diff --git a/src/renderer/src/components/activity/activity-portal-readiness-loop.react185.test.tsx b/src/renderer/src/components/activity/activity-portal-readiness-loop.react185.test.tsx
index ab134697b..13260d457 100644
--- a/src/renderer/src/components/activity/activity-portal-readiness-loop.react185.test.tsx
+++ b/src/renderer/src/components/activity/activity-portal-readiness-loop.react185.test.tsx
@@ -84,6 +84,33 @@ function installAnimationFrameController(): {
   }
 }
 
+function installMutationObserverController(): { notify: () => void } {
+  const callbacks = new Map<MutationObserver, MutationCallback>()
+  class ControlledMutationObserver implements MutationObserver {
+    constructor(callback: MutationCallback) {
+      callbacks.set(this, callback)
+    }
+
+    observe(): void {}
+
+    disconnect(): void {
+      callbacks.delete(this)
+    }
+
+    takeRecords(): MutationRecord[] {
+      return []
+    }
+  }
+  vi.stubGlobal('MutationObserver', ControlledMutationObserver)
+  return {
+    notify() {
+      for (const [observer, callback] of callbacks) {
+        callback([], observer)
+      }
+    }
+  }
+}
+
 async function flushPortalFramesUntil(
   frames: ReturnType<typeof installAnimationFrameController>,
   settled: () => boolean
@@ -347,6 +374,7 @@ describe('Activity portal pane switching', () => {
 
   it('releases a latched readiness once the terminal attaches', async () => {
     const frames = installAnimationFrameController()
+    const mutations = installMutationObserverController()
     const target = document.createElement('div')
     document.body.append(target)
     const buildRoot = (mode: 'hidden' | 'sibling' | 'ready'): void => {
@@ -402,7 +430,7 @@ describe('Activity portal pane switching', () => {
       const statusesBefore = statuses.length
       await act(async () => {
         buildRoot(mode)
-        await Promise.resolve()
+        mutations.notify()
       })
       expect(await flushPortalReadiness(frames)).toBe(true)
       if (mode !== 'sibling') {
@@ -426,7 +454,7 @@ describe('Activity portal pane switching', () => {
     for (let attempt = 0; attempt < PORTAL_READY_REAPPLY_ATTEMPTS && !sawReady; attempt += 1) {
       await act(async () => {
         buildRoot('ready')
-        await Promise.resolve()
+        mutations.notify()
       })
       expect(await flushPortalReadiness(frames)).toBe(true)
       await flushPortalFramesUntil(frames, () => statuses.at(-1) === 'ready')
diff --git a/src/renderer/src/components/right-sidebar/file-explorer-add-project-action.test.ts b/src/renderer/src/components/right-sidebar/file-explorer-add-project-action.test.ts
index 95fcdeda8..3f36fb046 100644
--- a/src/renderer/src/components/right-sidebar/file-explorer-add-project-action.test.ts
+++ b/src/renderer/src/components/right-sidebar/file-explorer-add-project-action.test.ts
@@ -56,4 +56,35 @@ describe('file explorer add project action', () => {
       connectionId: 'ssh-target-1'
     })
   })
+
+  it('routes an execution-host-only SSH project subfolder to its SSH target', () => {
+    expect(
+      buildAddProjectFromFolderModalData(folderNode, {
+        ...folderRepo,
+        executionHostId: 'ssh:ssh-target-1'
+      })
+    ).toEqual({
+      folderPath: '/projects/child-project',
+      connectionId: 'ssh-target-1'
+    })
+  })
+
+  it('routes a local project subfolder explicitly to local', () => {
+    expect(buildAddProjectFromFolderModalData(folderNode, folderRepo)).toEqual({
+      folderPath: '/projects/child-project',
+      runtimeEnvironmentId: null
+    })
+  })
+
+  it("routes a runtime project subfolder to the repo's runtime", () => {
+    expect(
+      buildAddProjectFromFolderModalData(folderNode, {
+        ...folderRepo,
+        executionHostId: 'runtime:runtime-a'
+      })
+    ).toEqual({
+      folderPath: '/projects/child-project',
+      runtimeEnvironmentId: 'runtime-a'
+    })
+  })
 })
diff --git a/src/renderer/src/components/right-sidebar/file-explorer-add-project-action.ts b/src/renderer/src/components/right-sidebar/file-explorer-add-project-action.ts
index 57d317abb..b8af63bcb 100644
--- a/src/renderer/src/components/right-sidebar/file-explorer-add-project-action.ts
+++ b/src/renderer/src/components/right-sidebar/file-explorer-add-project-action.ts
@@ -1,10 +1,12 @@
 import { isFolderRepo } from '../../../../shared/repo-kind'
+import { getRepoExecutionHostId, parseExecutionHostId } from '../../../../shared/execution-host'
 import type { Repo } from '../../../../shared/types'
 import type { TreeNode } from './file-explorer-types'
 
