
+    }
+  }
+}
+
+type PendingPrompt = {
+  modal: string
+  data: Record<string, unknown>
+  resolve: (decision: 'run' | 'skip') => void
+}
+
+function createTestState(overrides?: Partial<AppState>): {
+  state: AppState
+  pending: PendingPrompt[]
+} {
+  const pending: PendingPrompt[] = []
+  const trust: PersistedTrustedOrcaHooks = {}
+  const state = {
+    trustedOrcaHooks: trust,
+    repos: [{ id: 'repo-1', displayName: 'Repo One' }],
+    openModal: (modal: string, data: Record<string, unknown>) => {
+      pending.push({ modal, data, resolve: data.onResolve as (d: 'run' | 'skip') => void })
+    },
+    ...overrides
+  } as unknown as AppState
+  return { state, pending }
+}
+
+async function flush(): Promise<void> {
+  await new Promise((resolve) => setTimeout(resolve, 0))
+  await new Promise((resolve) => setTimeout(resolve, 0))
+}
+
+describe('ensureHooksConfirmed', () => {
+  beforeEach(() => {
+    hooksCheckMock.mockReset()
+    readIssueCommandMock.mockReset()
+    __resetTrustPromptChainForTests()
+  })
+
+  it('short-circuits to run when the persisted content hash matches the current script', async () => {
+    const { state, pending } = createTestState()
+    const script = 'pnpm install'
+    const hash = await hashOrcaHookScript(script)
+    state.trustedOrcaHooks['repo-1'] = {
+      setup: { contentHash: hash, approvedAt: 1 }
+    }
+    hooksCheckMock.mockResolvedValue({
+      hasHooks: true,
+      hooks: { scripts: { setup: script } },
+      mayNeedUpdate: false
+    })
+
+    const decision = await ensureHooksConfirmed(state, 'repo-1', 'setup')
+
+    expect(decision).toBe('run')
+    expect(pending).toHaveLength(0)
+  })
+
+  it('re-prompts when the script content differs from the persisted hash', async () => {
+    const { state, pending } = createTestState()
+    const staleHash = await hashOrcaHookScript('old script')
+    state.trustedOrcaHooks['repo-1'] = {
+      setup: { contentHash: staleHash, approvedAt: 1 }
+    }
+    hooksCheckMock.mockResolvedValue({
+      hasHooks: true,
+      hooks: { scripts: { setup: 'new script' } },
+      mayNeedUpdate: false
+    })
+
+    const promise = ensureHooksConfirmed(state, 'repo-1', 'setup')
+    await flush()
+
+    expect(pending).toHaveLength(1)
+    expect(pending[0].data.scriptContent).toBe('new script')
+
+    pending[0].resolve('run')
+    await expect(promise).resolves.toBe('run')
+  })
+
+  it('returns run without prompting when no script of that kind is configured', async () => {
+    const { state, pending } = createTestState()
+    hooksCheckMock.mockResolvedValue({
+      hasHooks: true,
+      hooks: { scripts: {} },
+      mayNeedUpdate: false
+    })
+
+    const decision = await ensureHooksConfirmed(state, 'repo-1', 'archive')
+
+    expect(decision).toBe('run')
+    expect(pending).toHaveLength(0)
+  })
+
+  it('returns run without prompting when issueCommand source is local (user-owned)', async () => {
+    const { state, pending } = createTestState()
+    readIssueCommandMock.mockResolvedValue({
+      source: 'local',
+      sharedContent: null,
+      localContent: 'user content',
+      effectiveContent: 'user content',
+      localFilePath: ''
+    })
+
+    const decision = await ensureHooksConfirmed(state, 'repo-1', 'issueCommand')
+
+    expect(decision).toBe('run')
+    expect(pending).toHaveLength(0)
+  })
+
+  it('opens a modal with the computed content hash and resolves with the user decision', async () => {
+    const { state, pending } = createTestState()
+    hooksCheckMock.mockResolvedValue({
+      hasHooks: true,
+      hooks: { scripts: { setup: 'pnpm install' } },
+      mayNeedUpdate: false
+    })
+
+    const promise = ensureHooksConfirmed(state, 'repo-1', 'setup')
+    await flush()
+
+    expect(pending).toHaveLength(1)
+    expect(pending[0].data).toMatchObject({
+      repoId: 'repo-1',
+      repoName: 'Repo One',
+      scriptKind: 'setup',
+      scriptContent: 'pnpm install',
+      contentHash: await hashOrcaHookScript('pnpm install')
+    })
+
+    pending[0].resolve('run')
+    await expect(promise).resolves.toBe('run')
+  })
+
+  it('serializes overlapping prompts so a second call waits for the first to resolve', async () => {
