feat(worktrees): add per-source visibility controls

src/main/ipc/repos-remote.test.ts

@@ -2189,6 +2189,39 @@ describe('repos:add + repos:clone', () => {
     })
   })
 
+  it('validates source definitions and preferences through local repos:update', () => {
+    const updated = {
+      id: 'repo-source-visibility',
+      path: '/tmp/repo-source-visibility',
+      displayName: 'repo-source-visibility',
+      kind: 'git',
+      badgeColor: '#22c55e'
+    }
+    mockStore.updateRepo.mockReturnValue(updated)
+
+    handlers.get('repos:update')!(null, {
+      repoId: updated.id,
+      updates: {
+        customWorktreeVisibilitySources: [
+          { id: 'team', rootPath: ' /srv/team ' },
+          { id: 'bad id', rootPath: '/srv/other' }
+        ],
+        worktreeVisibilitySourcePreferences: {
+          builtIn: { claude: 'show', gsd: 'invalid' },
+          custom: { team: 'hide' }
+        }
+      }
+    })
+
+    expect(mockStore.updateRepo).toHaveBeenCalledWith(updated.id, {
+      customWorktreeVisibilitySources: [{ id: 'team', rootPath: '/srv/team' }],
+      worktreeVisibilitySourcePreferences: {
+        builtIn: { claude: 'show' },
+        custom: { team: 'hide' }
+      }
+    })
+  })
+
   it('prepares and invalidates roots when project host setup update changes worktree base path', () => {
     const repo = {
       id: 'repo-setup-update-root',

src/main/ipc/repos.ts

@@ -118,6 +118,10 @@ import {
 } from '../project-groups/folder-workspace-path-status'
 import { getGitCloneFailureMessage } from '../../shared/git-clone-failure-message'
 import { prepareLocalWorktreeRootForRepo } from '../worktree-root-preparation'
+import {
+  normalizeCustomWorktreeVisibilitySources,
+  normalizeWorktreeVisibilitySourcePreferences
+} from '../../shared/worktree-visibility-sources'
 import { runWithGitReadCacheInvalidation } from '../git/status'
 import { isAdmissibleDirectSshAuthority } from '../../shared/ssh-retained-payload-admission'
 import { isCurrentSshProviderAuthority } from '../ssh/ssh-provider-authority'
@@ -2127,6 +2131,8 @@ export function registerRepoHandlers(mainWindow: BrowserWindow, store: Store): v
             | 'externalWorktreeInboxBaselinePaths'
             | 'importedExternalWorktreePaths'
             | 'agentWorktreeVisibility'
+            | 'customWorktreeVisibilitySources'
+            | 'worktreeVisibilitySourcePreferences'
             | 'projectGroupId'
             | 'projectGroupOrder'
           >
@@ -2205,6 +2211,26 @@ export function registerRepoHandlers(mainWindow: BrowserWindow, store: Store): v
       ) {
         delete updates.agentWorktreeVisibility
       }
+      if ('customWorktreeVisibilitySources' in updates) {
+        const normalized = normalizeCustomWorktreeVisibilitySources(
+          updates.customWorktreeVisibilitySources
+        )
+        if (!normalized) {
+          delete updates.customWorktreeVisibilitySources
+        } else {
+          updates.customWorktreeVisibilitySources = normalized
+        }
+      }
+      if ('worktreeVisibilitySourcePreferences' in updates) {
+        const normalized = normalizeWorktreeVisibilitySourcePreferences(
+          updates.worktreeVisibilitySourcePreferences
+        )
+        if (!normalized) {
+          delete updates.worktreeVisibilitySourcePreferences
+        } else {
+          updates.worktreeVisibilitySourcePreferences = normalized
+        }
+      }
       if (
         'externalWorktreeVisibilityPromptDismissedAt' in updates &&
         updates.externalWorktreeVisibilityPromptDismissedAt !== undefined &&

src/main/ipc/worktrees.ts

@@ -66,7 +66,10 @@ import {
   isLegacyRepoForExternalWorktreeVisibility,
   toDetectedWorktree
 } from '../../shared/worktree-ownership'
-import { createAgentScratchWorktreePathMatcher } from '../../shared/agent-scratch-worktrees'
+import {
+  createWorktreeVisibilitySourceMatcher,
+  normalizeCustomWorktreeVisibilitySources
+} from '../../shared/worktree-visibility-sources'
 import {
   assertWorktreeCleanForRemoval,
   forceDeleteLocalBranch,
@@ -850,10 +853,10 @@ function buildDetectedGitWorktrees(
   const liveWorktrees = dedupeWorktreesByPath(
     gitWorktrees.filter((gitWorktree) => !gitWorktree.prunable)
   )
-  const agentScratchWorktreePathMatcher = createAgentScratchWorktreePathMatcher([
-    repo.path,
-    ...liveWorktrees.map((worktree) => worktree.path)
-  ])
+  const worktreeVisibilitySourceMatcher = createWorktreeVisibilitySourceMatcher(
+    [repo.path, ...liveWorktrees.map((worktree) => worktree.path)],
+    normalizeCustomWorktreeVisibilitySources(repo.customWorktreeVisibilitySources) ?? []
+  )
   const detected = liveWorktrees.map((gitWorktree) => {
     const worktreeId = `${repo.id}::${gitWorktree.path}`
     let meta = store.getWorktreeMeta(worktreeId)
@@ -865,7 +868,7 @@ function buildDetectedGitWorktrees(
       settings,
       knownOrcaLayouts,
       isLegacyRepoForVisibility,
-      agentScratchWorktreePathMatcher
+      worktreeVisibilitySourceMatcher
     })
     if (!detected.visible) {
       return detected
@@ -879,7 +882,7 @@ function buildDetectedGitWorktrees(
       settings,
       knownOrcaLayouts,
       isLegacyRepoForVisibility,
-      agentScratchWorktreePathMatcher
+      worktreeVisibilitySourceMatcher
     })
   })
   return projectResolvedWorktreeLineage(detected, store.getAllWorktreeLineage?.() ?? {})
@@ -1081,10 +1084,10 @@ function buildDisconnectedDetectedWorktrees(
   worktrees: Worktree[]
 ): DetectedWorktree[] {
   const settings = store.getSettings()
-  const agentScratchWorktreePathMatcher = createAgentScratchWorktreePathMatcher([
-    repo.path,
-    ...worktrees.map((worktree) => worktree.path)
-  ])
+  const worktreeVisibilitySourceMatcher = createWorktreeVisibilitySourceMatcher(
+    [repo.path, ...worktrees.map((worktree) => worktree.path)],
+    normalizeCustomWorktreeVisibilitySources(repo.customWorktreeVisibilitySources) ?? []
+  )
   const detected = worktrees.map((worktree) => {
     const meta = store.getWorktreeMeta(worktree.id)
     const detected = toDetectedWorktree({
@@ -1094,7 +1097,7 @@ function buildDisconnectedDetectedWorktrees(
       settings,
       knownOrcaLayouts: [],
       isLegacyRepoForVisibility: true,
-      agentScratchWorktreePathMatcher
+      worktreeVisibilitySourceMatcher
     })
     return applyMetadataFallbackVisibility(detected)
   })

src/main/persistence.test.ts

@@ -4738,7 +4738,7 @@ describe('Store', () => {
     expect(updated!.externalWorktreeVisibilityLegacy).toBe(true)
   })
 
-  it('persists agent worktree visibility independently from external visibility', async () => {
+  it('keeps rollback agent visibility writes authoritative for both built-in sources', async () => {
     const store = await createStore()
     store.addRepo(makeRepo({ externalWorktreeVisibility: 'hide' }))
 
@@ -4746,17 +4746,53 @@ describe('Store', () => {
 
     expect(updated).toMatchObject({
       externalWorktreeVisibility: 'hide',
-      agentWorktreeVisibility: 'show'
+      agentWorktreeVisibility: 'show',
+      worktreeVisibilitySourcePreferences: {
+        builtIn: { claude: 'show', gsd: 'show' }
+      }
     })
 
     store.flush()
     const reloaded = await createStore()
     expect(reloaded.getRepo('r1')).toMatchObject({
       externalWorktreeVisibility: 'hide',
-      agentWorktreeVisibility: 'show'
+      agentWorktreeVisibility: 'show',
+      worktreeVisibilitySourcePreferences: {
+        builtIn: { claude: 'show', gsd: 'show' }
+      }
     })
   })
 
+  it('persists bounded custom worktree sources separately from their preferences', async () => {
+    const store = await createStore()
+    store.addRepo(makeRepo())
+
+    const updated = store.updateRepo('r1', {
+      customWorktreeVisibilitySources: [
+        { id: 'team', rootPath: ' /srv/team-worktrees ' },
+        { id: 'invalid', rootPath: '../relative' }
+      ],
+      worktreeVisibilitySourcePreferences: {
+        builtIn: { claude: 'show', gsd: 'hide' },
+        custom: { team: 'show' }
+      }
+    })
+
+    expect(updated).toMatchObject({
+      customWorktreeVisibilitySources: [{ id: 'team', rootPath: '/srv/team-worktrees' }],
+      worktreeVisibilitySourcePreferences: {
+        builtIn: { claude: 'show', gsd: 'hide' },
+        custom: { team: 'show' }
+      }
+    })
+
+    store.flush()
+    const reloaded = await createStore()
+    expect(reloaded.getRepo('r1')?.customWorktreeVisibilitySources).toEqual([
+      { id: 'team', rootPath: '/srv/team-worktrees' }
+    ])
+  })
+
   it('updateRepo clears source-control AI overrides independently from other clearable fields', async () => {
     const store = await createStore()
     store.addRepo(

src/main/persistence.ts

@@ -137,6 +137,10 @@ import {
 import { parseWorkspaceSessionSalvaging } from '../shared/workspace-session-salvage'
 import { normalizeUsagePercentageDisplay } from '../shared/usage-percentage-display'
 import { normalizeStatusBarUsageMode } from '../shared/status-bar-usage-mode'
+import {
+  normalizeCustomWorktreeVisibilitySources,
+  normalizeWorktreeVisibilitySourcePreferences
+} from '../shared/worktree-visibility-sources'
 import { isExistingPersistedProfile } from '../shared/project-order-manual-default-notice'
 import { resolveUsagePercentageDisplayChangeNoticeDismissed } from '../shared/usage-percentage-display-change-notice'
 import { normalizePRBotAuthorOverrides } from '../shared/pr-bot-author-overrides'
@@ -1463,6 +1467,8 @@ function sanitizeRepoUpdatesForPersistence<
       | 'worktreeBasePath'
       | 'projectHostSetupMethod'
       | 'forkSyncMode'
+      | 'customWorktreeVisibilitySources'
+      | 'worktreeVisibilitySourcePreferences'
     >
   >
 >(updates: T): T {
@@ -1523,6 +1529,26 @@ function sanitizeRepoUpdatesForPersistence<
       sanitized.forkSyncMode = forkSyncMode
     }
   }
+  if ('customWorktreeVisibilitySources' in sanitized) {
+    const sources = normalizeCustomWorktreeVisibilitySources(
+      sanitized.customWorktreeVisibilitySources
+    )
+    if (!sources) {
+      delete sanitized.customWorktreeVisibilitySources
+    } else {
+      sanitized.customWorktreeVisibilitySources = sources
+    }
+  }
+  if ('worktreeVisibilitySourcePreferences' in sanitized) {
+    const preferences = normalizeWorktreeVisibilitySourcePreferences(
+      sanitized.worktreeVisibilitySourcePreferences
+    )
+    if (!preferences) {
+      delete sanitized.worktreeVisibilitySourcePreferences
+    } else {
+      sanitized.worktreeVisibilitySourcePreferences = preferences
+    }
+  }
   return sanitized
 }
 
@@ -4920,6 +4946,8 @@ export class Store {
         | 'externalWorktreeInboxBaselinePaths'
         | 'importedExternalWorktreePaths'
         | 'agentWorktreeVisibility'
+        | 'customWorktreeVisibilitySources'
+        | 'worktreeVisibilitySourcePreferences'
         | 'projectGroupId'
         | 'projectGroupOrder'
         | 'projectHostSetupMethod'
@@ -4938,6 +4966,20 @@ export class Store {
       return null
     }
     const sanitizedUpdates = sanitizeRepoUpdatesForPersistence(updates)
+    if (
+      'agentWorktreeVisibility' in sanitizedUpdates &&
+      !('worktreeVisibilitySourcePreferences' in sanitizedUpdates) &&
+      (sanitizedUpdates.agentWorktreeVisibility === 'hide' ||
+        sanitizedUpdates.agentWorktreeVisibility === 'show')
+    ) {
+      sanitizedUpdates.worktreeVisibilitySourcePreferences = {
+        ...repo.worktreeVisibilitySourcePreferences,
+        builtIn: {
+          claude: sanitizedUpdates.agentWorktreeVisibility,
+          gsd: sanitizedUpdates.agentWorktreeVisibility
+        }
+      }
+    }
     if ('projectGroupId' in sanitizedUpdates) {
       const nextGroupId = sanitizedUpdates.projectGroupId
       if (
@@ -5103,6 +5145,8 @@ export class Store {
       sourceControlAi: rawSourceControlAi,
       projectHostSetupMethod: rawProjectHostSetupMethod,
       forkSyncMode: rawForkSyncMode,
+      customWorktreeVisibilitySources: rawCustomWorktreeVisibilitySources,
+      worktreeVisibilitySourcePreferences: rawWorktreeVisibilitySourcePreferences,
       ...repoWithoutIcon
     } = repo
     const repoIcon = sanitizeRepoIcon(rawRepoIcon)
@@ -5111,6 +5155,12 @@ export class Store {
     const sourceControlAi = normalizeRepoSourceControlAiOverrides(rawSourceControlAi)
     const projectHostSetupMethod = sanitizeRepoProjectHostSetupMethod(rawProjectHostSetupMethod)
     const forkSyncMode = sanitizeForkSyncMode(rawForkSyncMode)
+    const customWorktreeVisibilitySources = normalizeCustomWorktreeVisibilitySources(
+      rawCustomWorktreeVisibilitySources
+    )
+    const worktreeVisibilitySourcePreferences = normalizeWorktreeVisibilitySourcePreferences(
+      rawWorktreeVisibilitySourcePreferences
+    )
     // Why: never spawn git/gh username resolution in hydration — a stuck probe froze Windows startup for minutes (issue #7225); read only cache/persisted value.
     const gitUsername = isFolderRepo(repo)
       ? ''
@@ -5124,6 +5174,10 @@ export class Store {
       ...(sourceControlAi !== undefined ? { sourceControlAi } : {}),
       ...(projectHostSetupMethod !== undefined ? { projectHostSetupMethod } : {}),
       ...(forkSyncMode !== undefined ? { forkSyncMode } : {}),
+      ...(customWorktreeVisibilitySources !== undefined ? { customWorktreeVisibilitySources } : {}),
+      ...(worktreeVisibilitySourcePreferences !== undefined
+        ? { worktreeVisibilitySourcePreferences }
+        : {}),
       kind: isFolderRepo(repo) ? 'folder' : 'git',
       gitUsername,
       hookSettings: {

