fix(sidebar): unify linked worktree grouping and transient selection behavior

Tighten the follow-up linked-worktree behavior so saved linked worktrees stay attached to their main repository, remain leaf rows, and do not lose selection state when synthetic sidebar rows are active.

Changes:
- keep linked worktree rows as leaf nodes so only main worktrees own nested children in the sidebar
- use `Delete…` for both saved and synthetic linked worktree rows, while removing group-name actions from saved linked worktree rows
- ensure deleting a saved linked worktree also removes its Desktop repository entry so the stored list stays in sync with Git worktree deletion
- inherit the main repository's GitHub association when a linked worktree is added through the local repository flow and its main worktree is already known to Desktop
- keep saved linked worktrees in the same top-level group as their main repository after restart instead of dropping them into `Other`
- preserve transient synthetic worktree selections across repository-store updates so selecting a worktree from another repository family does not snap back to the previously selected saved repository
- keep alias support for saved linked worktrees while treating synthetic rows as transient sidebar-only entries
- retain the regression coverage for orphan linked rows staying flat and for the linked-worktree context menu behavior

Behavioral effect:
Linked worktrees now behave consistently as leaf rows whether they are saved or synthetic. Saved linked worktrees stay grouped under their real main repository, deleting a saved linked worktree updates both Git and Desktop state, and synthetic worktree selection no longer jumps back to an unrelated repository when the saved repository list refreshes.

Testing:
- yarn test:unit app/test/unit/repositories-list-grouping-test.ts
- yarn test:unit app/test/unit/repository-list-item-context-menu-test.ts
- yarn eslint app/src/ui/repositories-list/worktree-list-items.ts app/src/ui/repositories-list/repository-list-item-context-menu.ts app/src/ui/repositories-list/repositories-list.tsx app/src/ui/worktrees/delete-worktree-dialog.tsx app/src/ui/app.tsx app/src/models/popup.ts app/src/lib/stores/app-store.ts app/test/unit/repositories-list-grouping-test.ts app/test/unit/repository-list-item-context-menu-test.ts
- yarn compile:prod

Author: ignatremizov

app/src/lib/stores/app-store.ts

@@ -3033,7 +3033,20 @@ export class AppStore extends TypedBaseStore<IAppState> {
             r.id === selectedRepository.id
         ) || null
 
-      newSelectedRepository = r
+      if (r !== null) {
+        newSelectedRepository = r
+      } else if (
+        selectedRepository instanceof Repository &&
+        selectedRepository.id < 0
+      ) {
+        // Synthetic sidebar-only worktree rows are transient selections and
+        // won't exist in the saved repositories list. Preserve the current
+        // selection across repository store updates instead of falling back to
+        // the previously selected saved repository.
+        newSelectedRepository = selectedRepository
+      } else {
+        newSelectedRepository = null
+      }
     }
 
     if (newSelectedRepository === null && this.repositories.length > 0) {
@@ -7419,11 +7432,29 @@ export class AppStore extends TypedBaseStore<IAppState> {
           continue
         }
 
-        const addedRepo = await this.repositoriesStore.addRepository(
+        let addedRepo = await this.repositoriesStore.addRepository(
           validatedPath,
           login
         )
 
+        // When a linked worktree is added as a standalone repository and the
+        // main worktree is already known to Desktop, inherit that GitHub
+        // association up front so the saved row lands in the same top-level
+        // group after restart.
+        const mainWorktreeRepo = addedRepo.isLinkedWorktree
+          ? matchExistingRepository(repositories, addedRepo.mainWorktreePath)
+          : undefined
+
+        if (
+          mainWorktreeRepo !== undefined &&
+          isRepositoryWithGitHubRepository(mainWorktreeRepo)
+        ) {
+          addedRepo = await this.repositoriesStore.setGitHubRepository(
+            addedRepo,
+            mainWorktreeRepo.gitHubRepository
+          )
+        }
+
         // initialize the remotes for this new repository to ensure it can fetch
         // it's GitHub-related details using the GitHub API (if applicable)
         const gitStore = this.gitStoreCache.get(addedRepo)