+    const { state, pending } = createTestState()
+    hooksCheckMock.mockResolvedValue({
+      hasHooks: true,
+      hooks: { scripts: { setup: 'pnpm install', archive: 'echo bye' } },
+      mayNeedUpdate: false
+    })
+
+    const first = ensureHooksConfirmed(state, 'repo-1', 'setup')
+    const second = ensureHooksConfirmed(state, 'repo-1', 'archive')
+
+    await flush()
+
+    expect(pending).toHaveLength(1)
+    expect(pending[0].data.scriptKind).toBe('setup')
+
+    pending[0].resolve('skip')
+    await expect(first).resolves.toBe('skip')
+
+    await flush()
+
+    expect(pending).toHaveLength(2)
+    expect(pending[1].data.scriptKind).toBe('archive')
+
+    pending[1].resolve('run')
+    await expect(second).resolves.toBe('run')
+  })
+
+  it('fails closed when window.api.hooks.check throws', async () => {
+    const { state, pending } = createTestState()
+    hooksCheckMock.mockRejectedValue(new Error('boom'))
+
+    const decision = await ensureHooksConfirmed(state, 'repo-1', 'setup')
+
+    expect(decision).toBe('skip')
+    expect(pending).toHaveLength(0)
+  })
+})
diff --git a/src/renderer/src/lib/ensure-hooks-confirmed.ts b/src/renderer/src/lib/ensure-hooks-confirmed.ts
new file mode 100644
index 000000000..276c905df
--- /dev/null
+++ b/src/renderer/src/lib/ensure-hooks-confirmed.ts
@@ -0,0 +1,69 @@
+import type { AppState } from '@/store/types'
+import type { OrcaHooks } from '../../../shared/types'
+import { hashOrcaHookScript, type OrcaHookScriptKind } from './orca-hook-trust'
+
+export type HookScriptKind = OrcaHookScriptKind
+
+// Serialize the singleton modal callback so overlapping worktree actions cannot replace it.
+let trustPromptChain: Promise<unknown> = Promise.resolve()
+
+function enqueueTrustPrompt<T>(task: () => Promise<T>): Promise<T> {
+  const next = trustPromptChain.then(task, task)
+  trustPromptChain = next.catch(() => undefined)
+  return next
+}
+
+export function __resetTrustPromptChainForTests(): void {
+  trustPromptChain = Promise.resolve()
+}
+
+export async function ensureHooksConfirmed(
+  state: AppState,
+  repoId: string,
+  scriptKind: HookScriptKind
+): Promise<'run' | 'skip'> {
+  return enqueueTrustPrompt(async () => {
+    let scriptContent = ''
+    try {
+      if (scriptKind === 'issueCommand') {
+        // Local overrides are user-owned; only shared orca.yaml commands need repo trust.
+        const result = await window.api.hooks.readIssueCommand({ repoId })
+        if (result.source !== 'shared') {
+          return 'run'
+        }
+        scriptContent = (result.sharedContent ?? '').trim()
+      } else {
+        const result = await window.api.hooks.check({ repoId })
+        const yamlHooks = (result.hooks as OrcaHooks | null) ?? null
+        scriptContent = (yamlHooks?.scripts?.[scriptKind] ?? '').trim()
+      }
+    } catch {
+      // Fail closed: if we cannot inspect the script, we cannot trust it.
+      return 'skip'
+    }
+
+    if (!scriptContent) {
+      return 'run'
+    }
+
+    const contentHash = await hashOrcaHookScript(scriptContent)
+    const existingHash = state.trustedOrcaHooks[repoId]?.[scriptKind]?.contentHash
+    if (existingHash === contentHash) {
+      return 'run'
+    }
+
+    const repo = state.repos.find((r) => r.id === repoId)
+    const repoName = repo?.displayName ?? 'this repository'
+
+    return new Promise<'run' | 'skip'>((resolve) => {
+      state.openModal('confirm-orca-yaml-hooks', {
+        repoId,
+        repoName,
+        scriptKind,
+        scriptContent,
+        contentHash,
+        onResolve: (decision: 'run' | 'skip') => resolve(decision)
+      })
+    })
+  })
+}
diff --git a/src/renderer/src/lib/launch-work-item-direct.ts b/src/renderer/src/lib/launch-work-item-direct.ts
index eb645d53b..decb9219d 100644
--- a/src/renderer/src/lib/launch-work-item-direct.ts
+++ b/src/renderer/src/lib/launch-work-item-direct.ts
@@ -11,6 +11,7 @@ import {
   getWorkspaceSeedName
 } from '@/lib/new-workspace'
 import { getSuggestedCreatureName } from '@/components/sidebar/worktree-name-suggestions'
+import { ensureHooksConfirmed } from '@/lib/ensure-hooks-confirmed'
 import type { OrcaHooks, RepoHookSettings, SetupDecision, TuiAgent } from '../../../shared/types'
 