src/main/runtime/orca-runtime.ts

@@ -486,11 +486,12 @@ import {
   isLegacyRepoForExternalWorktreeVisibility,
   toDetectedWorktree
 } from '../../shared/worktree-ownership'
+import { isAgentScratchRepoRootPath } from '../../shared/agent-scratch-worktrees'
 import {
-  createAgentScratchWorktreePathMatcher,
-  isAgentScratchRepoRootPath,
-  type AgentScratchWorktreePathMatcher
-} from '../../shared/agent-scratch-worktrees'
+  createWorktreeVisibilitySourceMatcher,
+  normalizeCustomWorktreeVisibilitySources,
+  type WorktreeVisibilitySourceMatcher
+} from '../../shared/worktree-visibility-sources'
 import {
   BROWSER_HEADLESS_RUNTIME_CAPABILITY,
   BROWSER_CERTIFICATE_TRUST_RUNTIME_CAPABILITY,
@@ -19150,6 +19151,8 @@ export class OrcaRuntimeService {
         | 'externalWorktreeInboxBaselinePaths'
         | 'importedExternalWorktreePaths'
         | 'agentWorktreeVisibility'
+        | 'customWorktreeVisibilitySources'
+        | 'worktreeVisibilitySourcePreferences'
         | 'projectGroupId'
         | 'projectGroupOrder'
       >
@@ -20956,13 +20959,13 @@ export class OrcaRuntimeService {
       checkoutPaths.push(worktree.path)
       checkoutPathsByRepoId.set(worktree.repoId, checkoutPaths)
     }
-    const agentScratchMatchersByRepoId = new Map(
+    const visibilitySourceMatchersByRepoId = new Map(
       (this.store?.getRepos() ?? []).map((repo) => [
         repo.id,
-        createAgentScratchWorktreePathMatcher([
-          repo.path,
-          ...(checkoutPathsByRepoId.get(repo.id) ?? [])
-        ])
+        createWorktreeVisibilitySourceMatcher(
+          [repo.path, ...(checkoutPathsByRepoId.get(repo.id) ?? [])],
+          normalizeCustomWorktreeVisibilitySources(repo.customWorktreeVisibilitySources) ?? []
+        )
       ])
     )
     const worktrees = resolved.filter((worktree) => {
@@ -20971,7 +20974,7 @@ export class OrcaRuntimeService {
       }
       return this.isRuntimeWorktreeVisible(
         worktree,
-        agentScratchMatchersByRepoId.get(worktree.repoId)
+        visibilitySourceMatchersByRepoId.get(worktree.repoId)
       )
     })
     return {
@@ -21013,10 +21016,10 @@ export class OrcaRuntimeService {
     if (scan.ok) {
       pruneLineageForMissingRepoWorktrees(store, repo, scan.worktrees)
     }
-    const agentScratchWorktreePathMatcher = createAgentScratchWorktreePathMatcher([
-      repo.path,
-      ...scan.worktrees.map((worktree) => worktree.path)
-    ])
+    const worktreeVisibilitySourceMatcher = createWorktreeVisibilitySourceMatcher(
+      [repo.path, ...scan.worktrees.map((worktree) => worktree.path)],
+      normalizeCustomWorktreeVisibilitySources(repo.customWorktreeVisibilitySources) ?? []
+    )
     const detected = scan.worktrees.map((gitWorktree) => {
       const worktreeId = `${repo.id}::${gitWorktree.path}`
       const meta = store.getWorktreeMeta(worktreeId)
@@ -21027,7 +21030,7 @@ export class OrcaRuntimeService {
       const detectedWorktree = this.toRuntimeDetectedWorktree(
         repo,
         worktree,
-        agentScratchWorktreePathMatcher
+        worktreeVisibilitySourceMatcher
       )
       if (scan.ok) {
         return detectedWorktree
@@ -21094,19 +21097,19 @@ export class OrcaRuntimeService {
 
   private isRuntimeWorktreeVisible(
     worktree: Worktree,
-    agentScratchWorktreePathMatcher?: AgentScratchWorktreePathMatcher
+    worktreeVisibilitySourceMatcher?: WorktreeVisibilitySourceMatcher
   ): boolean {
     const repo = this.store?.getRepo(worktree.repoId)
     if (!repo || !this.store) {
       return true
     }
-    return this.toRuntimeDetectedWorktree(repo, worktree, agentScratchWorktreePathMatcher).visible
+    return this.toRuntimeDetectedWorktree(repo, worktree, worktreeVisibilitySourceMatcher).visible
   }
 
   private toRuntimeDetectedWorktree(
     repo: Repo,
     worktree: Worktree,
-    agentScratchWorktreePathMatcher?: AgentScratchWorktreePathMatcher
+    worktreeVisibilitySourceMatcher?: WorktreeVisibilitySourceMatcher
   ): DetectedWorktree {
     const settings = this.store?.getSettings()
     if (!settings) {
@@ -21124,7 +21127,7 @@ export class OrcaRuntimeService {
       settings,
       knownOrcaLayouts: buildKnownOrcaWorkspaceLayouts(settings, repo),
       isLegacyRepoForVisibility: isLegacyRepoForExternalWorktreeVisibility(repo),
-      agentScratchWorktreePathMatcher
+      worktreeVisibilitySourceMatcher
     })
   }
 

src/main/runtime/rpc/methods/repo-update-schema.ts

@@ -3,6 +3,10 @@ import { OptionalFiniteNumber, OptionalString } from '../schemas'
 import { sanitizeRepoIcon } from '../../../../shared/repo-icon'
 import { normalizeRepoBadgeColor } from '../../../../shared/repo-badge-color'
 import { normalizeRepoSourceControlAiOverrides } from '../../../../shared/source-control-ai'
+import {
+  normalizeCustomWorktreeVisibilitySources,
+  normalizeWorktreeVisibilitySourcePreferences
+} from '../../../../shared/worktree-visibility-sources'
 
 export const RepoSourceControlAiOverrides = z
   .unknown()
@@ -55,6 +59,14 @@ export function createRepoUpdateSchema<T extends z.ZodRawShape>(
       externalWorktreeInboxBaselinePaths: z.array(z.string()).optional(),
       importedExternalWorktreePaths: z.array(z.string()).optional(),
       agentWorktreeVisibility: z.enum(['hide', 'show']).optional(),
+      customWorktreeVisibilitySources: z
+        .unknown()
+        .transform((value) => normalizeCustomWorktreeVisibilitySources(value))
+        .optional(),
+      worktreeVisibilitySourcePreferences: z
+        .unknown()
+        .transform((value) => normalizeWorktreeVisibilitySourcePreferences(value))
+        .optional(),
       externalWorktreeDiscoverySuppressedAt: z.number().finite().nullable().optional(),
       projectGroupId: OptionalString.nullable().optional(),
       projectGroupOrder: OptionalFiniteNumber,

src/main/runtime/rpc/methods/repo.test.ts

@@ -330,6 +330,38 @@ describe('repo RPC methods', () => {
     })
   })
 
+  it('validates additive source settings at the remote RPC boundary', async () => {
+    const runtime = {
+      getRuntimeId: () => 'test-runtime',
+      updateRepo: vi.fn().mockResolvedValue({ id: 'repo-1', path: '/srv/repo' })
+    } as unknown as OrcaRuntimeService
+    const dispatcher = new RpcDispatcher({ runtime, methods: REPO_METHODS })
+
+    await dispatcher.dispatch(
+      makeRequest('repo.update', {
+        repo: 'repo-1',
+        updates: {
+          customWorktreeVisibilitySources: [
+            { id: 'team', rootPath: ' /srv/team ' },
+            { id: 'relative', rootPath: '../team' }
+          ],
+          worktreeVisibilitySourcePreferences: {
+            builtIn: { claude: 'show', gsd: 'bad' },
+            custom: { team: 'hide' }
+          }
+        }
+      })
+    )
+
+    expect(runtime.updateRepo).toHaveBeenCalledWith('repo-1', {
+      customWorktreeVisibilitySources: [{ id: 'team', rootPath: '/srv/team' }],
+      worktreeVisibilitySourcePreferences: {
+        builtIn: { claude: 'show' },
+        custom: { team: 'hide' }
+      }
+    })
+  })
+
   it('persists resolved GitHub upstream metadata updates', async () => {
     const runtime = {
       getRuntimeId: () => 'test-runtime',

src/preload/api-types.ts

@@ -1197,6 +1197,8 @@ export type PreloadApi = {
           | 'externalWorktreeInboxBaselinePaths'
           | 'importedExternalWorktreePaths'
           | 'agentWorktreeVisibility'
+          | 'customWorktreeVisibilitySources'
+          | 'worktreeVisibilitySourcePreferences'
           | 'projectGroupId'
           | 'projectGroupOrder'
           | 'forkSyncMode'

src/renderer/src/components/sidebar/HiddenWorktreeRecoveryList.tsx

@@ -0,0 +1,195 @@
+import React, { useId, useRef, useState } from 'react'
+import { FolderMinus, Search } from 'lucide-react'
+import { useVirtualizer } from '@tanstack/react-virtual'
+import { Button } from '@/components/ui/button'
+import { Input } from '@/components/ui/input'
+import { translate } from '@/i18n/i18n'
+import type { DetectedWorktreeListResult, Repo } from '../../../../shared/types'
+import {
+  getHiddenImportableExternalWorktrees,
+  getVisibleNonOrcaWorktrees
+} from '../../../../shared/external-worktree-inbox'
+import { relativePathInsideRoot } from '../../../../shared/cross-platform-path'
+
+type Props = {
+  repo: Repo
+  detected: DetectedWorktreeListResult | undefined
+  listState: 'checking' | 'ready' | 'failed'
+  busyPath: string | null
+  toggling: boolean
+  onShow: (worktreePath: string) => Promise<void>
+}
+
+export default function HiddenWorktreeRecoveryList({
+  repo,
+  detected,
+  listState,
+  busyPath,
+  toggling,
+  onShow
+}: Props): React.JSX.Element | null {
+  const [query, setQuery] = useState('')
+  const headingId = useId()
+  const listRef = useRef<HTMLDivElement>(null)
+  const hidden = getHiddenImportableExternalWorktrees(detected)
+  const normalizedQuery = query.trim().toLocaleLowerCase()
+  const filtered = normalizedQuery
+    ? hidden.filter(
+        (worktree) =>
+          worktree.displayName.toLocaleLowerCase().includes(normalizedQuery) ||
+          worktree.path.toLocaleLowerCase().includes(normalizedQuery)
+      )
+    : hidden
+  const discoveredCount = hidden.length + getVisibleNonOrcaWorktrees(detected).length
+  const virtualizer = useVirtualizer({
+    count: filtered.length,
+    getScrollElement: () => listRef.current,
+    estimateSize: () => 56,
+    getItemKey: (index) => filtered[index]?.id ?? index,
+    overscan: 3,
+    initialRect: { width: 480, height: 224 }
+  })
+
+  if (hidden.length === 0 && listState !== 'ready') {
+    return null
+  }
+
+  return (
+    <section className="grid min-w-0 gap-2">
+      <div className="flex items-center justify-between gap-3">
+        <div>
+          <h3 id={headingId} className="text-sm font-medium">
+            {translate(
+              'auto.components.sidebar.WorktreeVisibilityDialog.7d21c5e848',
+              'Hidden worktrees ({{value0}})',
+              { value0: hidden.length }
+            )}
+          </h3>
+          <p className="text-xs text-muted-foreground">
+            {translate(
+              'auto.components.sidebar.WorktreeVisibilityDialog.9b53f7a160',
+              'Show one without enabling its source.'
+            )}
+          </p>
+        </div>
+        {hidden.length >= 10 ? (
+          <div className="relative w-48 shrink-0">
+            <Search className="pointer-events-none absolute left-2.5 top-2 size-3.5 text-muted-foreground" />
+            <Input
+              type="search"
+              className="h-8 pl-8 text-xs"
+              value={query}
+              aria-label={translate(
+                'auto.components.sidebar.WorktreeVisibilityDialog.search',
+                'Search hidden worktrees'
+              )}
+              placeholder={translate(
+                'auto.components.sidebar.WorktreeVisibilityDialog.searchPlaceholder',
+                'Search {{value0}} worktrees…',
+                { value0: hidden.length }
+              )}
+              onChange={(event) => setQuery(event.target.value)}
+            />
+          </div>
+        ) : null}
+      </div>
+      {filtered.length > 0 ? (
+        <div
+          ref={listRef}
+          role="region"
+          aria-labelledby={headingId}
+          className="scrollbar-sleek max-h-56 min-w-0 overflow-y-auto"
+          tabIndex={0}
+          style={{ height: `${Math.min(virtualizer.getTotalSize(), 224)}px` }}
+        >
+          <ul className="relative min-w-0" style={{ height: `${virtualizer.getTotalSize()}px` }}>
+            {virtualizer.getVirtualItems().map((virtualRow) => {
+              const worktree = filtered[virtualRow.index]
+              if (!worktree) {
+                return null
+              }
+              const displayPath = relativePathInsideRoot(repo.path, worktree.path) || worktree.path
+              return (
+                <li
+                  key={worktree.id}
+                  ref={virtualizer.measureElement}
+                  data-index={virtualRow.index}
+                  className="absolute left-0 top-0 w-full pb-1"
+                  style={{ transform: `translateY(${virtualRow.start}px)` }}
+                  aria-posinset={virtualRow.index + 1}
+                  aria-setsize={filtered.length}
+                >
+                  <div className="flex min-w-0 items-center gap-3 rounded-md border border-border px-3 py-2 hover:bg-accent/50">
+                    <div className="min-w-0 flex-1">
+                      <div className="truncate text-sm">{worktree.displayName}</div>
+                      <div className="truncate font-mono text-xs text-muted-foreground">
+                        {displayPath}
+                      </div>
+                    </div>
+                    <Button
+                      type="button"
+                      variant="outline"
+                      size="sm"
+                      disabled={busyPath !== null || toggling || listState === 'checking'}
+                      onClick={() => void onShow(worktree.path)}
+                    >
+                      {busyPath === worktree.path
+                        ? translate(
+                            'auto.components.sidebar.WorktreeVisibilityDialog.2f80cd4b97',
+                            'Showing…'
+                          )
+                        : translate(
+                            'auto.components.sidebar.WorktreeVisibilityDialog.e64b81d3a9',
+                            'Show'
+                          )}
+                    </Button>
+                  </div>
+                </li>
+              )
+            })}
+          </ul>
+        </div>
+      ) : listState === 'ready' ? (
+        <div className="flex min-h-16 items-center gap-3 rounded-lg border border-border bg-muted/30 p-3">
+          <span className="flex size-7 shrink-0 items-center justify-center rounded-md border border-border bg-background text-muted-foreground">
+            <FolderMinus className="size-3.5" />
+          </span>
+          <div className="min-w-0">
+            <div className="text-[13px] font-medium">
+              {normalizedQuery
+                ? translate(
+                    'auto.components.sidebar.WorktreeVisibilityDialog.noMatches',
+                    'No matching worktrees'
+                  )
+                : discoveredCount > 0
+                  ? translate(
+                      'auto.components.sidebar.WorktreeVisibilityDialog.allShown',
+                      'All discovered worktrees are shown'
+                    )
+                  : translate(
+                      'auto.components.sidebar.WorktreeVisibilityDialog.noneFound',
+                      'No non-Orca worktrees found'
+                    )}
+            </div>
+            <div className="text-xs text-muted-foreground">
+              {normalizedQuery
+                ? translate(
+                    'auto.components.sidebar.WorktreeVisibilityDialog.tryDifferentSearch',
+                    'Try a different name or path.'
+                  )
+                : discoveredCount > 0
+                  ? translate(
+                      'auto.components.sidebar.WorktreeVisibilityDialog.disableSource',
+                      'Disable a source to manage its worktrees individually.'
+                    )
+                  : translate(
+                      'auto.components.sidebar.WorktreeVisibilityDialog.appearWhenDetected',
+                      'New worktrees will appear here when Orca detects them.'
+                    )}
+            </div>
+          </div>
+        </div>
+      ) : null}
+    </section>
+  )
+}

src/renderer/src/components/sidebar/WorktreeVisibilityDialog.test.tsx

@@ -38,6 +38,12 @@ vi.mock('@/components/ui/dialog', () => ({
   DialogTitle: ({ children }: { children: ReactNode }) => <div>{children}</div>
 }))
 