 export type AddProjectFromFolderModalData = {
   folderPath: string
   connectionId?: string
+  runtimeEnvironmentId?: string | null
 }
 
 export function canShowAddAsProjectAction(node: TreeNode, activeRepo: Repo | null): boolean {
@@ -15,8 +17,13 @@ export function buildAddProjectFromFolderModalData(
   node: TreeNode,
   activeRepo: Repo
 ): AddProjectFromFolderModalData {
+  // Why: subfolder paths must stay on their owning repo host, not the mutable global selection.
+  const host = parseExecutionHostId(getRepoExecutionHostId(activeRepo))
+  if (host?.kind === 'ssh') {
+    return { folderPath: node.path, connectionId: host.targetId }
+  }
   return {
     folderPath: node.path,
-    ...(activeRepo.connectionId ? { connectionId: activeRepo.connectionId } : {})
+    runtimeEnvironmentId: host?.kind === 'runtime' ? host.environmentId : null
   }
 }
diff --git a/src/renderer/src/components/sidebar/AddProjectFromFolderDialog.test.tsx b/src/renderer/src/components/sidebar/AddProjectFromFolderDialog.test.tsx
index ddff8f752..7310d450a 100644
--- a/src/renderer/src/components/sidebar/AddProjectFromFolderDialog.test.tsx
+++ b/src/renderer/src/components/sidebar/AddProjectFromFolderDialog.test.tsx
@@ -150,7 +150,9 @@ describe('AddProjectFromFolderDialog', () => {
     renderToStaticMarkup(<AddProjectFromFolderDialog />)
     await clickAddProject()
 
-    expect(mocks.state.addRepoPath).toHaveBeenCalledWith('/projects/child')
+    expect(mocks.state.addRepoPath).toHaveBeenCalledWith('/projects/child', 'git', {
+      runtimeEnvironmentId: null
+    })
     expect(mocks.state.fetchWorktrees).toHaveBeenCalledWith(repo.id, {
       requireAuthoritative: true,
       executionHostId: 'local'
@@ -179,13 +181,44 @@ describe('AddProjectFromFolderDialog', () => {
     renderToStaticMarkup(<AddProjectFromFolderDialog />)
     await clickAddProject()
 
-    expect(mocks.state.addRepoPath).toHaveBeenCalledWith('/projects/child')
+    expect(mocks.state.addRepoPath).toHaveBeenCalledWith('/projects/child', 'git', {
+      runtimeEnvironmentId: null
+    })
     expect(mocks.state.openModal).toHaveBeenCalledWith('confirm-non-git-folder', {
       folderPath: '/projects/child'
     })
     expect(mocks.state.fetchWorktrees).not.toHaveBeenCalled()
   })
 