 export type LaunchableWorkItem = {
@@ -164,6 +165,10 @@ export async function launchWorkItemDirect(args: LaunchWorkItemDirectArgs): Prom
     return
   }
 
+  const trustDecision = await ensureHooksConfirmed(useAppStore.getState(), repoId, 'setup')
+  const finalSetupDecision: SetupDecision =
+    trustDecision === 'skip' ? 'skip' : setupResolution.decision
+
   const workspaceName = getWorkspaceSeedName({
     explicitName: getLinkedWorkItemSuggestedName(item),
     prompt: '',
@@ -175,12 +180,7 @@ export async function launchWorkItemDirect(args: LaunchWorkItemDirectArgs): Prom
   let primaryTabId: string | null
   let startupPlan: ReturnType<typeof buildAgentStartupPlan> = null
   try {
-    const result = await store.createWorktree(
-      repoId,
-      workspaceName,
-      baseBranch,
-      setupResolution.decision
-    )
+    const result = await store.createWorktree(repoId, workspaceName, baseBranch, finalSetupDecision)
     worktreeId = result.worktree.id
 
     const detectedIds = new Set(await detectedAgentsPromise)
@@ -289,6 +289,10 @@ export async function launchFromBranch(args: LaunchFromBranchArgs): Promise<void
     return
   }
 
+  const trustDecision = await ensureHooksConfirmed(useAppStore.getState(), repoId, 'setup')
+  const finalSetupDecision: SetupDecision =
+    trustDecision === 'skip' ? 'skip' : setupResolution.decision
+
   // Why: branch-based launches don't carry a title hint, so fall back to the
   // repo's creature-name generator — same distinct, readable default the
   // quick-composer uses when the name field is blank.
@@ -306,12 +310,7 @@ export async function launchFromBranch(args: LaunchFromBranchArgs): Promise<void
   })
 