+vi.mock('@/components/ui/tooltip', () => ({
+  Tooltip: ({ children }: { children: ReactNode }) => <>{children}</>,
+  TooltipTrigger: ({ children }: { children: ReactNode }) => <>{children}</>,
+  TooltipContent: ({ children }: { children: ReactNode }) => <span>{children}</span>
+}))
+
 vi.mock('@/i18n/i18n', () => ({
   translate: (_key: string, fallback: string, values?: Record<string, unknown>) =>
     values
@@ -124,7 +130,22 @@ beforeEach(() => {
   mocks.state.modalData = { repoId: 'repo-1' }
   mocks.state.repos = [makeRepo()]
   mocks.state.detectedWorktreesByRepo = { 'repo-1': makeDetected() }
-  mocks.state.updateRepo.mockResolvedValue(true)
+  mocks.state.updateRepo.mockImplementation(
+    async (repoId: string, updates: Record<string, unknown>) => {
+      const repo = (mocks.state.repos as Repo[]).find((candidate) => candidate.id === repoId)
+      if (!repo) {
+        return false
+      }
+      for (const [key, value] of Object.entries(updates)) {
+        if (value === null) {
+          delete (repo as unknown as Record<string, unknown>)[key]
+        } else {
+          ;(repo as unknown as Record<string, unknown>)[key] = value
+        }
+      }
+      return true
+    }
+  )
   mocks.state.fetchWorktrees.mockResolvedValue(true)
   container = document.createElement('div')
   document.body.appendChild(container)
@@ -168,10 +189,12 @@ function buttonWithText(text: string): HTMLButtonElement {
   return button as HTMLButtonElement
 }
 
-function alwaysShowSwitch(): HTMLButtonElement {
-  const control = document.querySelector('[role="switch"]')
+function sourceSwitch(label = 'Claude Code'): HTMLButtonElement {
+  const control = document.querySelector(
+    `[role="switch"][aria-label="Show current and future worktrees from ${label}"]`
+  )
   if (!control) {
-    throw new Error('No Always show switch')
+    throw new Error(`No ${label} source switch`)
   }
   return control as HTMLButtonElement
 }
@@ -187,9 +210,7 @@ describe('WorktreeVisibilityDialog', () => {
     await renderDialog()
 
     expect(document.body.textContent).toContain('Hidden worktrees (1)')
-    expect(document.body.textContent).toContain(
-      'Choose which hidden worktrees to show individually.'
-    )
+    expect(document.body.textContent).toContain('Show one without enabling its source.')
     expect(document.body.textContent).toContain('scratch-1')
     expect(document.body.textContent).toContain('.claude/worktrees/scratch-1')
     expect(document.body.textContent).not.toContain('/repo/.claude')
@@ -212,6 +233,20 @@ describe('WorktreeVisibilityDialog', () => {
 
     expect(document.body.textContent).toContain('Hidden worktrees (500)')
     expect(document.querySelectorAll('ul > li').length).toBeLessThan(20)
+    const search = document.querySelector<HTMLInputElement>(
+      'input[aria-label="Search hidden worktrees"]'
+    )
+    expect(search).not.toBeNull()
+    await act(async () => {
+      Object.getOwnPropertyDescriptor(HTMLInputElement.prototype, 'value')?.set?.call(
+        search,
+        'scratch-499'
+      )
+      search!.dispatchEvent(new Event('input', { bubbles: true }))
+      search!.dispatchEvent(new Event('change', { bubbles: true }))
+    })
+    expect(document.body.textContent).toContain('scratch-499')
+    expect(document.body.textContent).not.toContain('scratch-0')
   })
 
   it('recovers a hidden worktree per path through the existing import exception', async () => {
@@ -234,7 +269,8 @@ describe('WorktreeVisibilityDialog', () => {
     mocks.state.detectedWorktreesByRepo = { 'repo-1': makeDetected([]) }
     await renderDialog()
 
-    expect(document.body.textContent).not.toContain('Hidden worktrees')
+    expect(document.body.textContent).toContain('Hidden worktrees (0)')
+    expect(document.body.textContent).toContain('No non-Orca worktrees found')
   })
 
   it('says it is checking instead of claiming nothing is hidden on a fallback snapshot', async () => {
@@ -289,7 +325,7 @@ describe('WorktreeVisibilityDialog', () => {
     mocks.state.fetchWorktrees.mockImplementation(() => new Promise(() => {}))
     await renderDialog()
 
-    expect(alwaysShowSwitch().disabled).toBe(true)
+    expect(sourceSwitch().disabled).toBe(true)
   })
 
   it('reports a failed refresh even while an older trusted snapshot is on screen', async () => {
@@ -323,7 +359,7 @@ describe('WorktreeVisibilityDialog', () => {
 
     await click(buttonWithText('Show'))
 
-    expect(alwaysShowSwitch().disabled).toBe(true)
+    expect(sourceSwitch().disabled).toBe(true)
   })
 
   it('locks row actions and retry while the repo-wide toggle is in flight', async () => {
@@ -331,7 +367,7 @@ describe('WorktreeVisibilityDialog', () => {
     mocks.state.updateRepo.mockImplementation(() => new Promise(() => {}))
     await renderDialog()
 
-    await click(alwaysShowSwitch())
+    await click(sourceSwitch())
 
     expect(buttonWithText('Show').disabled).toBe(true)
     expect(buttonWithText('Try again').disabled).toBe(true)
@@ -392,12 +428,12 @@ describe('WorktreeVisibilityDialog', () => {
     mocks.state.updateRepo.mockReturnValueOnce(update.promise)
     await renderDialog()
     mocks.state.fetchWorktrees.mockClear()
-    await click(alwaysShowSwitch())
+    await click(sourceSwitch())
 
     await act(async () => root.render(null))
     await renderDialog()
 
-    expect(alwaysShowSwitch().disabled).toBe(true)
+    expect(sourceSwitch().disabled).toBe(true)
     expect(buttonWithText('Show').disabled).toBe(true)
     expect(mocks.state.fetchWorktrees).not.toHaveBeenCalled()
 
@@ -406,7 +442,7 @@ describe('WorktreeVisibilityDialog', () => {
       await update.promise
       await Promise.resolve()
     })
-    expect(alwaysShowSwitch().disabled).toBe(false)
+    expect(sourceSwitch().disabled).toBe(false)
   })
 
   it('does not carry a mutation fence across same-id repos on different hosts', async () => {
@@ -465,7 +501,20 @@ describe('WorktreeVisibilityDialog', () => {
     await renderDialog()
     mocks.state.fetchWorktrees.mockClear()
 
-    await click(alwaysShowSwitch())
+    await click(sourceSwitch())
+
+    expect(document.querySelector('[role="alert"]')?.textContent).toContain(
+      'Could not update worktree visibility. Try again.'
+    )
+    expect(mocks.state.fetchWorktrees).not.toHaveBeenCalled()
+  })
+
+  it('does not report success when an older host strips additive source settings (STA-4092)', async () => {
+    mocks.state.updateRepo.mockResolvedValue(true)
+    await renderDialog()
+    mocks.state.fetchWorktrees.mockClear()
+
+    await click(sourceSwitch())
 
     expect(document.querySelector('[role="alert"]')?.textContent).toContain(
       'Could not update worktree visibility. Try again.'
@@ -477,7 +526,7 @@ describe('WorktreeVisibilityDialog', () => {
     await renderDialog()
     mocks.state.fetchWorktrees.mockResolvedValue(false)
 
-    await click(alwaysShowSwitch())
+    await click(sourceSwitch())
 
     expect(mocks.state.fetchWorktrees).toHaveBeenLastCalledWith('repo-1', {
       requireAuthoritative: true
@@ -487,54 +536,107 @@ describe('WorktreeVisibilityDialog', () => {
     )
   })
 
-  it('enables the persistent policy for regular and agent worktrees', async () => {
+  it('toggles built-in sources independently', async () => {
     await renderDialog()
 
-    expect(document.body.textContent).toContain('Always show')
-    expect(document.body.textContent).toContain('1 worktree currently hidden')
-    expect(alwaysShowSwitch().getAttribute('aria-checked')).toBe('false')
+    expect(sourceSwitch('Claude Code').getAttribute('aria-checked')).toBe('false')
+    expect(sourceSwitch('GSD').getAttribute('aria-checked')).toBe('false')
 
-    await click(alwaysShowSwitch())
+    await click(sourceSwitch('Claude Code'))
 
     expect(mocks.state.updateRepo).toHaveBeenCalledWith('repo-1', {
-      externalWorktreeVisibility: 'show',
-      agentWorktreeVisibility: 'show',
-      externalWorktreeDiscoverySuppressedAt: null
+      worktreeVisibilitySourcePreferences: {
+        builtIn: { claude: 'show', gsd: 'hide' }
+      }
     })
     expect(mocks.state.closeModal).not.toHaveBeenCalled()
   })
 
-  it('keeps the combined switch off until the agent policy is explicitly enabled', async () => {
+  it('migrates legacy Always show to both built-in source rows', async () => {
+    mocks.state.repos = [makeRepo({ agentWorktreeVisibility: 'show' })]
+    await renderDialog()
+
+    expect(sourceSwitch('Claude Code').getAttribute('aria-checked')).toBe('true')
+    expect(sourceSwitch('GSD').getAttribute('aria-checked')).toBe('true')
+
+    await click(sourceSwitch('Claude Code'))
+
+    expect(mocks.state.updateRepo).toHaveBeenCalledWith('repo-1', {
+      worktreeVisibilitySourcePreferences: {
+        builtIn: { claude: 'hide', gsd: 'show' }
+      }
+    })
+  })
+
+  it('keeps ordinary non-Orca visibility on its own source row', async () => {
     mocks.state.repos = [makeRepo({ externalWorktreeVisibility: 'show' })]
     await renderDialog()
 
-    expect(alwaysShowSwitch().getAttribute('aria-checked')).toBe('false')
-    expect(document.body.textContent).toContain('scratch-1')
-
-    await click(alwaysShowSwitch())
+    expect(sourceSwitch('Other locations').getAttribute('aria-checked')).toBe('true')
+    await click(sourceSwitch('Other locations'))
 
     expect(mocks.state.updateRepo).toHaveBeenCalledWith('repo-1', {
-      externalWorktreeVisibility: 'show',
-      agentWorktreeVisibility: 'show',
-      externalWorktreeDiscoverySuppressedAt: null
+      externalWorktreeVisibility: 'hide'
     })
   })
 
-  it('turns the persistent policy off without closing the dialog', async () => {
+  it('adds custom locations disabled by default', async () => {
+    await renderDialog()
+    await click(buttonWithText('Add location'))
+    const input = document.querySelector<HTMLInputElement>('#custom-worktree-root')
+    expect(input).not.toBeNull()
+    await act(async () => {
+      Object.getOwnPropertyDescriptor(HTMLInputElement.prototype, 'value')?.set?.call(
+        input,
+        '/srv/team-worktrees'
+      )
+      input!.dispatchEvent(new Event('input', { bubbles: true }))
+      input!.dispatchEvent(new Event('change', { bubbles: true }))
+    })
+    await click(buttonWithText('Add'))
+
+    expect(mocks.state.updateRepo).toHaveBeenCalledWith(
+      'repo-1',
+      expect.objectContaining({
+        customWorktreeVisibilitySources: [
+          expect.objectContaining({ rootPath: '/srv/team-worktrees' })
+        ],
+        worktreeVisibilitySourcePreferences: expect.objectContaining({
+          custom: expect.objectContaining({})
+        })
+      })
+    )
+    const update = mocks.state.updateRepo.mock.calls.at(-1)?.[1] as {
+      customWorktreeVisibilitySources: { id: string }[]
+      worktreeVisibilitySourcePreferences: { custom: Record<string, string> }
+    }
+    expect(
+      update.worktreeVisibilitySourcePreferences.custom[
+        update.customWorktreeVisibilitySources[0]!.id
+      ]
+    ).toBe('hide')
+  })
+
+  it('removes custom locations without changing other source preferences', async () => {
     mocks.state.repos = [
-      makeRepo({ externalWorktreeVisibility: 'show', agentWorktreeVisibility: 'show' })
+      makeRepo({
+        customWorktreeVisibilitySources: [{ id: 'team', rootPath: '/srv/team-worktrees' }],
+        worktreeVisibilitySourcePreferences: { custom: { team: 'hide' } }
+      })
     ]
     await renderDialog()
 
-    expect(document.body.textContent).toContain('0 worktrees currently shown')
-    expect(alwaysShowSwitch().getAttribute('aria-checked')).toBe('true')
+    expect(sourceSwitch('team-worktrees').getAttribute('aria-checked')).toBe('false')
+    const remove = document.querySelector<HTMLButtonElement>(
+      'button[aria-label="Remove team-worktrees"]'
+    )
+    expect(remove).not.toBeNull()
+    await click(remove!)
 