+  it("routes a runtime project's subfolder and completion to the owning runtime", async () => {
+    const repo = makeRepo({ id: 'runtime-repo', executionHostId: 'runtime:runtime-a' })
+    mocks.state.modalData = {
+      folderPath: '/srv/projects/child',
+      runtimeEnvironmentId: 'runtime-a'
+    }
+    mocks.state.addRepoPath.mockResolvedValue(repo)
+    const { default: AddProjectFromFolderDialog } = await import('./AddProjectFromFolderDialog')
+
+    renderToStaticMarkup(<AddProjectFromFolderDialog />)
+    await clickAddProject()
+
+    expect(mocks.state.addRepoPath).toHaveBeenCalledWith('/srv/projects/child', 'git', {
+      runtimeEnvironmentId: 'runtime-a'
+    })
+    expect(mocks.state.fetchWorktrees).toHaveBeenCalledWith(repo.id, {
+      requireAuthoritative: true,
+      executionHostId: 'runtime:runtime-a'
+    })
+    expect(mocks.finishProjectAddWithDefaultCheckout).toHaveBeenCalledWith({
+      repoId: repo.id,
+      source: 'runtime_server_path',
+      selectedPath: '/srv/projects/child',
+      executionHostId: 'runtime:runtime-a',
+      closeModal: mocks.state.closeModal,
+      setHideDefaultBranchWorkspace: mocks.state.setHideDefaultBranchWorkspace
+    })
+  })
+
   it('adds an SSH Git folder through the remote repo import path', async () => {
     const repo = makeRepo({ id: 'remote-repo', connectionId: 'ssh-target-1' })
     mocks.state.modalData = {
diff --git a/src/renderer/src/components/sidebar/AddProjectFromFolderDialog.tsx b/src/renderer/src/components/sidebar/AddProjectFromFolderDialog.tsx
index 78a0f2b02..f3ef3b43c 100644
--- a/src/renderer/src/components/sidebar/AddProjectFromFolderDialog.tsx
+++ b/src/renderer/src/components/sidebar/AddProjectFromFolderDialog.tsx
@@ -39,6 +39,8 @@ const AddProjectFromFolderDialog = React.memo(function AddProjectFromFolderDialo
   const [previousOpen, setPreviousOpen] = useState(isOpen)
   const folderPath = typeof modalData.folderPath === 'string' ? modalData.folderPath : ''
   const connectionId = typeof modalData.connectionId === 'string' ? modalData.connectionId : ''
+  const runtimeEnvironmentId =
+    typeof modalData.runtimeEnvironmentId === 'string' ? modalData.runtimeEnvironmentId : null
 
   if (isOpen !== previousOpen) {
     setPreviousOpen(isOpen)
@@ -55,9 +57,12 @@ const AddProjectFromFolderDialog = React.memo(function AddProjectFromFolderDialo
     closeModal()
     openModal('confirm-non-git-folder', {
       folderPath,
-      ...(connectionId ? { connectionId } : {})
+      ...(connectionId ? { connectionId } : {}),
+      // Absence === local: NonGitFolderDialog coerces a missing/empty
+      // runtimeEnvironmentId to null, so omitting the spread signals local.
+      ...(runtimeEnvironmentId ? { runtimeEnvironmentId } : {})
     })
-  }, [closeModal, connectionId, folderPath, openModal])
+  }, [closeModal, connectionId, folderPath, openModal, runtimeEnvironmentId])
 
   const handleConfirm = useCallback(async () => {
     if (!folderPath || isAdding) {
@@ -94,7 +99,7 @@ const AddProjectFromFolderDialog = React.memo(function AddProjectFromFolderDialo
           { description: repo.displayName }
         )
       } else {
-        repo = await addRepoPath(folderPath)
+        repo = await addRepoPath(folderPath, 'git', { runtimeEnvironmentId })
       }
 