app/src/models/popup.ts

@@ -513,5 +513,7 @@ export type PopupDetail =
       type: PopupType.DeleteWorktree
       repository: Repository
       worktreePath: string
+      storedRepositoryToRemove?: Repository
+      isDeletingCurrentWorktree?: boolean
     }
 export type Popup = IBasePopup & PopupDetail

app/src/ui/app.tsx

@@ -2763,6 +2763,8 @@ export class App extends React.Component<IAppProps, IAppState> {
             key="delete-worktree"
             repository={popup.repository}
             worktreePath={popup.worktreePath}
+            storedRepositoryToRemove={popup.storedRepositoryToRemove}
+            isDeletingCurrentWorktree={popup.isDeletingCurrentWorktree}
             dispatcher={this.props.dispatcher}
             onDismissed={onPopupDismissedFn}
           />

app/src/ui/repositories-list/repositories-list.tsx

@@ -449,6 +449,10 @@ export class RepositoriesList extends React.Component<
         : item.repository instanceof Repository
         ? item.repository
         : null
+    const storedRepositoryToRemove =
+      item.repository instanceof Repository && !item.isVirtualLinkedWorktree
+        ? item.repository
+        : undefined
 
     if (repository === null) {
       return
@@ -458,6 +462,11 @@ export class RepositoriesList extends React.Component<
       type: PopupType.DeleteWorktree,
       repository,
       worktreePath,
+      storedRepositoryToRemove,
+      isDeletingCurrentWorktree:
+        this.props.selectedRepository !== null &&
+        normalizePath(this.props.selectedRepository.path) ===
+          normalizePath(worktreePath),
     })
   }
 
@@ -490,7 +499,11 @@ export class RepositoriesList extends React.Component<
       onOpenInExternalEditor: this.props.onOpenInExternalEditor,
       askForConfirmationOnRemoveRepository:
         this.props.askForConfirmationOnRemoveRepository,
-      isLinkedWorktreeRow: item.isVirtualLinkedWorktree,
+      isLinkedWorktreeRow:
+        item.isVirtualLinkedWorktree ||
+        (item.repository instanceof Repository &&
+          item.repository.isLinkedWorktree),
+      isVirtualLinkedWorktreeRow: item.isVirtualLinkedWorktree,
       isPrunableWorktreeRow: item.isPrunableWorktree,
       externalEditorLabel: this.props.externalEditorLabel,
       onChangeRepositoryAlias: this.onChangeRepositoryAlias,

app/src/ui/repositories-list/repository-list-item-context-menu.ts

@@ -19,6 +19,7 @@ interface IRepositoryListItemContextMenuConfig {
   externalEditorLabel: string | undefined
   askForConfirmationOnRemoveRepository: boolean
   readonly isLinkedWorktreeRow?: boolean
+  readonly isVirtualLinkedWorktreeRow?: boolean
   readonly isPrunableWorktreeRow?: boolean
   onViewInBrowser: (repository: Repositoryish) => void
   onOpenInNewWindow?: (repository: Repositoryish) => void
@@ -159,7 +160,10 @@ const buildAliasMenuItems = (
 ): ReadonlyArray<IMenuItem> => {
   const { repository } = config
 
-  if (!(repository instanceof Repository) || config.isLinkedWorktreeRow) {
+  if (
+    !(repository instanceof Repository) ||
+    config.isVirtualLinkedWorktreeRow
+  ) {
     return []
   }
 
@@ -186,7 +190,11 @@ const buildGroupNameMenuItems = (
 ): ReadonlyArray<IMenuItem> => {
   const { repository } = config
 
-  if (!(repository instanceof Repository) || config.isLinkedWorktreeRow) {
+  if (
+    !(repository instanceof Repository) ||
+    config.isLinkedWorktreeRow ||
+    config.isVirtualLinkedWorktreeRow
+  ) {
     return []
   }
 

app/src/ui/repositories-list/worktree-list-items.ts

@@ -23,14 +23,22 @@ export const getDisplayTitle = (repository: Repositoryish) =>
     ? repository.alias
     : repository.name
 