-    await click(alwaysShowSwitch())
-
-    expect(mocks.state.updateRepo).toHaveBeenCalledWith('repo-1', {
-      externalWorktreeVisibility: 'hide',
-      agentWorktreeVisibility: 'hide'
-    })
+    expect(mocks.state.updateRepo).toHaveBeenCalledWith(
+      'repo-1',
+      expect.objectContaining({ customWorktreeVisibilitySources: [] })
+    )
     expect(mocks.state.closeModal).not.toHaveBeenCalled()
   })
 })

src/renderer/src/components/sidebar/WorktreeVisibilityDialog.tsx

@@ -1,6 +1,4 @@
-import React, { useCallback, useEffect, useId, useLayoutEffect, useRef, useState } from 'react'
-import { Eye, EyeOff } from 'lucide-react'
-import { useVirtualizer } from '@tanstack/react-virtual'
+import React, { useCallback, useEffect, useLayoutEffect, useRef, useState } from 'react'
 import { useAppStore } from '@/store'
 import {
   Dialog,
@@ -10,19 +8,11 @@ import {
   DialogTitle
 } from '@/components/ui/dialog'
 import { Button } from '@/components/ui/button'
-import { Label } from '@/components/ui/label'
-import { Switch } from '@/components/ui/switch'
-import {
-  getHiddenImportableExternalWorktrees,
-  getVisibleNonOrcaWorktrees
-} from '../../../../shared/external-worktree-inbox'
 import { isGitRepoKind } from '../../../../shared/repo-kind'
-import { relativePathInsideRoot } from '../../../../shared/cross-platform-path'
 import {
-  effectiveAgentWorktreeVisibility,
   effectiveExternalWorktreeVisibility,
   isLegacyRepoForExternalWorktreeVisibility
-} from '../../../../shared/worktree-ownership'
+} from '../../../../shared/external-worktree-visibility'
 import { translate } from '@/i18n/i18n'
 import {
   importNewExternalWorktreeInboxPaths,
@@ -41,6 +31,26 @@ import {
   type ActiveVisibilityMutation,
   useVisibilityMutationFence
 } from './worktree-visibility-mutation-fence'
+import WorktreeVisibilitySourceList, {
+  type WorktreeVisibilitySourceRow
+} from './WorktreeVisibilitySourceList'
+import type { CustomWorktreeVisibilitySource, Repo } from '../../../../shared/types'
+import {
+  MAX_CUSTOM_WORKTREE_VISIBILITY_SOURCES,
+  buildWorktreeSourcePreferenceUpdate,
+  effectiveBuiltInWorktreeSourceVisibility,
+  effectiveCustomWorktreeSourceVisibility,
+  normalizeCustomWorktreeVisibilitySources,
+  removeCustomWorktreeSourcePreference
+} from '../../../../shared/worktree-visibility-sources'
+import HiddenWorktreeRecoveryList from './HiddenWorktreeRecoveryList'
+
+function getLatestRepoForScope(scope: string): Repo | null {
+  return (
+    useAppStore.getState().repos.find((candidate) => getRepoHostIdentity(candidate) === scope) ??
+    null
+  )
+}
 
 export default function WorktreeVisibilityDialog(): React.JSX.Element | null {
   const activeModal = useAppStore((s) => s.activeModal)
@@ -55,9 +65,6 @@ export default function WorktreeVisibilityDialog(): React.JSX.Element | null {
   const [busyPath, setBusyPath] = useState<string | null>(null)
   const [isToggling, setIsToggling] = useState(false)
   const [listState, setListState] = useState<'checking' | 'ready' | 'failed'>('checking')
-  const alwaysShowSwitchId = useId()
-  const hiddenListHeadingId = useId()
-  const hiddenListRef = useRef<HTMLDivElement>(null)
 
   const isOpen = activeModal === 'worktree-visibility'
   const repoId = typeof modalData.repoId === 'string' ? modalData.repoId : ''
@@ -76,25 +83,6 @@ export default function WorktreeVisibilityDialog(): React.JSX.Element | null {
   const effectiveBusyPath =
     busyPath ?? (activeMutation?.kind === 'row' ? activeMutation.path : null)
   const effectivelyToggling = isToggling || activeMutation?.kind === 'toggle'
-  const showOther = repo
-    ? effectiveExternalWorktreeVisibility(repo, isLegacyRepoForExternalWorktreeVisibility(repo)) ===
-      'show'
-    : false
-  const showAgentScratch = repo ? effectiveAgentWorktreeVisibility(repo) === 'show' : false
-  const alwaysShow = showOther && showAgentScratch
-  const hiddenImportable = getHiddenImportableExternalWorktrees(detected)
-  const hiddenCount = hiddenImportable.length
-  const otherCount = getVisibleNonOrcaWorktrees(detected).length
-  const hiddenWorktreeLabel = `${hiddenCount} ${hiddenCount === 1 ? 'worktree' : 'worktrees'}`
-  const shownWorktreeLabel = `${otherCount} ${otherCount === 1 ? 'worktree' : 'worktrees'}`
-  const hiddenListVirtualizer = useVirtualizer({
-    count: hiddenImportable.length,
-    getScrollElement: () => hiddenListRef.current,
-    estimateSize: () => 56,
-    getItemKey: (index) => hiddenImportable[index]?.id ?? index,
-    overscan: 3,
-    initialRect: { width: 480, height: 224 }
-  })
 
   useLayoutEffect(() => {
     currentMutationScopeRef.current = mutationScope
@@ -188,26 +176,22 @@ export default function WorktreeVisibilityDialog(): React.JSX.Element | null {
     [refreshTargetRepo, repo, updateTargetRepo]
   )
 
-  const handleAlwaysShowChange = useCallback(
-    async (checked: boolean) => {
-      if (!repoId || checked === alwaysShow) {
-        return
+  const commitSourceUpdate = useCallback(
+    async (
+      updates: Parameters<typeof updateTargetRepo>[1],
+      isAccepted: (latestRepo: Repo) => boolean
+    ): Promise<boolean> => {
+      if (!repoId) {
+        return false
       }
       const mutation: ActiveVisibilityMutation = { kind: 'toggle' }
       startVisibilityMutation(mutationScope, mutation)
       setActionState(null)
       setIsToggling(true)
       try {
-        const updated = await updateTargetRepo(repoId, {
-          externalWorktreeVisibility: checked ? 'show' : 'hide',
-          agentWorktreeVisibility: checked ? 'show' : 'hide',
-          // Why: showing hidden externals again should re-enable the inbox if the
-          // user previously opted out of discovery prompts for this repo.
-          // Why: null is the transport sentinel for clearing on remote runtime paths
-          // where `undefined` is stripped before persistence.
-          ...(checked ? { externalWorktreeDiscoverySuppressedAt: null } : {})
-        })
-        if (!updated) {
+        const updated = await updateTargetRepo(repoId, updates)
+        const latestRepo = getLatestRepoForScope(mutationScope)
+        if (!updated || !latestRepo || !isAccepted(latestRepo)) {
           if (currentMutationScopeRef.current === mutationScope) {
             setActionState({
               pending: false,
@@ -217,12 +201,13 @@ export default function WorktreeVisibilityDialog(): React.JSX.Element | null {
               )
             })
           }
-          return
+          return false
         }
         const refreshed = await refreshTargetRepo(repoId, { requireAuthoritative: true })
         if (currentMutationScopeRef.current === mutationScope) {
           setListState(refreshed ? 'ready' : 'failed')
         }
+        return true
       } finally {
         finishVisibilityMutation(mutationScope, mutation)
         if (currentMutationScopeRef.current === mutationScope) {
@@ -230,7 +215,105 @@ export default function WorktreeVisibilityDialog(): React.JSX.Element | null {
         }
       }
     },
-    [alwaysShow, mutationScope, refreshTargetRepo, repoId, updateTargetRepo]
+    [mutationScope, refreshTargetRepo, repoId, updateTargetRepo]
+  )
+
+  const handleSourceToggle = useCallback(
+    async (source: WorktreeVisibilitySourceRow, checked: boolean) => {
+      if (!repo) {
+        return
+      }
+      const visibility = checked ? 'show' : 'hide'
+      if (source.kind === 'other') {
+        await commitSourceUpdate(
+          {
+            externalWorktreeVisibility: visibility,
+            ...(checked ? { externalWorktreeDiscoverySuppressedAt: null } : {})
+          },
+          (latestRepo) =>
+            effectiveExternalWorktreeVisibility(
+              latestRepo,
+              isLegacyRepoForExternalWorktreeVisibility(latestRepo)
+            ) === visibility
+        )
+        return
+      }
+      const match =
+        source.kind === 'built-in'
+          ? ({ kind: 'built-in', id: source.id } as const)
+          : ({ kind: 'custom', id: source.source.id } as const)
+      await commitSourceUpdate(
+        {
+          worktreeVisibilitySourcePreferences: buildWorktreeSourcePreferenceUpdate(
+            repo,
+            match,
+            visibility
+          )
+        },
+        (latestRepo) =>
+          source.kind === 'built-in'
+            ? effectiveBuiltInWorktreeSourceVisibility(latestRepo, source.id) === visibility
+            : effectiveCustomWorktreeSourceVisibility(latestRepo, source.source.id) === visibility
+      )
+    },
+    [commitSourceUpdate, repo]
+  )
+
+  const handleAddSource = useCallback(
+    async (rootPath: string): Promise<boolean> => {
+      if (!repo) {
+        return false
+      }
+      const existing = normalizeCustomWorktreeVisibilitySources(
+        repo.customWorktreeVisibilitySources
+      )
+      if ((existing?.length ?? 0) >= MAX_CUSTOM_WORKTREE_VISIBILITY_SOURCES) {
+        return false
+      }
+      const id = crypto.randomUUID().replaceAll('-', '')
+      const next = normalizeCustomWorktreeVisibilitySources([...(existing ?? []), { id, rootPath }])
+      if (!next || next.length !== (existing?.length ?? 0) + 1) {
+        return false
+      }
+      return commitSourceUpdate(
+        {
+          customWorktreeVisibilitySources: next,
+          worktreeVisibilitySourcePreferences: buildWorktreeSourcePreferenceUpdate(
+            repo,
+            { kind: 'custom', id },
+            'hide'
+          )
+        },
+        (latestRepo) =>
+          normalizeCustomWorktreeVisibilitySources(
+            latestRepo.customWorktreeVisibilitySources
+          )?.some((source) => source.id === id) === true &&
+          effectiveCustomWorktreeSourceVisibility(latestRepo, id) === 'hide'
+      )
+    },
+    [commitSourceUpdate, repo]
+  )
+
+  const handleRemoveSource = useCallback(
+    async (source: CustomWorktreeVisibilitySource) => {
+      if (!repo) {
+        return
+      }
+      const next = (
+        normalizeCustomWorktreeVisibilitySources(repo.customWorktreeVisibilitySources) ?? []
+      ).filter((candidate) => candidate.id !== source.id)
+      await commitSourceUpdate(
+        {
+          customWorktreeVisibilitySources: next,
+          worktreeVisibilitySourcePreferences: removeCustomWorktreeSourcePreference(repo, source.id)
+        },
+        (latestRepo) =>
+          !normalizeCustomWorktreeVisibilitySources(
+            latestRepo.customWorktreeVisibilitySources
+          )?.some((candidate) => candidate.id === source.id)
+      )
+    },
+    [commitSourceUpdate, repo]
   )
 
   if (!isOpen || !repo || !isGitRepoKind(repo)) {
@@ -239,7 +322,7 @@ export default function WorktreeVisibilityDialog(): React.JSX.Element | null {
 
   return (
     <Dialog open onOpenChange={(open) => !open && closeModal()}>
-      <DialogContent className="sm:max-w-lg">
+      <DialogContent className="scrollbar-sleek max-h-[calc(100vh-6rem)] overflow-y-auto sm:max-w-lg">
         <DialogHeader>
           <div className="flex items-center gap-1.5">
             <DialogTitle>
@@ -253,51 +336,14 @@ export default function WorktreeVisibilityDialog(): React.JSX.Element | null {
           <DialogDescription>{repo.displayName}</DialogDescription>
         </DialogHeader>
 
-        <div className="flex items-center gap-3 rounded-lg border border-border bg-muted/30 p-3">
-          <div className="flex size-8 shrink-0 items-center justify-center rounded-md bg-background text-muted-foreground">
-            {alwaysShow ? <Eye className="size-4" /> : <EyeOff className="size-4" />}
-          </div>
-          <div className="min-w-0 flex-1">
-            <div className="text-sm font-medium">
-              {alwaysShow
-                ? translate(
-                    'auto.components.sidebar.WorktreeVisibilityDialog.3e045d4cb8',
-                    'Shown in sidebar'
-                  )
-                : translate(
-                    'auto.components.sidebar.WorktreeVisibilityDialog.5d02a5647f',
-                    'Hidden from sidebar'
-                  )}
-            </div>
-            <div className="text-xs text-muted-foreground">
-              {alwaysShow
-                ? translate(
-                    'auto.components.sidebar.WorktreeVisibilityDialog.8372e4bbd9',
-                    '{{value0}} currently shown',
-                    { value0: shownWorktreeLabel }
-                  )
-                : translate(
-                    'auto.components.sidebar.WorktreeVisibilityDialog.25ddf19920',
-                    '{{value0}} currently hidden',
-                    { value0: hiddenWorktreeLabel }
-                  )}
-            </div>
-          </div>
-          <Label htmlFor={alwaysShowSwitchId} className="shrink-0 gap-2">
-            {translate(
-              'auto.components.sidebar.WorktreeVisibilityDialog.f1f71b9f02',
-              'Always show'
-            )}
-            <Switch
-              id={alwaysShowSwitchId}
-              checked={alwaysShow}
-              disabled={
-                effectiveBusyPath !== null || effectivelyToggling || listState === 'checking'
-              }
-              onCheckedChange={(checked) => void handleAlwaysShowChange(checked)}
-            />
-          </Label>
-        </div>
+        <WorktreeVisibilitySourceList
+          repo={repo}
+          worktrees={detected?.authoritative ? detected.worktrees : []}
+          disabled={effectiveBusyPath !== null || effectivelyToggling || listState === 'checking'}
+          onAdd={handleAddSource}
+          onRemove={handleRemoveSource}
+          onToggle={handleSourceToggle}
+        />
 
         {listState === 'checking' ? (
           <p aria-live="polite" className="text-xs text-muted-foreground">
@@ -328,89 +374,14 @@ export default function WorktreeVisibilityDialog(): React.JSX.Element | null {
           </div>
         ) : null}
 