   try {
-    const result = await store.createWorktree(
-      repoId,
-      workspaceName,
-      baseBranch,
-      setupResolution.decision
-    )
+    const result = await store.createWorktree(repoId, workspaceName, baseBranch, finalSetupDecision)
     const detectedIds = new Set(await detectedAgentsPromise)
     const effectiveAgent = pickAgent(settings?.defaultTuiAgent, detectedIds)
     const startupPlan =
diff --git a/src/renderer/src/lib/orca-hook-trust.ts b/src/renderer/src/lib/orca-hook-trust.ts
new file mode 100644
index 000000000..034b9b52a
--- /dev/null
+++ b/src/renderer/src/lib/orca-hook-trust.ts
@@ -0,0 +1,13 @@
+export type OrcaHookScriptKind = 'setup' | 'archive' | 'issueCommand'
+
+export async function hashOrcaHookScript(content: string): Promise<string> {
+  const normalized = content.trim()
+  const bytes = new TextEncoder().encode(normalized)
+  const digest = await crypto.subtle.digest('SHA-256', bytes)
+  const hex: string[] = []
+  const view = new Uint8Array(digest)
+  for (let i = 0; i < view.length; i += 1) {
+    hex.push(view[i].toString(16).padStart(2, '0'))
+  }
+  return hex.join('')
+}
diff --git a/src/renderer/src/store/slices/repos.ts b/src/renderer/src/store/slices/repos.ts
index 62bba77aa..8ab45b17b 100644
--- a/src/renderer/src/store/slices/repos.ts
+++ b/src/renderer/src/store/slices/repos.ts
@@ -69,6 +69,9 @@ export const createRepoSlice: StateCreator<AppState, [], [], RepoSlice> = (set,
         return null
       }
       const alreadyAdded = get().repos.some((r) => r.id === repo.id)
+      if (alreadyAdded) {
+        get().clearOrcaHookTrustForRepo(repo.id)
+      }
       set((s) => {
         if (s.repos.some((r) => r.id === repo.id)) {
           return s
@@ -103,6 +106,9 @@ export const createRepoSlice: StateCreator<AppState, [], [], RepoSlice> = (set,
       }
       const repo = result.repo
       const alreadyAdded = get().repos.some((r) => r.id === repo.id)
+      if (alreadyAdded) {
+        get().clearOrcaHookTrustForRepo(repo.id)
+      }
       set((s) => {
         if (s.repos.some((r) => r.id === repo.id)) {
           return s
@@ -139,6 +145,8 @@ export const createRepoSlice: StateCreator<AppState, [], [], RepoSlice> = (set,
     try {
       await window.api.repos.remove({ repoId })
 
+      get().clearOrcaHookTrustForRepo(repoId)
+
       // Kill PTYs for all worktrees belonging to this repo
       const worktreeIds = (get().worktreesByRepo[repoId] ?? []).map((w) => w.id)
       const killedTabIds = new Set<string>()
diff --git a/src/renderer/src/store/slices/ui.ts b/src/renderer/src/store/slices/ui.ts
index 6e0306139..6adc7d3ec 100644
--- a/src/renderer/src/store/slices/ui.ts
+++ b/src/renderer/src/store/slices/ui.ts
@@ -4,6 +4,7 @@ import type { AppState } from '../types'
 import { findPrevLiveWorktreeHistoryIndex } from './worktree-nav-history'
 import type {
   ChangelogData,
+  PersistedTrustedOrcaHooks,
   PersistedUIState,
   StatusBarItem,
   TaskViewPresetId,
@@ -13,10 +14,9 @@ import type {
 } from '../../../../shared/types'
 import { PER_REPO_FETCH_LIMIT } from '../../../../shared/work-items'
 
-// Why: mirrors the preset→query mapping in getTaskPresetQuery (new-workspace.ts).
+// Why: mirrors the preset→query mapping used by TaskPage's preset buttons.
 // Keeping a local copy here avoids a store ↔ lib circular import while letting
 // openTaskPage warm exactly the cache key the page will read on mount.
-// Must stay in sync with getTaskPresetQuery — see DESIGN-gh-issues-improve.md.
 function presetToQuery(presetId: TaskViewPresetId | null): string {
   switch (presetId) {
     case 'issues':
@@ -25,10 +25,10 @@ function presetToQuery(presetId: TaskViewPresetId | null): string {
       return 'assignee:@me is:issue is:open'
     case 'prs':
       return 'is:pr is:open'
-    case 'my-prs':
-      return 'author:@me is:pr is:open'
     case 'review':
       return 'review-requested:@me is:pr is:open'
+    case 'my-prs':
+      return 'author:@me is:pr is:open'
     default:
       return 'is:open'
   }
@@ -37,6 +37,7 @@ import {
   DEFAULT_STATUS_BAR_ITEMS,
   DEFAULT_WORKTREE_CARD_PROPERTIES
 } from '../../../../shared/constants'
+import type { OrcaHookScriptKind } from '../../lib/orca-hook-trust'
 
 const MIN_SIDEBAR_WIDTH = 220
 const MAX_LEFT_SIDEBAR_WIDTH = 500
@@ -46,6 +47,19 @@ const MAX_LEFT_SIDEBAR_WIDTH = 500
 // corrupted/manually-edited values rather than as a product limit.
 const MAX_RIGHT_SIDEBAR_WIDTH = 4000
 