+const getLinkedWorktreeDisplayTitle = (
+  repository: Repositoryish,
+  worktreePath?: string
+) =>
+  repository instanceof Repository && repository.alias != null
+    ? repository.alias
+    : Path.basename(worktreePath ?? repository.path)
+
 export const getRepositoryListTitle = (
   repository: Repositoryish,
   showWorktreesInSidebar: boolean
 ) =>
   showWorktreesInSidebar &&
   repository instanceof Repository &&
   repository.isLinkedWorktree
-    ? Path.basename(repository.path)
+    ? getLinkedWorktreeDisplayTitle(repository)
     : getDisplayTitle(repository)
 
 const getVirtualRepositoryId = (worktreePath: string) => {
@@ -138,7 +146,7 @@ export function toSortedRepositoryListItems({
         : null
     const title =
       isLinkedWorktree || isVirtualLinkedWorktree
-        ? Path.basename(worktreePath)
+        ? getLinkedWorktreeDisplayTitle(repository, worktreePath)
         : getDisplayTitle(repository)
     const defaultBranchName =
       repoState?.defaultBranchName ??
@@ -313,12 +321,6 @@ export function toSortedRepositoryListItems({
 
   for (const repository of orphanLinkedRepos) {
     items.push(toListItem(repository, false))
-    appendVirtualWorktreeItems(
-      items,
-      repository,
-      repository,
-      emittedVirtualPaths
-    )
   }
 
   return items

app/src/ui/worktrees/delete-worktree-dialog.tsx

@@ -16,6 +16,8 @@ import {
 interface IDeleteWorktreeDialogProps {
   readonly repository: Repository
   readonly worktreePath: string
+  readonly storedRepositoryToRemove?: Repository
+  readonly isDeletingCurrentWorktree?: boolean
   readonly dispatcher: Dispatcher
   readonly onDismissed: () => void
 }
@@ -66,9 +68,13 @@ export class DeleteWorktreeDialog extends React.Component<
   private onDeleteWorktree = async () => {
     this.setState({ isDeleting: true })
 
-    const { repository, worktreePath, dispatcher } = this.props
-    const isDeletingCurrentWorktree =
-      normalizePath(repository.path) === normalizePath(worktreePath)
+    const {
+      repository,
+      worktreePath,
+      dispatcher,
+      storedRepositoryToRemove,
+      isDeletingCurrentWorktree = false,
+    } = this.props
 
     const mainPathForCleanup = await getMainWorktreePath(repository)
 
@@ -94,9 +100,13 @@ export class DeleteWorktreeDialog extends React.Component<
         const mainRepo = addedRepos[0]
         await dispatcher.selectRepository(mainRepo)
         await removeWorktree(mainRepo, worktreePath)
-        await dispatcher.removeRepository(repository, false)
       } else {
         await removeWorktree(repository, worktreePath)
+      }
+
+      if (storedRepositoryToRemove !== undefined) {
+        await dispatcher.removeRepository(storedRepositoryToRemove, false)
+      } else if (!isDeletingCurrentWorktree) {
         await dispatcher.refreshRepository(repository)
       }
     } catch (e) {