-        {hiddenImportable.length > 0 ? (
-          <div className="grid min-w-0 gap-2">
-            <div>
-              <h3 id={hiddenListHeadingId} className="text-sm font-medium">
-                {translate(
-                  'auto.components.sidebar.WorktreeVisibilityDialog.7d21c5e848',
-                  'Hidden worktrees ({{value0}})',
-                  { value0: hiddenImportable.length }
-                )}
-              </h3>
-              <p className="text-xs text-muted-foreground">
-                {translate(
-                  'auto.components.sidebar.WorktreeVisibilityDialog.9b53f7a160',
-                  'Choose which hidden worktrees to show individually.'
-                )}
-              </p>
-            </div>
-            <div
-              ref={hiddenListRef}
-              aria-labelledby={hiddenListHeadingId}
-              className="scrollbar-sleek max-h-56 min-w-0 overflow-y-auto"
-              tabIndex={0}
-              style={{
-                height: `${Math.min(hiddenListVirtualizer.getTotalSize(), 224)}px`
-              }}
-            >
-              <ul
-                className="relative min-w-0"
-                style={{ height: `${hiddenListVirtualizer.getTotalSize()}px` }}
-              >
-                {hiddenListVirtualizer.getVirtualItems().map((virtualRow) => {
-                  const worktree = hiddenImportable[virtualRow.index]
-                  if (!worktree) {
-                    return null
-                  }
-                  const displayPath =
-                    relativePathInsideRoot(repo.path, worktree.path) || worktree.path
-                  return (
-                    <li
-                      key={worktree.id}
-                      ref={hiddenListVirtualizer.measureElement}
-                      data-index={virtualRow.index}
-                      className="absolute left-0 top-0 w-full pb-1"
-                      style={{ transform: `translateY(${virtualRow.start}px)` }}
-                      aria-posinset={virtualRow.index + 1}
-                      aria-setsize={hiddenImportable.length}
-                    >
-                      <div className="flex min-w-0 items-center gap-3 rounded-md border border-border px-3 py-2">
-                        <div className="min-w-0 flex-1">
-                          <div className="truncate text-sm">{worktree.displayName}</div>
-                          <div className="truncate text-xs text-muted-foreground">
-                            {displayPath}
-                          </div>
-                        </div>
-                        <Button
-                          type="button"
-                          variant="outline"
-                          size="sm"
-                          disabled={
-                            effectiveBusyPath !== null ||
-                            effectivelyToggling ||
-                            listState === 'checking'
-                          }
-                          onClick={() => void handleShowWorktree(worktree.path)}
-                        >
-                          {effectiveBusyPath === worktree.path
-                            ? translate(
-                                'auto.components.sidebar.WorktreeVisibilityDialog.2f80cd4b97',
-                                'Showing…'
-                              )
-                            : translate(
-                                'auto.components.sidebar.WorktreeVisibilityDialog.e64b81d3a9',
-                                'Show'
-                              )}
-                        </Button>
-                      </div>
-                    </li>
-                  )
-                })}
-              </ul>
-            </div>
-          </div>
-        ) : null}
+        <HiddenWorktreeRecoveryList
+          repo={repo}
+          detected={detected}
+          listState={listState}
+          busyPath={effectiveBusyPath}
+          toggling={effectivelyToggling}
+          onShow={handleShowWorktree}
+        />
 
         {actionState?.error ? (
           <p className="text-xs text-destructive" role="alert">

src/renderer/src/components/sidebar/WorktreeVisibilityHelpPopover.test.tsx

@@ -67,9 +67,8 @@ describe('WorktreeVisibilityHelpPopover', () => {
 
     expect(trigger.getAttribute('aria-expanded')).toBe('true')
     expect(content()?.getAttribute('aria-label')).toBe('Which worktrees are hidden by default?')
-    expect(content()?.textContent).toContain('current and future non-Orca worktrees')
-    expect(content()?.textContent).toContain('.claude/worktrees/*')
-    expect(content()?.textContent).toContain('.gsd-workspaces/*')
+    expect(content()?.textContent).toContain('current and future worktrees')
+    expect(content()?.textContent).toContain('show individual worktrees below')
 
     await dispatch(
       hoverTarget!,

src/renderer/src/components/sidebar/WorktreeVisibilityHelpPopover.tsx

@@ -26,7 +26,6 @@ export default function WorktreeVisibilityHelpPopover(): React.JSX.Element {
             className="size-5 text-muted-foreground hover:bg-transparent hover:text-foreground dark:hover:bg-transparent"
             aria-label={title}
             aria-expanded={open}
-            title={title}
             onClick={() => setOpen(true)}
           >
             <CircleHelp className="size-3.5" />
@@ -51,13 +50,13 @@ export default function WorktreeVisibilityHelpPopover(): React.JSX.Element {
             <li>
               {translate(
                 'auto.components.sidebar.WorktreeVisibilityHelpPopover.54a7c2f183',
-                'For newly added repositories, worktrees created manually or by another tool are hidden by default to avoid unexpected sidebar clutter.'
+                'Other worktrees start hidden to avoid unexpected sidebar clutter.'
               )}
             </li>
             <li>
               {translate(
                 'auto.components.sidebar.WorktreeVisibilityHelpPopover.b9e0d43675',
-                'Always show includes current and future non-Orca worktrees, including agent worktrees under .claude/worktrees/* and .gsd-workspaces/*. When it is off, use Show below to add one individually.'
+                'Enable a source for all current and future worktrees, or show individual worktrees below.'
               )}
             </li>
           </ul>

src/renderer/src/components/sidebar/WorktreeVisibilitySourceList.tsx

@@ -0,0 +1,302 @@
+import React, { useMemo, useState } from 'react'
+import { Folder, Grid2X2, Plus, SquareTerminal, Trash2 } from 'lucide-react'
+import { Button } from '@/components/ui/button'
+import { Input } from '@/components/ui/input'
+import { Label } from '@/components/ui/label'
+import { Popover, PopoverContent, PopoverTrigger } from '@/components/ui/popover'
+import { Switch } from '@/components/ui/switch'
+import { Tooltip, TooltipContent, TooltipTrigger } from '@/components/ui/tooltip'
+import { translate } from '@/i18n/i18n'
+import type {
+  BuiltInWorktreeVisibilitySourceId,
+  CustomWorktreeVisibilitySource,
+  DetectedWorktree,
+  Repo
+} from '../../../../shared/types'
+import {
+  createWorktreeVisibilitySourceMatcher,
+  effectiveBuiltInWorktreeSourceVisibility,
+  effectiveCustomWorktreeSourceVisibility,
+  normalizeCustomWorktreeVisibilitySources,
+  type WorktreeVisibilitySourceMatch
+} from '../../../../shared/worktree-visibility-sources'
+import {
+  effectiveExternalWorktreeVisibility,
+  isLegacyRepoForExternalWorktreeVisibility
+} from '../../../../shared/external-worktree-visibility'
+import { getRuntimePathBasename } from '../../../../shared/cross-platform-path'
+
+export type WorktreeVisibilitySourceRow =
+  | { kind: 'built-in'; id: BuiltInWorktreeVisibilitySourceId }
+  | { kind: 'custom'; source: CustomWorktreeVisibilitySource }
+  | { kind: 'other' }
+
+type Props = {
+  repo: Repo
+  worktrees: readonly DetectedWorktree[]
+  disabled: boolean
+  onAdd: (rootPath: string) => Promise<boolean>
+  onRemove: (source: CustomWorktreeVisibilitySource) => Promise<void>
+  onToggle: (source: WorktreeVisibilitySourceRow, enabled: boolean) => Promise<void>
+}
+
+function getSourceLabel(source: WorktreeVisibilitySourceRow): string {
+  if (source.kind === 'built-in') {
+    return source.id === 'claude'
+      ? translate('auto.components.sidebar.WorktreeVisibilitySourceList.claude', 'Claude Code')
+      : translate('auto.components.sidebar.WorktreeVisibilitySourceList.gsd', 'GSD')
+  }
+  if (source.kind === 'other') {
+    return translate(
+      'auto.components.sidebar.WorktreeVisibilitySourceList.other',
+      'Other locations'
+    )
+  }
+  return (
+    getRuntimePathBasename(source.source.rootPath) ||
+    translate('auto.components.sidebar.WorktreeVisibilitySourceList.custom', 'Custom location')
+  )
+}
+
+function getSourcePath(source: WorktreeVisibilitySourceRow): string {
+  if (source.kind === 'built-in') {
+    return source.id === 'claude' ? '.claude/worktrees/*' : '.gsd-workspaces/*'
+  }
+  if (source.kind === 'other') {
+    return translate(
+      'auto.components.sidebar.WorktreeVisibilitySourceList.otherPath',
+      'Outside listed sources'
+    )
+  }
+  return `${source.source.rootPath.replace(/[\\/]+$/, '')}/*`
+}
+
+function isSourceEnabled(repo: Repo, source: WorktreeVisibilitySourceRow): boolean {
+  if (source.kind === 'built-in') {
+    return effectiveBuiltInWorktreeSourceVisibility(repo, source.id) === 'show'
+  }
+  if (source.kind === 'custom') {
+    return effectiveCustomWorktreeSourceVisibility(repo, source.source.id) === 'show'
+  }
+  return (
+    effectiveExternalWorktreeVisibility(repo, isLegacyRepoForExternalWorktreeVisibility(repo)) ===
+    'show'
+  )
+}
+
+function matchesRow(
+  source: WorktreeVisibilitySourceRow,
+  match: WorktreeVisibilitySourceMatch | null
+): boolean {
+  if (source.kind === 'other') {
+    return match === null
+  }
+  if (source.kind === 'built-in') {
+    return match?.kind === 'built-in' && match.id === source.id
+  }
+  return match?.kind === 'custom' && match.id === source.source.id
+}
+
+export default function WorktreeVisibilitySourceList({
+  repo,
+  worktrees,
+  disabled,
+  onAdd,
+  onRemove,
+  onToggle
+}: Props): React.JSX.Element {
+  const [addOpen, setAddOpen] = useState(false)
+  const [rootPath, setRootPath] = useState('')
+  const [inputError, setInputError] = useState<string | null>(null)
+  const customSources = normalizeCustomWorktreeVisibilitySources(
+    repo.customWorktreeVisibilitySources
+  )
+  const sources: WorktreeVisibilitySourceRow[] = [
+    { kind: 'built-in', id: 'claude' },
+    { kind: 'built-in', id: 'gsd' },
+    ...(customSources ?? []).map((source) => ({ kind: 'custom' as const, source })),
+    { kind: 'other' }
+  ]
+  const classify = useMemo(
+    () =>
+      createWorktreeVisibilitySourceMatcher(
+        [repo.path, ...worktrees.map((worktree) => worktree.path)],
+        customSources ?? []
+      ),
+    [customSources, repo.path, worktrees]
+  )
+
+  const handleAdd = async (event: React.FormEvent) => {
+    event.preventDefault()
+    setInputError(null)
+    const added = await onAdd(rootPath)
+    if (added) {
+      setRootPath('')
+      setAddOpen(false)
+      return
+    }
+    setInputError(
+      translate(
+        'auto.components.sidebar.WorktreeVisibilitySourceList.invalidPath',
+        'Enter a unique absolute path for this host.'
+      )
+    )
+  }
+
+  return (
+    <section className="grid min-w-0 gap-2" aria-labelledby="worktree-sources-heading">
+      <div>
+        <h3 id="worktree-sources-heading" className="text-sm font-medium">
+          {translate('auto.components.sidebar.WorktreeVisibilitySourceList.sources', 'Sources')}
+        </h3>
+        <p className="text-xs text-muted-foreground">
+          {translate(
+            'auto.components.sidebar.WorktreeVisibilitySourceList.sourcesDescription',
+            'Enabled sources include current and future worktrees in the sidebar.'
+          )}
+        </p>
+      </div>
+      <div className="overflow-hidden rounded-lg border border-border bg-muted/30">
+        {sources.map((source, index) => {
+          const label = getSourceLabel(source)
+          const count = worktrees.filter(
+            (worktree) =>
+              !worktree.selectedCheckout &&
+              worktree.ownership !== 'orca-managed' &&
+              matchesRow(source, worktree.visibilitySource ?? classify(worktree.path))
+          ).length
+          const key =
+            source.kind === 'custom'
+              ? `custom:${source.source.id}`
+              : `${source.kind}:${source.kind === 'built-in' ? source.id : ''}`
+          return (
+            <div
+              key={key}
+              className={`grid min-h-14 grid-cols-[28px_minmax(0,1fr)_auto] items-center gap-2.5 px-2.5 py-2 ${index > 0 ? 'border-t border-border' : ''}`}
+            >
+              <span className="flex size-7 items-center justify-center rounded-md border border-border bg-background text-muted-foreground">
+                {source.kind === 'built-in' ? (
+                  source.id === 'claude' ? (
+                    <SquareTerminal className="size-3.5" />
+                  ) : (
+                    <Grid2X2 className="size-3.5" />
+                  )
+                ) : (
+                  <Folder className="size-3.5" />
+                )}
+              </span>
+              <span className="min-w-0">
+                <span className="flex min-w-0 items-center gap-1.5">
+                  <span className="truncate text-[13px] font-medium">{label}</span>
+                  <span className="shrink-0 text-[11px] text-muted-foreground">
+                    {translate(
+                      'auto.components.sidebar.WorktreeVisibilitySourceList.found',
+                      '{{value0}} found',
+                      { value0: count }
+                    )}
+                  </span>
+                </span>
+                <span className="block truncate font-mono text-[11px] text-muted-foreground">
+                  {getSourcePath(source)}
+                </span>
+              </span>
+              <span className="flex items-center gap-1">
+                {source.kind === 'custom' ? (
+                  <Tooltip>
+                    <TooltipTrigger asChild>
+                      <Button
+                        type="button"
+                        variant="ghost"
+                        size="icon-xs"
+                        className="text-muted-foreground hover:text-destructive"
+                        disabled={disabled}
+                        aria-label={translate(
+                          'auto.components.sidebar.WorktreeVisibilitySourceList.remove',
+                          'Remove {{value0}}',
+                          { value0: label }
+                        )}
+                        onClick={() => void onRemove(source.source)}
+                      >
+                        <Trash2 />
+                      </Button>
+                    </TooltipTrigger>
+                    <TooltipContent side="top" sideOffset={4}>
+                      {translate(
+                        'auto.components.sidebar.WorktreeVisibilitySourceList.removeLocation',
+                        'Remove custom location'
+                      )}
+                    </TooltipContent>
+                  </Tooltip>
+                ) : null}
+                <Switch
+                  checked={isSourceEnabled(repo, source)}
+                  disabled={disabled}
+                  aria-label={translate(
+                    'auto.components.sidebar.WorktreeVisibilitySourceList.toggle',
+                    'Show current and future worktrees from {{value0}}',
+                    { value0: label }
+                  )}
+                  onCheckedChange={(checked) => void onToggle(source, checked)}
+                />
+              </span>
+            </div>
+          )
+        })}
+      </div>
+      <Popover open={addOpen} onOpenChange={setAddOpen}>
+        <PopoverTrigger asChild>
+          <Button type="button" variant="outline" size="sm" className="w-fit" disabled={disabled}>
+            <Plus />
+            {translate(
+              'auto.components.sidebar.WorktreeVisibilitySourceList.addLocation',
+              'Add location'
+            )}
+          </Button>
+        </PopoverTrigger>
+        <PopoverContent
+          align="start"
+          side="bottom"
+          className="w-[390px] max-w-[calc(100vw-6rem)] p-3"
+        >
+          <form className="grid gap-2" onSubmit={(event) => void handleAdd(event)}>
+            <Label htmlFor="custom-worktree-root">
+              {translate(
+                'auto.components.sidebar.WorktreeVisibilitySourceList.worktreeRoot',
+                'Worktree root'
+              )}
+            </Label>
+            <div className="flex items-center gap-2">
+              <Input
+                id="custom-worktree-root"
+                className="font-mono text-xs"
+                value={rootPath}
+                autoComplete="off"
+                spellCheck={false}
+                aria-invalid={inputError ? true : undefined}
+                aria-describedby="custom-worktree-root-help"
+                onChange={(event) => {
+                  setRootPath(event.target.value)
+                  setInputError(null)
+                }}
+              />
+              <Button type="submit" size="sm" disabled={disabled || !rootPath.trim()}>
+                {translate('auto.components.sidebar.WorktreeVisibilitySourceList.add', 'Add')}
+              </Button>
+            </div>
+            <p
+              id="custom-worktree-root-help"
+              className={`text-[11px] ${inputError ? 'text-destructive' : 'text-muted-foreground'}`}
+              role={inputError ? 'alert' : undefined}
+            >
+              {inputError ??
+                translate(
+                  'auto.components.sidebar.WorktreeVisibilitySourceList.rootHelp',
+                  'Orca will recognize worktrees beneath this folder.'
+                )}
+            </p>
+          </form>
+        </PopoverContent>
+      </Popover>
+    </section>
+  )
+}