       if (!mountedRef.current || gen !== addGenRef.current) {
@@ -109,14 +114,18 @@ const AddProjectFromFolderDialog = React.memo(function AddProjectFromFolderDialo
       }
       // Why: after the repo is already added, a non-authoritative refresh
       // should still close onto the project row instead of trapping the user.
-      const ownerOptions = worktreeRefreshOptions(null, connectionId)
+      const ownerOptions = worktreeRefreshOptions(runtimeEnvironmentId, connectionId)
       await fetchWorktrees(repo.id, ownerOptions)
       if (!mountedRef.current || gen !== addGenRef.current) {
         return
       }
       await finishProjectAddWithDefaultCheckout({
         repoId: repo.id,
-        source: connectionId ? 'ssh_remote_path' : 'local_folder_picker',
+        source: connectionId
+          ? 'ssh_remote_path'
+          : runtimeEnvironmentId
+            ? 'runtime_server_path'
+            : 'local_folder_picker',
         selectedPath: folderPath,
         executionHostId: ownerOptions.executionHostId,
         closeModal,
@@ -147,6 +156,7 @@ const AddProjectFromFolderDialog = React.memo(function AddProjectFromFolderDialo
     isAdding,
     mountedRef,
     openNonGitConfirmation,
+    runtimeEnvironmentId,
     setHideDefaultBranchWorkspace
   ])
 
diff --git a/src/renderer/src/components/sidebar/project-added-default-checkout.test.ts b/src/renderer/src/components/sidebar/project-added-default-checkout.test.ts
index 0f5ad7cfe..8b4b42d8d 100644
--- a/src/renderer/src/components/sidebar/project-added-default-checkout.test.ts
+++ b/src/renderer/src/components/sidebar/project-added-default-checkout.test.ts
@@ -221,6 +221,26 @@ describe('finishProjectAddWithDefaultCheckout', () => {
     })
   })
 
+  it('activates a runtime-owned checkout even when its physical host is private SSH', async () => {
+    const runtimeMain = makeWorktree({
+      id: 'repo-1::runtime-ssh',
+      hostId: 'ssh:private-target',
+      runtimeOwnerEnvironmentId: 'env-1'
+    })
+    mocks.state.worktreesByRepo = { 'repo-1': [runtimeMain] }
+
+    await openProjectDefaultCheckout({
+      repoId: 'repo-1',
+      source: 'runtime_server_path',
+      executionHostId: 'runtime:env-1',
+      setHideDefaultBranchWorkspace: vi.fn()
+    })
+
+    expect(mocks.activateAndRevealWorktree).toHaveBeenCalledWith(runtimeMain.id, {
+      executionHostId: 'runtime:env-1'
+    })
+  })
+
   it('passes a contained selected path through as the initial terminal cwd', async () => {
     mocks.state.worktreesByRepo = {
       'repo-1': [makeWorktree()]
diff --git a/src/renderer/src/components/sidebar/project-added-default-checkout.ts b/src/renderer/src/components/sidebar/project-added-default-checkout.ts
index 0c7fc74f7..dabf089a8 100644
--- a/src/renderer/src/components/sidebar/project-added-default-checkout.ts
+++ b/src/renderer/src/components/sidebar/project-added-default-checkout.ts
@@ -9,7 +9,7 @@ import type { DetectedWorktreeListResult, Worktree } from '../../../../shared/ty
 import { relativePathInsideRoot } from '../../../../shared/cross-platform-path'
 import { markOnboardingProjectAdded } from '@/lib/onboarding-project-checklist'
 import { finalizeImportedRepoAfterSkip } from './add-repo-skip-finalization'
-import type { ExecutionHostId } from '../../../../shared/execution-host'
+import { parseExecutionHostId, type ExecutionHostId } from '../../../../shared/execution-host'
 
 type DefaultCheckoutHandoffReason = EventProps<'add_repo_default_checkout_handoff'>['reason']
 