app/test/unit/repositories-list-grouping-test.ts

@@ -390,4 +390,92 @@ describe('repository list grouping', () => {
       await rm(tempRoot, { recursive: true, force: true })
     }
   })
+
+  it('does not synthesize linked worktree siblings under orphan linked worktrees', async () => {
+    const tempRoot = await mkdtemp(
+      path.join(os.tmpdir(), 'github-desktop-plus-worktree-orphan-leaf-')
+    )
+    try {
+      const mainRepoPath = path.join(tempRoot, 'repo')
+      const linkedRepoPath = path.join(tempRoot, 'repo-feature-a')
+      const secondLinkedRepoPath = path.join(tempRoot, 'repo-feature-b')
+
+      await mkdir(path.join(mainRepoPath, '.git'), { recursive: true })
+      await mkdir(path.join(mainRepoPath, '.git', 'worktrees', 'feature-a'), {
+        recursive: true,
+      })
+      await mkdir(path.join(mainRepoPath, '.git', 'worktrees', 'feature-b'), {
+        recursive: true,
+      })
+      await mkdir(linkedRepoPath, { recursive: true })
+      await writeFile(
+        path.join(linkedRepoPath, '.git'),
+        'gitdir: ../repo/.git/worktrees/feature-a\n'
+      )
+      await writeFile(
+        path.join(mainRepoPath, '.git', 'worktrees', 'feature-a', 'commondir'),
+        '../..\n'
+      )
+      await writeFile(
+        path.join(mainRepoPath, '.git', 'worktrees', 'feature-b', 'commondir'),
+        '../..\n'
+      )
+
+      const linkedRepo = new Repository(
+        linkedRepoPath,
+        20,
+        gitHubRepoFixture({ owner: 'example', name: 'repo' }),
+        false,
+        'custom alias'
+      )
+
+      cache.set(linkedRepo.id, {
+        aheadBehind: null,
+        changedFilesCount: 0,
+        branchName: 'feature/a',
+        defaultBranchName: 'main',
+        allWorktrees: [
+          {
+            path: mainRepoPath,
+            head: 'a',
+            branch: 'refs/heads/main',
+            isDetached: false,
+            type: 'main',
+            isLocked: false,
+            isPrunable: false,
+          },
+          {
+            path: linkedRepoPath,
+            head: 'b',
+            branch: 'refs/heads/feature/a',
+            isDetached: false,
+            type: 'linked',
+            isLocked: false,
+            isPrunable: false,
+          },
+          {
+            path: secondLinkedRepoPath,
+            head: 'c',
+            branch: 'refs/heads/feature/b',
+            isDetached: false,
+            type: 'linked',
+            isLocked: false,
+            isPrunable: false,
+          },
+        ],
+      })
+
+      const grouped = groupRepositories([linkedRepo], cache, [], {
+        showWorktreesInSidebar: true,
+      })
+
+      assert.equal(grouped.length, 1)
+      assert.equal(grouped[0].items.length, 1)
+      assert.equal(grouped[0].items[0].repository.path, linkedRepoPath)
+      assert.equal(grouped[0].items[0].isNestedWorktree, false)
+      assert.equal(grouped[0].items[0].title, 'custom alias')
+    } finally {
+      await rm(tempRoot, { recursive: true, force: true })
+    }
+  })
 })

app/test/unit/repository-list-item-context-menu-test.ts

@@ -66,6 +66,7 @@ describe('repository list item context menu', () => {
     const items = generateRepositoryListContextMenu(
       buildConfig({
         isLinkedWorktreeRow: true,
+        isVirtualLinkedWorktreeRow: true,
         onRemoveRepository: () => {
           removedRepository = true
         },
@@ -98,6 +99,26 @@ describe('repository list item context menu', () => {
     assert.equal(removedRepository, false)
   })
 
+  it('keeps alias and group name actions for saved linked worktree rows', () => {
+    const items = generateRepositoryListContextMenu(
+      buildConfig({
+        isLinkedWorktreeRow: true,
+        isVirtualLinkedWorktreeRow: false,
+        onRemoveLinkedWorktree: () => {},
+      })
+    )
+    const labels = items.flatMap(item => ('label' in item ? [item.label] : []))
+
+    assert(labels.includes('Change alias') || labels.includes('Change Alias'))
+    assert(labels.includes('Remove alias') || labels.includes('Remove Alias'))
+    assert(!labels.includes('Change group name'))
+    assert(!labels.includes('Change Group Name'))
+    assert(!labels.includes('Restore group name'))
+    assert(!labels.includes('Restore Group Name'))
+    assert(labels.includes('Delete…'))
+    assert(!labels.includes('Remove…'))
+  })
+
   it('shows a prune action for stale worktree rows and keeps remove semantics', () => {
     let prunedStaleWorktrees = false
     let removedRepository = false
@@ -140,6 +161,7 @@ describe('repository list item context menu', () => {
     const items = generateRepositoryListContextMenu(
       buildConfig({
         isLinkedWorktreeRow: true,
+        isVirtualLinkedWorktreeRow: true,
         isPrunableWorktreeRow: true,
         onPruneStaleWorktrees: () => {},
       })