src/renderer/src/i18n/locales/en.json

@@ -4903,8 +4903,8 @@
         "WorktreeVisibilityHelpPopover": {
           "c41f2d7e90": "Which worktrees are hidden by default?",
           "8db4e19a26": "This setting never hides worktrees created through Orca.",
-          "54a7c2f183": "For newly added repositories, worktrees created manually or by another tool are hidden by default to avoid unexpected sidebar clutter.",
-          "b9e0d43675": "Always show includes current and future non-Orca worktrees, including agent worktrees under .claude/worktrees/* and .gsd-workspaces/*. When it is off, use Show below to add one individually."
+          "54a7c2f183": "Other worktrees start hidden to avoid unexpected sidebar clutter.",
+          "b9e0d43675": "Enable a source for all current and future worktrees, or show individual worktrees below."
         },
         "WorktreeVisibilityDialog": {
           "83a5ba8dd1": "Non-Orca worktrees",
@@ -4918,10 +4918,18 @@
           "b8d24e61f5": "Could not list this repo's worktrees.",
           "c5e70a93b1": "Try again",
           "7d21c5e848": "Hidden worktrees ({{value0}})",
-          "9b53f7a160": "Choose which hidden worktrees to show individually.",
+          "9b53f7a160": "Show one without enabling its source.",
           "2f80cd4b97": "Showing…",
           "e64b81d3a9": "Show",
-          "d40d436fc2": "Could not update worktree visibility. Try again."
+          "d40d436fc2": "Could not update worktree visibility. Try again.",
+          "search": "Search hidden worktrees",
+          "searchPlaceholder": "Search {{value0}} worktrees…",
+          "noMatches": "No matching worktrees",
+          "allShown": "All discovered worktrees are shown",
+          "noneFound": "No non-Orca worktrees found",
+          "tryDifferentSearch": "Try a different name or path.",
+          "disableSource": "Disable a source to manage its worktrees individually.",
+          "appearWhenDetected": "New worktrees will appear here when Orca detects them."
         },
         "add": {
           "repo": {
@@ -5419,6 +5427,24 @@
         },
         "WorktreeListScrollToTopButton": {
           "jumpToTop": "Jump to top"
+        },
+        "WorktreeVisibilitySourceList": {
+          "claude": "Claude Code",
+          "gsd": "GSD",
+          "other": "Other locations",
+          "custom": "Custom location",
+          "otherPath": "Outside listed sources",
+          "invalidPath": "Enter a unique absolute path for this host.",
+          "sources": "Sources",
+          "sourcesDescription": "Enabled sources include current and future worktrees in the sidebar.",
+          "found": "{{value0}} found",
+          "remove": "Remove {{value0}}",
+          "removeLocation": "Remove custom location",
+          "toggle": "Show current and future worktrees from {{value0}}",
+          "addLocation": "Add location",
+          "worktreeRoot": "Worktree root",
+          "add": "Add",
+          "rootHelp": "Orca will recognize worktrees beneath this folder."
         }
       },
       "shared": {

src/renderer/src/i18n/locales/es.json

@@ -4700,8 +4700,8 @@
         "WorktreeVisibilityHelpPopover": {
           "c41f2d7e90": "¿Qué worktrees se ocultan de forma predeterminada?",
           "8db4e19a26": "Este ajuste nunca oculta los worktrees creados mediante Orca.",
-          "54a7c2f183": "En los repositorios recién añadidos, los worktrees creados manualmente o con otra herramienta se ocultan de forma predeterminada para evitar elementos inesperados en la barra lateral.",
-          "b9e0d43675": "«Mostrar siempre» incluye los worktrees ajenos a Orca actuales y futuros, incluidos los worktrees de agentes en .claude/worktrees/* y .gsd-workspaces/*. Cuando está desactivado, usa «Mostrar» abajo para añadir uno individualmente."
+          "54a7c2f183": "Los demás worktrees empiezan ocultos para evitar saturar inesperadamente la barra lateral.",
+          "b9e0d43675": "Activa una fuente para mostrar todos sus worktrees actuales y futuros, o muestra worktrees individuales abajo."
         },
         "WorktreeVisibilityDialog": {
           "83a5ba8dd1": "Worktrees que no son de Orca",
@@ -4715,10 +4715,36 @@
           "b8d24e61f5": "No se pudieron listar los worktrees de este repositorio.",
           "c5e70a93b1": "Reintentar",
           "7d21c5e848": "Worktrees ocultos ({{value0}})",
-          "9b53f7a160": "Elige qué worktrees ocultos mostrar de forma individual.",
+          "9b53f7a160": "Muestra uno sin activar su fuente.",
           "2f80cd4b97": "Mostrando…",
           "e64b81d3a9": "Mostrar",
-          "d40d436fc2": "No se pudo actualizar la visibilidad de los worktrees. Inténtalo de nuevo."
+          "d40d436fc2": "No se pudo actualizar la visibilidad de los worktrees. Inténtalo de nuevo.",
+          "search": "Buscar worktrees ocultos",
+          "searchPlaceholder": "Buscar en {{value0}} worktrees…",
+          "noMatches": "No hay worktrees coincidentes",
+          "allShown": "Todos los worktrees detectados se muestran",
+          "noneFound": "No se encontraron worktrees ajenos a Orca",
+          "tryDifferentSearch": "Prueba con otro nombre o ruta.",
+          "disableSource": "Desactiva una fuente para gestionar sus worktrees individualmente.",
+          "appearWhenDetected": "Los worktrees nuevos aparecerán aquí cuando Orca los detecte."
+        },
+        "WorktreeVisibilitySourceList": {
+          "claude": "Claude Code",
+          "gsd": "GSD",
+          "other": "Otras ubicaciones",
+          "custom": "Ubicación personalizada",
+          "otherPath": "Fuera de las fuentes listadas",
+          "invalidPath": "Introduce una ruta absoluta única para este host.",
+          "sources": "Fuentes",
+          "sourcesDescription": "Las fuentes activadas incluyen los worktrees actuales y futuros en la barra lateral.",
+          "found": "{{value0}} encontrados",
+          "remove": "Eliminar {{value0}}",
+          "removeLocation": "Eliminar ubicación personalizada",
+          "toggle": "Mostrar los worktrees actuales y futuros de {{value0}}",
+          "addLocation": "Añadir ubicación",
+          "worktreeRoot": "Raíz de worktrees",
+          "add": "Añadir",
+          "rootHelp": "Orca reconocerá los worktrees dentro de esta carpeta."
         },
         "add": {
           "repo": {

src/renderer/src/i18n/locales/ja.json

@@ -4681,8 +4681,8 @@
         "WorktreeVisibilityHelpPopover": {
           "c41f2d7e90": "デフォルトで非表示になるワークツリー",
           "8db4e19a26": "この設定では、Orca で作成されたワークツリーが非表示になることはありません。",
-          "54a7c2f183": "新しく追加したリポジトリでは、手動または別のツールで作成したワークツリーは、意図しない項目でサイドバーが埋まらないよう、デフォルトでは非表示です。",
-          "b9e0d43675": "「常に表示」では、.claude/worktrees/* および .gsd-workspaces/* にある Agent ワークツリーを含む、Orca 以外で作成された現在および今後のワークツリーが表示されます。オフの場合は、下の「表示」を使用して個別に追加できます。"
+          "54a7c2f183": "その他のワークツリーは、サイドバーが意図せず煩雑にならないようデフォルトで非表示です。",
+          "b9e0d43675": "ソースを有効にすると現在および今後のワークツリーをすべて表示できます。下から個別に表示することもできます。"
         },
         "WorktreeVisibilityDialog": {
           "83a5ba8dd1": "Orca 以外のワークツリー",
@@ -4696,10 +4696,36 @@
           "b8d24e61f5": "このリポジトリのワークツリーを一覧できませんでした。",
           "c5e70a93b1": "再試行",
           "7d21c5e848": "非表示のワークツリー（{{value0}}）",
-          "9b53f7a160": "個別にサイドバーへ表示する非表示のワークツリーを選択します。",
+          "9b53f7a160": "ソースを有効にせずに個別に表示します。",
           "2f80cd4b97": "表示中…",
           "e64b81d3a9": "表示",
-          "d40d436fc2": "ワークツリーの表示設定を更新できませんでした。もう一度お試しください。"
+          "d40d436fc2": "ワークツリーの表示設定を更新できませんでした。もう一度お試しください。",
+          "search": "非表示のワークツリーを検索",
+          "searchPlaceholder": "{{value0}} 件のワークツリーを検索…",
+          "noMatches": "一致するワークツリーはありません",
+          "allShown": "検出されたワークツリーはすべて表示されています",
+          "noneFound": "Orca 以外のワークツリーは見つかりませんでした",
+          "tryDifferentSearch": "別の名前またはパスをお試しください。",
+          "disableSource": "ソースを無効にするとワークツリーを個別に管理できます。",
+          "appearWhenDetected": "Orca が新しいワークツリーを検出すると、ここに表示されます。"
+        },
+        "WorktreeVisibilitySourceList": {
+          "claude": "Claude Code",
+          "gsd": "GSD",
+          "other": "その他の場所",
+          "custom": "カスタムの場所",
+          "otherPath": "一覧にないソース",
+          "invalidPath": "このホストの一意な絶対パスを入力してください。",
+          "sources": "ソース",
+          "sourcesDescription": "有効なソースの現在および今後のワークツリーがサイドバーに表示されます。",
+          "found": "{{value0}} 件検出",
+          "remove": "{{value0}} を削除",
+          "removeLocation": "カスタムの場所を削除",
+          "toggle": "{{value0}} の現在および今後のワークツリーを表示",
+          "addLocation": "場所を追加",
+          "worktreeRoot": "ワークツリールート",
+          "add": "追加",
+          "rootHelp": "Orca はこのフォルダー配下のワークツリーを認識します。"
         },
         "add": {
           "repo": {

src/renderer/src/i18n/locales/ko.json

@@ -4681,8 +4681,8 @@
         "WorktreeVisibilityHelpPopover": {
           "c41f2d7e90": "기본적으로 숨겨지는 워크트리",
           "8db4e19a26": "이 설정은 Orca에서 만든 워크트리를 숨기지 않습니다.",
-          "54a7c2f183": "새로 추가한 저장소에서는 직접 만들거나 다른 도구에서 만든 워크트리가 예기치 않은 항목으로 사이드바를 복잡하게 하지 않도록 기본적으로 숨겨집니다.",
-          "b9e0d43675": "'항상 표시'는 .claude/worktrees/* 및 .gsd-workspaces/* 아래의 에이전트 워크트리를 포함하여 현재와 앞으로 생성되는 Orca 외부 워크트리를 표시합니다. 꺼져 있을 때는 아래의 '표시'를 사용해 하나씩 추가할 수 있습니다."
+          "54a7c2f183": "다른 워크트리는 사이드바가 예기치 않게 복잡해지지 않도록 기본적으로 숨겨집니다.",
+          "b9e0d43675": "소스를 활성화해 현재와 앞으로 생성되는 모든 워크트리를 표시하거나 아래에서 개별 워크트리를 표시하세요."
         },
         "WorktreeVisibilityDialog": {
           "83a5ba8dd1": "Orca 외부 워크트리",
@@ -4696,10 +4696,36 @@
           "b8d24e61f5": "이 저장소의 워크트리를 나열할 수 없습니다.",
           "c5e70a93b1": "다시 시도",
           "7d21c5e848": "숨겨진 워크트리({{value0}})",
-          "9b53f7a160": "개별적으로 사이드바에 표시할 숨겨진 워크트리를 선택하세요.",
+          "9b53f7a160": "소스를 활성화하지 않고 하나만 표시합니다.",
           "2f80cd4b97": "표시 중…",
           "e64b81d3a9": "표시",
-          "d40d436fc2": "워크트리 표시 설정을 업데이트하지 못했습니다. 다시 시도하세요."
+          "d40d436fc2": "워크트리 표시 설정을 업데이트하지 못했습니다. 다시 시도하세요.",
+          "search": "숨겨진 워크트리 검색",
+          "searchPlaceholder": "워크트리 {{value0}}개 검색…",
+          "noMatches": "일치하는 워크트리가 없습니다",
+          "allShown": "발견된 모든 워크트리가 표시 중입니다",
+          "noneFound": "Orca 외부 워크트리를 찾지 못했습니다",
+          "tryDifferentSearch": "다른 이름이나 경로를 시도하세요.",
+          "disableSource": "소스를 비활성화하면 워크트리를 개별적으로 관리할 수 있습니다.",
+          "appearWhenDetected": "Orca가 새 워크트리를 발견하면 여기에 표시됩니다."
+        },
+        "WorktreeVisibilitySourceList": {
+          "claude": "Claude Code",
+          "gsd": "GSD",
+          "other": "기타 위치",
+          "custom": "사용자 지정 위치",
+          "otherPath": "목록에 없는 소스",
+          "invalidPath": "이 호스트의 고유한 절대 경로를 입력하세요.",
+          "sources": "소스",
+          "sourcesDescription": "활성화된 소스의 현재와 앞으로 생성되는 워크트리가 사이드바에 표시됩니다.",
+          "found": "{{value0}}개 발견",
+          "remove": "{{value0}} 제거",
+          "removeLocation": "사용자 지정 위치 제거",
+          "toggle": "{{value0}}의 현재와 앞으로 생성되는 워크트리 표시",
+          "addLocation": "위치 추가",
+          "worktreeRoot": "워크트리 루트",
+          "add": "추가",
+          "rootHelp": "Orca는 이 폴더 아래의 워크트리를 인식합니다."
         },
         "add": {
           "repo": {