@@ -24,12 +24,21 @@ function getProjectWorktreesForHost<T extends Worktree>(
   if (!executionHostId) {
     return [...worktrees]
   }
+  const parsedHost = parseExecutionHostId(executionHostId)
   return worktrees.filter((worktree) => {
-    if (worktree.hostId) {
+    if (parsedHost?.kind === 'runtime') {
+      if (worktree.runtimeOwnerEnvironmentId) {
+        return worktree.runtimeOwnerEnvironmentId === parsedHost.environmentId
+      }
+      // Reachable: a colliding repo id can carry a runtime-qualified hostId with
+      // no runtimeOwnerEnvironmentId, so match it against the execution host.
       return worktree.hostId === executionHostId
     }
     if (worktree.runtimeOwnerEnvironmentId) {
-      return executionHostId === `runtime:${encodeURIComponent(worktree.runtimeOwnerEnvironmentId)}`
+      return false
+    }
+    if (worktree.hostId) {
+      return worktree.hostId === executionHostId
     }
     return executionHostId === 'local'
   })
diff --git a/src/renderer/src/lib/worktree-runtime-owner-index.test.ts b/src/renderer/src/lib/worktree-runtime-owner-index.test.ts
new file mode 100644
index 000000000..0de6397e3
--- /dev/null
+++ b/src/renderer/src/lib/worktree-runtime-owner-index.test.ts
@@ -0,0 +1,90 @@
+import { describe, expect, it } from 'vitest'
+import { findIndexedWorktreeOwnerForHost } from './worktree-runtime-owner-index'
+
+describe('worktree runtime owner index', () => {
+  it('indexes paired worktrees by both runtime owner and physical host', () => {
+    const paired = {
+      id: 'repo-1::same-id',
+      repoId: 'repo-1',
+      hostId: 'ssh:private-target' as const,
+      runtimeOwnerEnvironmentId: 'hub-a'
+    }
+    const directSsh = {
+      id: 'repo-1::direct',
+      repoId: 'repo-1',
+      hostId: 'ssh:direct-target' as const
+    }
+    const worktreesByRepo = { 'repo-1': [paired, directSsh] }
+
+    expect(findIndexedWorktreeOwnerForHost(worktreesByRepo, paired.id, 'runtime:hub-a')).toBe(
+      paired
+    )
+    expect(findIndexedWorktreeOwnerForHost(worktreesByRepo, paired.id, 'ssh:private-target')).toBe(
+      paired
+    )
+    expect(
+      findIndexedWorktreeOwnerForHost(worktreesByRepo, directSsh.id, 'ssh:direct-target')
+    ).toBe(directSsh)
+    expect(
+      findIndexedWorktreeOwnerForHost(worktreesByRepo, directSsh.id, 'runtime:hub-a')
+    ).toBeNull()
+  })
+
+  it('fails closed when direct and paired worktrees share a physical host alias', () => {
+    const direct = {
+      id: 'same-id',
+      repoId: 'direct-repo',
+      hostId: 'ssh:private-target' as const
+    }
+    const paired = {
+      id: 'same-id',
+      repoId: 'paired-repo',
+      hostId: 'ssh:private-target' as const,
+      runtimeOwnerEnvironmentId: 'hub-a'
+    }
+
+    for (const worktrees of [
+      [direct, paired],
+      [paired, direct]
+    ]) {
+      const worktreesByRepo = { repo: worktrees }
+      expect(
+        findIndexedWorktreeOwnerForHost(worktreesByRepo, 'same-id', 'ssh:private-target')
+      ).toBeNull()
+      expect(findIndexedWorktreeOwnerForHost(worktreesByRepo, 'same-id', 'runtime:hub-a')).toBe(
+        paired
+      )
+    }
+  })
+
+  it('fails closed when paired worktrees share a runtime host alias', () => {
+    const pairedA = {
+      id: 'same-id',
+      repoId: 'repo-a',
+      hostId: 'ssh:private-a' as const,
+      runtimeOwnerEnvironmentId: 'hub-a'
+    }
+    const pairedB = {
+      id: 'same-id',
+      repoId: 'repo-b',
+      hostId: 'ssh:private-b' as const,
+      runtimeOwnerEnvironmentId: 'hub-a'
+    }
+
+    for (const worktrees of [
+      [pairedA, pairedB],
+      [pairedB, pairedA]
+    ]) {
+      const worktreesByRepo = { repo: worktrees }
+      expect(
+        findIndexedWorktreeOwnerForHost(worktreesByRepo, 'same-id', 'runtime:hub-a')
+      ).toBeNull()
+      expect(findIndexedWorktreeOwnerForHost(worktreesByRepo, 'same-id', 'ssh:private-a')).toBe(
+        pairedA
+      )
+      expect(findIndexedWorktreeOwnerForHost(worktreesByRepo, 'same-id', 'ssh:private-b')).toBe(
+        pairedB
+      )
+    }
+  })
+})
diff --git a/src/renderer/src/lib/worktree-runtime-owner-index.ts b/src/renderer/src/lib/worktree-runtime-owner-index.ts
index c9d2afbc4..25b1af478 100644
--- a/src/renderer/src/lib/worktree-runtime-owner-index.ts
+++ b/src/renderer/src/lib/worktree-runtime-owner-index.ts
@@ -156,13 +156,33 @@ function worktreeOwnerIdentity(owner: WorktreeOwnerRecord): string {
   ])
 }
 