+function filterTrustedOrcaHooksToValidRepos(
+  trust: PersistedTrustedOrcaHooks,
+  validRepoIds: Set<string>
+): PersistedTrustedOrcaHooks {
+  const next: PersistedTrustedOrcaHooks = {}
+  for (const [repoId, entry] of Object.entries(trust)) {
+    if (validRepoIds.has(repoId)) {
+      next[repoId] = entry
+    }
+  }
+  return next
+}
+
 function sanitizePersistedSidebarWidth(width: unknown, fallback: number, maxWidth: number): number {
   if (typeof width !== 'number' || !Number.isFinite(width)) {
     return fallback
@@ -131,6 +145,7 @@ export type UISlice = {
     | 'quick-open'
     | 'worktree-palette'
     | 'new-workspace-composer'
+    | 'confirm-orca-yaml-hooks'
   modalData: Record<string, unknown>
   openModal: (modal: UISlice['activeModal'], data?: Record<string, unknown>) => void
   closeModal: () => void
@@ -145,6 +160,13 @@ export type UISlice = {
    *  tab every time. */
   createFromSubTab: 'prs' | 'issues' | 'branches' | 'linear'
   setCreateFromSubTab: (tab: 'prs' | 'issues' | 'branches' | 'linear') => void
+  trustedOrcaHooks: PersistedTrustedOrcaHooks
+  markOrcaHookScriptConfirmed: (
+    repoId: string,
+    kind: OrcaHookScriptKind,
+    contentHash: string
+  ) => void
+  clearOrcaHookTrustForRepo: (repoId: string) => void
   searchQuery: string
   setSearchQuery: (q: string) => void
   groupBy: 'none' | 'repo' | 'pr-status'
@@ -333,6 +355,33 @@ export const createUISlice: StateCreator<AppState, [], [], UISlice> = (set, get)
   createFromSubTab: 'prs',
   setCreateFromSubTab: (tab) => set({ createFromSubTab: tab }),
 
+  trustedOrcaHooks: {},
+  markOrcaHookScriptConfirmed: (repoId, kind, contentHash) =>
+    set((s) => {
+      const existing = s.trustedOrcaHooks[repoId]
+      const currentEntry = existing?.[kind]
+      if (currentEntry?.contentHash === contentHash) {
+        return s
+      }
+      const nextRepo = {
+        ...existing,
+        [kind]: { contentHash, approvedAt: Date.now() }
+      }
+      const next = { ...s.trustedOrcaHooks, [repoId]: nextRepo }
+      window.api.ui.set({ trustedOrcaHooks: next }).catch(console.error)
+      return { trustedOrcaHooks: next }
+    }),
+  clearOrcaHookTrustForRepo: (repoId) =>
+    set((s) => {
+      if (!(repoId in s.trustedOrcaHooks)) {
+        return s
+      }
+      const next = { ...s.trustedOrcaHooks }
+      delete next[repoId]
+      window.api.ui.set({ trustedOrcaHooks: next }).catch(console.error)
+      return { trustedOrcaHooks: next }
+    }),
+
   searchQuery: '',
   setSearchQuery: (q) => set({ searchQuery: q }),
 
@@ -449,6 +498,10 @@ export const createUISlice: StateCreator<AppState, [], [], UISlice> = (set, get)
         updateReassuranceSeen: ui.updateReassuranceSeen ?? false,
         browserDefaultUrl: ui.browserDefaultUrl ?? null,
         browserDefaultSearchEngine: ui.browserDefaultSearchEngine ?? null,
+        trustedOrcaHooks: filterTrustedOrcaHooksToValidRepos(
+          ui.trustedOrcaHooks ?? {},
+          validRepoIds
+        ),
         persistedUIReady: true
       }
     }),
diff --git a/src/renderer/src/store/slices/worktrees.test.ts b/src/renderer/src/store/slices/worktrees.test.ts
index 46672086d..eeec95cd2 100644
--- a/src/renderer/src/store/slices/worktrees.test.ts
+++ b/src/renderer/src/store/slices/worktrees.test.ts
@@ -15,6 +15,9 @@ const mockApi = {
   },
   pty: {
     kill: vi.fn().mockResolvedValue(undefined)
+  },
+  hooks: {
+    check: vi.fn().mockResolvedValue({ hasHooks: false, hooks: null, mayNeedUpdate: false })
   }
 }
 