src/renderer/src/i18n/locales/zh.json

@@ -4693,8 +4693,8 @@
         "WorktreeVisibilityHelpPopover": {
           "c41f2d7e90": "哪些工作树默认隐藏？",
           "8db4e19a26": "此设置不会隐藏通过 Orca 创建的工作树。",
-          "54a7c2f183": "对于新添加的仓库，手动或通过其他工具创建的工作树默认隐藏，以免侧边栏出现意外内容。",
-          "b9e0d43675": "“始终显示”会显示当前及以后创建的非 Orca 工作树，包括 .claude/worktrees/* 和 .gsd-workspaces/* 下的智能体工作树。关闭时，可使用下方的“显示”逐个添加。"
+          "54a7c2f183": "其他工作树默认隐藏，以免侧边栏意外变得杂乱。",
+          "b9e0d43675": "启用来源可显示其当前及未来的所有工作树，也可以在下方单独显示工作树。"
         },
         "WorktreeVisibilityDialog": {
           "83a5ba8dd1": "非 Orca 工作树",
@@ -4708,10 +4708,36 @@
           "b8d24e61f5": "无法列出此仓库的工作树。",
           "c5e70a93b1": "重试",
           "7d21c5e848": "已隐藏的工作树（{{value0}}）",
-          "9b53f7a160": "选择要单独显示的隐藏工作树。",
+          "9b53f7a160": "无需启用来源即可单独显示一个工作树。",
           "2f80cd4b97": "显示中…",
           "e64b81d3a9": "显示",
-          "d40d436fc2": "无法更新工作树可见性。请重试。"
+          "d40d436fc2": "无法更新工作树可见性。请重试。",
+          "search": "搜索隐藏的工作树",
+          "searchPlaceholder": "搜索 {{value0}} 个工作树…",
+          "noMatches": "没有匹配的工作树",
+          "allShown": "已显示所有检测到的工作树",
+          "noneFound": "未找到非 Orca 工作树",
+          "tryDifferentSearch": "请尝试其他名称或路径。",
+          "disableSource": "禁用来源后可单独管理其工作树。",
+          "appearWhenDetected": "Orca 检测到新工作树后，它们会显示在这里。"
+        },
+        "WorktreeVisibilitySourceList": {
+          "claude": "Claude Code",
+          "gsd": "GSD",
+          "other": "其他位置",
+          "custom": "自定义位置",
+          "otherPath": "所列来源之外",
+          "invalidPath": "请输入此主机上唯一的绝对路径。",
+          "sources": "来源",
+          "sourcesDescription": "已启用来源的当前及未来工作树会显示在侧边栏中。",
+          "found": "找到 {{value0}} 个",
+          "remove": "移除 {{value0}}",
+          "removeLocation": "移除自定义位置",
+          "toggle": "显示 {{value0}} 的当前及未来工作树",
+          "addLocation": "添加位置",
+          "worktreeRoot": "工作树根目录",
+          "add": "添加",
+          "rootHelp": "Orca 会识别此文件夹下的工作树。"
         },
         "add": {
           "repo": {

src/renderer/src/store/slices/repos.ts

@@ -87,6 +87,10 @@ import {
   type ExecutionHostId
 } from '../../../../shared/execution-host'
 import { isRemovedRuntimeHostId } from './stale-runtime-host-rows'
+import {
+  normalizeCustomWorktreeVisibilitySources,
+  normalizeWorktreeVisibilitySourcePreferences
+} from '../../../../shared/worktree-visibility-sources'
 import { cleanupEphemeralVmRuntimesForDeleted } from '@/lib/ephemeral-vm-runtime-cleanup'
 import { folderWorkspaceKey, parseWorkspaceKey } from '../../../../shared/workspace-scope'
 import { formatFolderWorkspaceCreateError } from '../../lib/folder-workspace-path-status'
@@ -133,6 +137,8 @@ export type RepoUpdate = Partial<
     | 'externalWorktreeInboxBaselinePaths'
     | 'importedExternalWorktreePaths'
     | 'agentWorktreeVisibility'
+    | 'customWorktreeVisibilitySources'
+    | 'worktreeVisibilitySourcePreferences'
     | 'projectGroupId'
     | 'projectGroupOrder'
   >
@@ -272,6 +278,26 @@ function sanitizeRepoUpdate(updates: RepoUpdate): RepoUpdate {
   ) {
     delete sanitized.forkSyncMode
   }
+  if ('customWorktreeVisibilitySources' in sanitized) {
+    const sources = normalizeCustomWorktreeVisibilitySources(
+      sanitized.customWorktreeVisibilitySources
+    )
+    if (!sources) {
+      delete sanitized.customWorktreeVisibilitySources
+    } else {
+      sanitized.customWorktreeVisibilitySources = sources
+    }
+  }
+  if ('worktreeVisibilitySourcePreferences' in sanitized) {
+    const preferences = normalizeWorktreeVisibilitySourcePreferences(
+      sanitized.worktreeVisibilitySourcePreferences
+    )
+    if (!preferences) {
+      delete sanitized.worktreeVisibilitySourcePreferences
+    } else {
+      sanitized.worktreeVisibilitySourcePreferences = preferences
+    }
+  }
   return sanitized
 }
 

src/shared/agent-scratch-worktrees.ts

@@ -1,4 +1,8 @@
 import { normalizeRuntimePathForComparison } from './cross-platform-path'
+import {
+  createWorktreeVisibilitySourceMatcher,
+  type WorktreeVisibilitySourceMatcher
+} from './worktree-visibility-sources'
 
 /** Why: agent CLIs reserve these repo-root paths for scratch; broader matches
  *  can hide legitimate user worktrees (#9388). */
@@ -9,29 +13,17 @@ const AGENT_SCRATCH_PATH_PREFIXES: readonly (readonly string[])[] = [
 
 export type AgentScratchWorktreePathMatcher = (worktreePath: string) => boolean
 
+export function createAgentScratchWorktreeSourceMatcher(
+  checkoutPaths: readonly string[]
+): WorktreeVisibilitySourceMatcher {
+  return createWorktreeVisibilitySourceMatcher(checkoutPaths)
+}
+
 export function createAgentScratchWorktreePathMatcher(
   checkoutPaths: readonly string[]
 ): AgentScratchWorktreePathMatcher {
-  const checkoutPathKeys = new Set(checkoutPaths.map(normalizeRuntimePathForComparison))
-  return (worktreePath) => {
-    const segments = normalizeRuntimePathForComparison(worktreePath).split('/')
-    for (const prefix of AGENT_SCRATCH_PATH_PREFIXES) {
-      for (let index = 0; index + prefix.length < segments.length; index += 1) {
-        if (!prefix.every((segment, offset) => segments[index + offset] === segment)) {
-          continue
-        }
-        const checkoutPath = segments.slice(0, index).join('/')
-        // Why: splitting strips the separator from filesystem roots, but normalized checkout keys retain it.
-        const checkoutPathKey = /^[a-z]:$/i.test(checkoutPath)
-          ? `${checkoutPath}/`
-          : checkoutPath || '/'
-        if (checkoutPathKeys.has(checkoutPathKey)) {
-          return true
-        }
-      }
-    }
-    return false
-  }
+  const classify = createAgentScratchWorktreeSourceMatcher(checkoutPaths)
+  return (worktreePath) => classify(worktreePath)?.kind === 'built-in'
 }
 
 export function isAgentScratchWorktreePath(repoPath: string, worktreePath: string): boolean {

src/shared/types.ts

@@ -111,6 +111,18 @@ export type IssueSourcePreference = 'upstream' | 'origin' | 'auto'
 export type { ForkSyncMode, GitForkSyncExpectedUpstream, GitForkSyncResult } from './git-fork-sync'
 export type ExternalWorktreeVisibility = 'hide' | 'show'
 
+export type BuiltInWorktreeVisibilitySourceId = 'claude' | 'gsd'
+
+export type CustomWorktreeVisibilitySource = {
+  id: string
+  rootPath: string
+}
+
+export type WorktreeVisibilitySourcePreferences = {
+  builtIn?: Partial<Record<BuiltInWorktreeVisibilitySourceId, ExternalWorktreeVisibility>>
+  custom?: Record<string, ExternalWorktreeVisibility>
+}
+
 export type ProjectProviderIdentity = {
   provider: 'github'
   owner: string
@@ -291,6 +303,10 @@ export type Repo = {
   importedExternalWorktreePaths?: string[]
   /** Opt-in repo policy for coding-agent scratch worktrees; absent means hide. */
   agentWorktreeVisibility?: ExternalWorktreeVisibility
+  /** User-defined roots classified independently from ordinary external worktrees. */
+  customWorktreeVisibilitySources?: CustomWorktreeVisibilitySource[]
+  /** Per-source visibility; absent built-ins inherit the legacy agent policy. */
+  worktreeVisibilitySourcePreferences?: WorktreeVisibilitySourcePreferences
   /** User permanently opted out of the new-external-worktree inbox for this repo. */
   externalWorktreeDiscoverySuppressedAt?: number
   /** Paths (relative to the primary checkout) that should be APFS clone-copied
@@ -707,6 +723,10 @@ export type DetectedWorktree = Worktree & {
   ownership: WorktreeOwnership
   selectedCheckout: boolean
   visible: boolean
+  /** Optional additive source identity; older hosts omit it. */
+  visibilitySource?:
+    | { kind: 'built-in'; id: BuiltInWorktreeVisibilitySourceId }
+    | { kind: 'custom'; id: string }
 }
 
 export type DetectedWorktreeListResult = {

src/shared/worktree-ownership.test.ts

@@ -513,6 +513,56 @@ describe('agent scratch worktrees', () => {
     }
   })
 
+  it('applies built-in source preferences independently after legacy migration', () => {
+    const repo = makeRepo({
+      agentWorktreeVisibility: 'show',
+      worktreeVisibilitySourcePreferences: {
+        builtIn: { claude: 'hide', gsd: 'show' }
+      }
+    })
+    const settings = makeSettings()
+
+    expect(
+      toDetectedWorktree({
+        repo,
+        settings,
+        worktree: makeWorktree({ path: scratchPath, isMainWorktree: false }),
+        knownOrcaLayouts: buildKnownOrcaWorkspaceLayouts(settings, repo)
+      }).visible
+    ).toBe(false)
+    expect(
+      toDetectedWorktree({
+        repo,
+        settings,
+        worktree: makeWorktree({
+          path: '/repos/app/.gsd-workspaces/phase-1',
+          isMainWorktree: false
+        }),
+        knownOrcaLayouts: buildKnownOrcaWorkspaceLayouts(settings, repo)
+      }).visible
+    ).toBe(true)
+  })
+
+  it('lets a custom source override ordinary external visibility', () => {
+    const customPath = '/srv/team-worktrees/feature'
+    const repo = makeRepo({
+      externalWorktreeVisibility: 'show',
+      customWorktreeVisibilitySources: [{ id: 'team', rootPath: '/srv/team-worktrees' }],
+      worktreeVisibilitySourcePreferences: { custom: { team: 'hide' } }
+    })
+    const settings = makeSettings()
+    const detected = toDetectedWorktree({
+      repo,
+      settings,
+      worktree: makeWorktree({ path: customPath, isMainWorktree: false }),
+      knownOrcaLayouts: buildKnownOrcaWorkspaceLayouts(settings, repo)
+    })
+
+    expect(detected.visibilitySource).toEqual({ kind: 'custom', id: 'team' })
+    expect(detected.visible).toBe(false)
+    expect(applyMetadataFallbackVisibility(detected).visible).toBe(false)
+  })
+
   it('still shows agent scratch for the selected checkout or an explicit import', () => {
     const repo = makeRepo({
       externalWorktreeVisibility: 'hide',

src/shared/worktree-ownership.ts

@@ -11,6 +11,12 @@ import {
   isAgentScratchWorktreePath,
   type AgentScratchWorktreePathMatcher
 } from './agent-scratch-worktrees'
+import {
+  createWorktreeVisibilitySourceMatcher,
+  effectiveWorktreeSourceVisibility,
+  normalizeCustomWorktreeVisibilitySources,
+  type WorktreeVisibilitySourceMatcher
+} from './worktree-visibility-sources'
 import { isExplicitlyImportedExternalWorktreePath } from './external-worktree-inbox'
 import {
   effectiveAgentWorktreeVisibility,
@@ -145,6 +151,7 @@ export function classifyWorktreeOwnership(args: {
   settings: Pick<GlobalSettings, 'workspaceDir' | 'nestWorkspaces' | 'workspaceDirHistory'>
   knownOrcaLayouts: OrcaWorkspaceLayout[]
   agentScratchWorktreePathMatcher?: AgentScratchWorktreePathMatcher
+  worktreeVisibilitySourceMatcher?: WorktreeVisibilitySourceMatcher
 }): WorktreeOwnership {
   if (hasStrongOrcaMetadata(args.meta)) {
     return 'orca-managed'
@@ -153,8 +160,9 @@ export function classifyWorktreeOwnership(args: {
   // Why: sub-agent scratch worktrees (e.g. .claude/worktrees) are tool
   // plumbing, not workspaces; classify before layout heuristics (#9388).
   if (
-    args.agentScratchWorktreePathMatcher?.(args.worktree.path) ??
-    isAgentScratchWorktreePath(args.repo.path, args.worktree.path)
+    args.worktreeVisibilitySourceMatcher?.(args.worktree.path)?.kind === 'built-in' ||
+    (args.agentScratchWorktreePathMatcher?.(args.worktree.path) ??
+      isAgentScratchWorktreePath(args.repo.path, args.worktree.path))
   ) {
     return 'agent-scratch'
   }
@@ -180,8 +188,19 @@ export function toDetectedWorktree(args: {
   knownOrcaLayouts: OrcaWorkspaceLayout[]
   isLegacyRepoForVisibility?: boolean
   agentScratchWorktreePathMatcher?: AgentScratchWorktreePathMatcher
+  worktreeVisibilitySourceMatcher?: WorktreeVisibilitySourceMatcher
 }): DetectedWorktree {
-  const ownership = classifyWorktreeOwnership(args)
+  const sourceMatcher =
+    args.worktreeVisibilitySourceMatcher ??
+    createWorktreeVisibilitySourceMatcher(
+      [args.repo.path],
+      normalizeCustomWorktreeVisibilitySources(args.repo.customWorktreeVisibilitySources) ?? []
+    )
+  const visibilitySource = sourceMatcher(args.worktree.path)
+  const ownership = classifyWorktreeOwnership({
+    ...args,
+    worktreeVisibilitySourceMatcher: sourceMatcher
+  })
   const selectedCheckout = areRuntimePathsEqual(args.worktree.path, args.repo.path)
   const isLegacyRepoForVisibility =
     args.isLegacyRepoForVisibility ?? isLegacyRepoForExternalWorktreeVisibility(args.repo)
@@ -191,14 +210,16 @@ export function toDetectedWorktree(args: {
     repo: args.repo,
     isLegacyRepoForVisibility,
     isSelectedCheckout: selectedCheckout,
-    importedExternalWorktreePaths: args.repo.importedExternalWorktreePaths
+    importedExternalWorktreePaths: args.repo.importedExternalWorktreePaths,
+    visibilitySource
   })
 
   return {
     ...args.worktree,
     ownership,
     selectedCheckout,
-    visible
+    visible,
+    ...(visibilitySource ? { visibilitySource } : {})
   }
 }
 