-function worktreeOwnerHostId(owner: WorktreeOwnerRecord): ExecutionHostId {
-  return (
-    parseExecutionHostId(owner.hostId)?.id ??
-    (owner.runtimeOwnerEnvironmentId
-      ? toRuntimeExecutionHostId(owner.runtimeOwnerEnvironmentId)
-      : 'local')
-  )
+function addWorktreeOwnerIndexEntry(
+  index: Map<string, IndexedWorktreeOwnerResolution>,
+  key: string,
+  owner: WorktreeOwnerRecord
+): void {
+  const current = index.get(key)
+  if (!current) {
+    index.set(key, { kind: 'resolved', owner })
+  } else if (
+    current.kind === 'resolved' &&
+    worktreeOwnerIdentity(current.owner) !== worktreeOwnerIdentity(owner)
+  ) {
+    index.set(key, { kind: 'ambiguous' })
+  }
+}
+
+function worktreeOwnerHostIds(owner: WorktreeOwnerRecord): ExecutionHostId[] {
+  const physicalHostId = parseExecutionHostId(owner.hostId)?.id
+  const runtimeEnvironmentId = owner.runtimeOwnerEnvironmentId?.trim()
+  if (!runtimeEnvironmentId) {
+    return [physicalHostId ?? 'local']
+  }
+  const runtimeHostId = toRuntimeExecutionHostId(runtimeEnvironmentId)
+  // Why: paired HUB worktrees need logical-runtime lookup without losing their physical SSH route.
+  return physicalHostId && physicalHostId !== runtimeHostId
+    ? [physicalHostId, runtimeHostId]
+    : [runtimeHostId]
 }
 
 export function resolveIndexedWorktreeOwner(
@@ -178,19 +198,10 @@ export function resolveIndexedWorktreeOwner(
     for (const worktrees of Object.values(worktreesByRepo)) {
       for (const worktree of worktrees) {
         const id = worktree.id
-        const current = next.get(id)
-        if (!current) {
-          next.set(id, { kind: 'resolved', owner: worktree })
-        } else if (
-          current.kind === 'resolved' &&
-          worktreeOwnerIdentity(current.owner) !== worktreeOwnerIdentity(worktree)
-        ) {
-          next.set(id, { kind: 'ambiguous' })
+        addWorktreeOwnerIndexEntry(next, id, worktree)
+        for (const hostId of worktreeOwnerHostIds(worktree)) {
+          addWorktreeOwnerIndexEntry(next, `${id}\0${hostId}`, worktree)
         }
-        next.set(`${id}\0${worktreeOwnerHostId(worktree)}`, {
-          kind: 'resolved',
-          owner: worktree
-        })
       }
     }
     index = next