@@ -30,6 +33,9 @@ function createTestStore() {
         // Why: this test isolates the worktree slice, so it only provides the
         // state surface that `createWorktreeSlice` reads and writes.
         ...createWorktreeSlice(...a),
+        trustedOrcaHooks: {},
+        repos: [],
+        openModal: vi.fn(),
         shutdownWorktreeTerminals: vi.fn().mockResolvedValue(undefined),
         tabsByWorktree: {},
         tabBarOrderByWorktree: {},
diff --git a/src/renderer/src/store/slices/worktrees.ts b/src/renderer/src/store/slices/worktrees.ts
index f3279d6cf..55d9cae08 100644
--- a/src/renderer/src/store/slices/worktrees.ts
+++ b/src/renderer/src/store/slices/worktrees.ts
@@ -8,6 +8,7 @@ import {
   getRepoIdFromWorktreeId,
   type WorktreeSlice
 } from './worktree-helpers'
+import { ensureHooksConfirmed } from '@/lib/ensure-hooks-confirmed'
 export type { WorktreeSlice, WorktreeDeleteState } from './worktree-helpers'
 
 function areWorktreesEqual(current: Worktree[] | undefined, next: Worktree[]): boolean {
@@ -141,12 +142,16 @@ export const createWorktreeSlice: StateCreator<AppState, [], [], WorktreeSlice>
     }))
 
     try {
+      const repoIdForTrust = getRepoIdFromWorktreeId(worktreeId)
+      const trustDecision = await ensureHooksConfirmed(get(), repoIdForTrust, 'archive')
+      const skipArchive = trustDecision === 'skip'
+
       // Why: setup-enabled worktrees now commonly have a live shell open as soon as
       // they are created. We must tear those PTYs down before asking Git to remove
       // the working tree or Windows and some shells can keep the directory in use
       // and make delete look broken even though the git state itself is fine.
       await get().shutdownWorktreeTerminals(worktreeId)
-      await window.api.worktrees.remove({ worktreeId, force })
+      await window.api.worktrees.remove({ worktreeId, force, skipArchive })
       const tabs = get().tabsByWorktree[worktreeId] ?? []
       const tabIds = new Set(tabs.map((t) => t.id))
 
diff --git a/src/shared/constants.ts b/src/shared/constants.ts
index 5ab06f31a..69d4332c6 100644
--- a/src/shared/constants.ts
+++ b/src/shared/constants.ts
@@ -232,7 +232,8 @@ export function getDefaultUIState(): PersistedUIState {
     statusBarItems: [...DEFAULT_STATUS_BAR_ITEMS],
     statusBarVisible: true,
     dismissedUpdateVersion: null,
-    lastUpdateCheckAt: null
+    lastUpdateCheckAt: null,
+    trustedOrcaHooks: {}
   }
 }
 
diff --git a/src/shared/types.ts b/src/shared/types.ts
index 9b22a1f3a..d9c5d30ee 100644
--- a/src/shared/types.ts
+++ b/src/shared/types.ts
@@ -1117,8 +1117,22 @@ export type PersistedUIState = {
   /** Once the user has starred Orca (from any entry point) we permanently
    *  suppress the nag — no further thresholds, no notifications. */
   starNagCompleted?: boolean
+  trustedOrcaHooks?: PersistedTrustedOrcaHooks
 }
 
+export type PersistedTrustedOrcaHookEntry = {
+  contentHash: string
+  approvedAt: number
+}
+
+export type PersistedTrustedOrcaHookRepo = {
+  setup?: PersistedTrustedOrcaHookEntry
+  archive?: PersistedTrustedOrcaHookEntry
+  issueCommand?: PersistedTrustedOrcaHookEntry
+}
+
+export type PersistedTrustedOrcaHooks = Record<string, PersistedTrustedOrcaHookRepo>
+
 // ─── Persistence shape ──────────────────────────────────────────────
 export type PersistedState = {
   schemaVersion: number