@@ -209,6 +230,7 @@ export function shouldShowWorktree(args: {
   isLegacyRepoForVisibility: boolean
   isSelectedCheckout: boolean
   importedExternalWorktreePaths?: readonly string[] | undefined
+  visibilitySource?: ReturnType<WorktreeVisibilitySourceMatcher>
 }): boolean {
   if (args.isSelectedCheckout) {
     return true
@@ -223,6 +245,9 @@ export function shouldShowWorktree(args: {
   ) {
     return true
   }
+  if (args.visibilitySource) {
+    return effectiveWorktreeSourceVisibility(args.repo, args.visibilitySource) === 'show'
+  }
   if (args.ownership === 'agent-scratch') {
     return effectiveAgentWorktreeVisibility(args.repo) === 'show'
   }
@@ -233,7 +258,7 @@ export function shouldShowWorktree(args: {
 }
 
 export function applyMetadataFallbackVisibility(detected: DetectedWorktree): DetectedWorktree {
-  if (detected.ownership === 'agent-scratch') {
+  if (detected.ownership === 'agent-scratch' || detected.visibilitySource) {
     // Why: retain scratch policy, including explicit imports, while ordinary fallback fails open.
     return detected
   }

src/shared/worktree-visibility-sources.test.ts

@@ -0,0 +1,93 @@
+import { describe, expect, it } from 'vitest'
+import type { Repo } from './types'
+import {
+  buildWorktreeSourcePreferenceUpdate,
+  createWorktreeVisibilitySourceMatcher,
+  effectiveBuiltInWorktreeSourceVisibility,
+  normalizeCustomWorktreeVisibilitySources,
+  normalizeWorktreeVisibilitySourcePreferences
+} from './worktree-visibility-sources'
+
+function repo(overrides: Partial<Repo> = {}): Repo {
+  return {
+    id: 'repo-1',
+    path: '/repo',
+    displayName: 'repo',
+    addedAt: 1,
+    ...overrides,
+    badgeColor: overrides.badgeColor ?? '#fff'
+  }
+}
+
+describe('worktree visibility sources', () => {
+  it('classifies each built-in independently across linked checkouts', () => {
+    const classify = createWorktreeVisibilitySourceMatcher(['/repo', '/worktrees/feature'])
+    expect(classify('/repo/.claude/worktrees/review')).toEqual({
+      kind: 'built-in',
+      id: 'claude'
+    })
+    expect(classify('/worktrees/feature/.gsd-workspaces/phase-1')).toEqual({
+      kind: 'built-in',
+      id: 'gsd'
+    })
+    expect(classify('/other/.claude/worktrees/review')).toBeNull()
+  })
+
+  it('matches custom descendants with Windows and WSL comparison semantics', () => {
+    const windows = createWorktreeVisibilitySourceMatcher(
+      [],
+      [{ id: 'team', rootPath: 'C:\\Users\\Dev\\Team' }]
+    )
+    expect(windows('c:\\users\\dev\\team\\feature')).toEqual({
+      kind: 'custom',
+      id: 'team'
+    })
+
+    const wsl = createWorktreeVisibilitySourceMatcher(
+      [],
+      [{ id: 'linux', rootPath: '//wsl$/Ubuntu/home/dev/team' }]
+    )
+    expect(wsl('//wsl.localhost/Ubuntu/home/dev/team/feature')).toEqual({
+      kind: 'custom',
+      id: 'linux'
+    })
+    expect(wsl('//wsl.localhost/Ubuntu/home/Dev/team/feature')).toBeNull()
+  })
+
+  it('gives built-ins precedence over overlapping custom roots', () => {
+    const classify = createWorktreeVisibilitySourceMatcher(
+      ['/repo'],
+      [{ id: 'overlap', rootPath: '/repo/.claude/worktrees' }]
+    )
+    expect(classify('/repo/.claude/worktrees/review')).toEqual({
+      kind: 'built-in',
+      id: 'claude'
+    })
+  })
+
+  it('migrates the optional legacy agent policy lazily for both built-ins', () => {
+    const legacy = repo({ agentWorktreeVisibility: 'show' })
+    expect(effectiveBuiltInWorktreeSourceVisibility(legacy, 'claude')).toBe('show')
+    expect(effectiveBuiltInWorktreeSourceVisibility(legacy, 'gsd')).toBe('show')
+    expect(
+      buildWorktreeSourcePreferenceUpdate(legacy, { kind: 'built-in', id: 'claude' }, 'hide')
+    ).toEqual({ builtIn: { claude: 'hide', gsd: 'show' } })
+  })
+
+  it('bounds and sanitizes persisted source definitions and preferences', () => {
+    expect(
+      normalizeCustomWorktreeVisibilitySources([
+        { id: 'team', rootPath: ' /srv/team/ ' },
+        { id: 'duplicate-root', rootPath: '/srv/team' },
+        { id: 'relative', rootPath: '../team' },
+        { id: 'bad id', rootPath: '/srv/other' }
+      ])
+    ).toEqual([{ id: 'team', rootPath: '/srv/team/' }])
+    expect(
+      normalizeWorktreeVisibilitySourcePreferences({
+        builtIn: { claude: 'show', gsd: 'invalid', unknown: 'show' },
+        custom: { team: 'hide', nope: 'invalid' }
+      })
+    ).toEqual({ builtIn: { claude: 'show' }, custom: { team: 'hide' } })
+  })
+})

src/shared/worktree-visibility-sources.ts

@@ -0,0 +1,233 @@
+import {
+  createNormalizedPathInsideOrEqualMatcher,
+  isRuntimePathAbsolute,
+  normalizeRuntimePathForComparison
+} from './cross-platform-path'
+import type {
+  BuiltInWorktreeVisibilitySourceId,
+  CustomWorktreeVisibilitySource,
+  ExternalWorktreeVisibility,
+  Repo,
+  WorktreeVisibilitySourcePreferences
+} from './types'
+
+export const MAX_CUSTOM_WORKTREE_VISIBILITY_SOURCES = 32
+const MAX_SOURCE_ID_LENGTH = 128
+const MAX_SOURCE_PATH_LENGTH = 4096
+
+export const BUILT_IN_WORKTREE_VISIBILITY_SOURCES: readonly {
+  id: BuiltInWorktreeVisibilitySourceId
+  relativeRootSegments: readonly string[]
+}[] = [
+  { id: 'claude', relativeRootSegments: ['.claude', 'worktrees'] },
+  { id: 'gsd', relativeRootSegments: ['.gsd-workspaces'] }
+]
+
+export type WorktreeVisibilitySourceMatch =
+  | { kind: 'built-in'; id: BuiltInWorktreeVisibilitySourceId }
+  | { kind: 'custom'; id: string }
+
+export type WorktreeVisibilitySourceMatcher = (
+  worktreePath: string
+) => WorktreeVisibilitySourceMatch | null
+
+function isValidSourceId(value: string): boolean {
+  return value.length > 0 && value.length <= MAX_SOURCE_ID_LENGTH && /^[A-Za-z0-9_-]+$/.test(value)
+}
+
+function normalizeSourceRootPath(value: string): string | null {
+  const trimmed = value.trim()
+  if (
+    !trimmed ||
+    trimmed.length > MAX_SOURCE_PATH_LENGTH ||
+    trimmed.includes('\0') ||
+    !isRuntimePathAbsolute(trimmed)
+  ) {
+    return null
+  }
+  return trimmed
+}
+
+export function normalizeCustomWorktreeVisibilitySources(
+  value: unknown
+): CustomWorktreeVisibilitySource[] | undefined {
+  if (!Array.isArray(value)) {
+    return undefined
+  }
+  const ids = new Set<string>()
+  const roots = new Set<string>()
+  const normalized: CustomWorktreeVisibilitySource[] = []
+  for (const candidate of value.slice(0, MAX_CUSTOM_WORKTREE_VISIBILITY_SOURCES)) {
+    if (!candidate || typeof candidate !== 'object') {
+      continue
+    }
+    const { id, rootPath } = candidate as { id?: unknown; rootPath?: unknown }
+    if (typeof id !== 'string' || !isValidSourceId(id) || typeof rootPath !== 'string') {
+      continue
+    }
+    const normalizedRootPath = normalizeSourceRootPath(rootPath)
+    const rootKey = normalizedRootPath
+      ? normalizeRuntimePathForComparison(normalizedRootPath)
+      : null
+    if (!normalizedRootPath || !rootKey || ids.has(id) || roots.has(rootKey)) {
+      continue
+    }
+    ids.add(id)
+    roots.add(rootKey)
+    normalized.push({ id, rootPath: normalizedRootPath })
+  }
+  return normalized
+}
+
+function normalizeVisibility(value: unknown): ExternalWorktreeVisibility | undefined {
+  return value === 'hide' || value === 'show' ? value : undefined
+}
+
+export function normalizeWorktreeVisibilitySourcePreferences(
+  value: unknown
+): WorktreeVisibilitySourcePreferences | undefined {
+  if (!value || typeof value !== 'object' || Array.isArray(value)) {
+    return undefined
+  }
+  const raw = value as { builtIn?: unknown; custom?: unknown }
+  const builtInValue =
+    raw.builtIn && typeof raw.builtIn === 'object' && !Array.isArray(raw.builtIn)
+      ? (raw.builtIn as Record<string, unknown>)
+      : {}
+  const builtIn = Object.fromEntries(
+    BUILT_IN_WORKTREE_VISIBILITY_SOURCES.flatMap(({ id }) => {
+      const visibility = normalizeVisibility(builtInValue[id])
+      return visibility ? [[id, visibility]] : []
+    })
+  ) as WorktreeVisibilitySourcePreferences['builtIn']
+  const customValue =
+    raw.custom && typeof raw.custom === 'object' && !Array.isArray(raw.custom)
+      ? (raw.custom as Record<string, unknown>)
+      : {}
+  const custom = Object.fromEntries(
+    Object.entries(customValue)
+      .filter(([id, visibility]) => isValidSourceId(id) && normalizeVisibility(visibility))
+      .slice(0, MAX_CUSTOM_WORKTREE_VISIBILITY_SOURCES)
+      .map(([id, visibility]) => [id, normalizeVisibility(visibility)!])
+  )
+  return {
+    ...(Object.keys(builtIn ?? {}).length > 0 ? { builtIn } : {}),
+    ...(Object.keys(custom).length > 0 ? { custom } : {})
+  }
+}
+
+function createDescendantMatcher(rootPath: string): (candidatePath: string) => boolean {
+  const matchesInsideOrEqual = createNormalizedPathInsideOrEqualMatcher(rootPath)
+  const normalizedRoot = normalizeRuntimePathForComparison(rootPath)
+  return (candidatePath) => {
+    const normalizedCandidate = normalizeRuntimePathForComparison(candidatePath)
+    return normalizedCandidate !== normalizedRoot && matchesInsideOrEqual(normalizedCandidate)
+  }
+}
+
+export function createWorktreeVisibilitySourceMatcher(
+  checkoutPaths: readonly string[],
+  customSources: readonly CustomWorktreeVisibilitySource[] = []
+): WorktreeVisibilitySourceMatcher {
+  const builtInMatchers = checkoutPaths.flatMap((checkoutPath) =>
+    BUILT_IN_WORKTREE_VISIBILITY_SOURCES.map(({ id, relativeRootSegments }) => ({
+      id,
+      matches: createDescendantMatcher(
+        `${checkoutPath.replace(/[\\/]+$/, '')}/${relativeRootSegments.join('/')}`
+      )
+    }))
+  )
+  const customMatchers = customSources.map(({ id, rootPath }) => ({
+    id,
+    matches: createDescendantMatcher(rootPath)
+  }))
+  return (worktreePath) => {
+    for (const source of builtInMatchers) {
+      if (source.matches(worktreePath)) {
+        return { kind: 'built-in', id: source.id }
+      }
+    }
+    for (const source of customMatchers) {
+      if (source.matches(worktreePath)) {
+        return { kind: 'custom', id: source.id }
+      }
+    }
+    return null
+  }
+}
+
+export function effectiveBuiltInWorktreeSourceVisibility(
+  repo: Pick<Repo, 'agentWorktreeVisibility' | 'worktreeVisibilitySourcePreferences'>,
+  sourceId: BuiltInWorktreeVisibilitySourceId
+): ExternalWorktreeVisibility {
+  const explicit = normalizeWorktreeVisibilitySourcePreferences(
+    repo.worktreeVisibilitySourcePreferences
+  )?.builtIn?.[sourceId]
+  if (explicit) {
+    return explicit
+  }
+  return repo.agentWorktreeVisibility === 'show' ? 'show' : 'hide'
+}
+
+export function effectiveCustomWorktreeSourceVisibility(
+  repo: Pick<Repo, 'worktreeVisibilitySourcePreferences'>,
+  sourceId: string
+): ExternalWorktreeVisibility {
+  return normalizeWorktreeVisibilitySourcePreferences(repo.worktreeVisibilitySourcePreferences)
+    ?.custom?.[sourceId] === 'show'
+    ? 'show'
+    : 'hide'
+}
+
+export function effectiveWorktreeSourceVisibility(
+  repo: Pick<Repo, 'agentWorktreeVisibility' | 'worktreeVisibilitySourcePreferences'>,
+  source: WorktreeVisibilitySourceMatch
+): ExternalWorktreeVisibility {
+  return source.kind === 'built-in'
+    ? effectiveBuiltInWorktreeSourceVisibility(repo, source.id)
+    : effectiveCustomWorktreeSourceVisibility(repo, source.id)
+}
+
+export function buildWorktreeSourcePreferenceUpdate(
+  repo: Pick<Repo, 'agentWorktreeVisibility' | 'worktreeVisibilitySourcePreferences'>,
+  source: WorktreeVisibilitySourceMatch,
+  visibility: ExternalWorktreeVisibility
+): WorktreeVisibilitySourcePreferences {
+  const current = normalizeWorktreeVisibilitySourcePreferences(
+    repo.worktreeVisibilitySourcePreferences
+  )
+  const builtIn = {
+    claude: effectiveBuiltInWorktreeSourceVisibility(repo, 'claude'),
+    gsd: effectiveBuiltInWorktreeSourceVisibility(repo, 'gsd'),
+    ...current?.builtIn
+  }
+  const custom = { ...current?.custom }
+  if (source.kind === 'built-in') {
+    builtIn[source.id] = visibility
+  } else {
+    custom[source.id] = visibility
+  }
+  return {
+    builtIn,
+    ...(Object.keys(custom).length > 0 ? { custom } : {})
+  }
+}
+
+export function removeCustomWorktreeSourcePreference(
+  repo: Pick<Repo, 'agentWorktreeVisibility' | 'worktreeVisibilitySourcePreferences'>,
+  sourceId: string
+): WorktreeVisibilitySourcePreferences {
+  const current = normalizeWorktreeVisibilitySourcePreferences(
+    repo.worktreeVisibilitySourcePreferences
+  )
+  const custom = { ...current?.custom }
+  delete custom[sourceId]
+  return {
+    builtIn: {
+      claude: effectiveBuiltInWorktreeSourceVisibility(repo, 'claude'),
+      gsd: effectiveBuiltInWorktreeSourceVisibility(repo, 'gsd'),
+      ...current?.builtIn
+    },
+    ...(Object.keys(custom).length > 0 ? { custom } : {})
+  }
+}