diff --git a/apps/desktop/DESIGN.md b/apps/desktop/DESIGN.md
index 53075c5d49bb..a9d585441ff1 100644
--- a/apps/desktop/DESIGN.md
+++ b/apps/desktop/DESIGN.md
@@ -192,7 +192,12 @@ Notes:
   semantics when unifying appearance.
 - Respect `AppShell` overlay ownership. Persistent terminal/content layers,
   route overlays, dialogs, and boot surfaces must not compete through ad-hoc
-  z-index literals.
+  z-index literals. Pick a rung of the ladder in `styles.css` instead —
+  `--z-modal-backdrop` / `--z-modal` / `--z-modal-popover`, `--z-over-modal`
+  (toasts, tooltips, command surfaces) and `--z-over-modal-content`,
+  `--z-switcher-backdrop` / `--z-switcher`, then the boot chain
+  `--z-connecting` → `--z-onboarding` → `--z-setup` → `--z-crash`. Plain
+  `z-10`/`z-20` are still right for stacking *within* one component.
 
 ## Iconography & brand
 
diff --git a/apps/desktop/e2e/fixtures.ts b/apps/desktop/e2e/fixtures.ts
index 1dabc674d043..3427d42c9bf3 100644
--- a/apps/desktop/e2e/fixtures.ts
+++ b/apps/desktop/e2e/fixtures.ts
@@ -230,6 +230,10 @@ export function buildAppEnv(sandbox: Sandbox, extra: Record<string, string> = {}
     HERMES_DESKTOP_IGNORE_EXISTING: '1',
     HERMES_DESKTOP_HERMES_ROOT: REPO_ROOT,
     HERMES_DESKTOP_APP_NAME: `HermesE2E-${Date.now()}`,
+    // `app.close()` in teardown must exit even when a spec leaves a turn
+    // mid-flight — otherwise the quit confirmation waits on a click that no
+    // one is there to make, and the worker dies on a teardown timeout.
+    HERMES_DESKTOP_SKIP_QUIT_CONFIRM: '1',
     // Clear dev-server override — we want the built dist/, not a vite server.
     // The dev-server check in main.ts looks for this env var; if it's set,
     // it loads from the vite URL instead of the local file.
diff --git a/apps/desktop/electron/main.ts b/apps/desktop/electron/main.ts
index d88e1f787601..7ac24c57f8ed 100644
--- a/apps/desktop/electron/main.ts
+++ b/apps/desktop/electron/main.ts
@@ -146,6 +146,7 @@ import { rehomePrimaryConnection } from './primary-connection-rehome'
 import { decideProfileDeleteAction, profileNameFromDeleteRequest, resolveRouteProfile } from './profile-delete-routing'
 import { fetchPrimaryProfileSessions } from './profile-session-routing'
 import { createQuickEntryShortcut, quickEntryWindowBounds, sanitizeQuickEntrySettings } from './quick-entry'
+import { type ActiveWork, mergeActiveWork, normalizeActiveWork, quitPromptFor } from './quit-guard'
 import * as remoteLifecycle from './remote-lifecycle'
 import {
   RemoteLivenessTracker,
@@ -607,6 +608,10 @@ const DESKTOP_LOG_DISCARD_BYTES = DESKTOP_LOG_MAX_BYTES * 4
 const desktopLogBackupPath = n => `${DESKTOP_LOG_PATH}.${n}`
 const BOOT_FAKE_MODE = process.env.HERMES_DESKTOP_BOOT_FAKE === '1'
 const BOOT_FAKE_ERROR = process.env.HERMES_DESKTOP_BOOT_FAKE_ERROR || ''
+// Automated teardown (Playwright's app.close(), harness scripts) quits with
+// nobody to answer a modal, so the active-work confirmation would hang the
+// caller instead of letting the process exit. Force quits set this.
+const SKIP_QUIT_CONFIRM = process.env.HERMES_DESKTOP_SKIP_QUIT_CONFIRM === '1'
 
 const BOOT_FAKE_STEP_MS = (() => {
   const raw = Number.parseInt(String(process.env.HERMES_DESKTOP_BOOT_FAKE_STEP_MS || ''), 10)
@@ -2510,6 +2515,12 @@ let updateInFlight = false
 // actually dies and the hand-off script can proceed immediately.
 let isQuittingForHandoff = false
 
+// Quit-guard latches: one while the confirmation is on screen (a second
+// Cmd-Q must not stack dialogs), one after the user has said "quit anyway"
+// (the app.quit() that follows re-enters before-quit and must pass through).
+let quitPromptOpen = false
+let quitConfirmedWithActiveWork = false
+
 // Resolve the staged updater binary. The Tauri installer copies itself to
 // HERMES_HOME/hermes-setup.exe on a successful install (see
 // apps/bootstrap-installer paths::copy_self_to_hermes_home). That binary owns
@@ -10134,6 +10145,20 @@ ipcMain.handle('hermes:watchPreviewFile', (_event, url) => watchPreviewFile(Stri
 
 ipcMain.handle('hermes:stopPreviewFileWatch', (_event, id) => stopPreviewFileWatch(String(id || '')))
 
+// Each renderer reports the turns it has in flight; the quit guard reads the
+// merged picture. Keyed by webContents id so a closed window stops counting.
+const activeWorkByWebContents = new Map<number, ActiveWork>()
+
+ipcMain.on('hermes:active-work', (event, payload) => {
+  const id = event.sender.id
+
+  if (!activeWorkByWebContents.has(id)) {
+    event.sender.once('destroyed', () => activeWorkByWebContents.delete(id))
+  }
+
+  activeWorkByWebContents.set(id, normalizeActiveWork(payload))
+})
+
 ipcMain.on('hermes:titlebar-theme', (_event, payload) => {
   if (!payload || !isHexColor(payload.background) || !isHexColor(payload.foreground)) {
     return
@@ -11399,7 +11424,58 @@ function configureSpellChecker() {
   }
 }
 
+// Ask before a quit kills a turn in flight. True when the quit was intercepted
+// and the confirmation is on screen; "Quit Anyway" re-enters before-quit with
+// the latch set and falls straight through to the teardown below.
+function heldQuitForActiveWork(event: Electron.Event): boolean {
+  if (SKIP_QUIT_CONFIRM || quitConfirmedWithActiveWork || quitPromptOpen) {
+    return false
+  }
+
+  const prompt = quitPromptFor(mergeActiveWork(activeWorkByWebContents.values()), isQuittingForHandoff)
+  const parent = BrowserWindow.getFocusedWindow() ?? BrowserWindow.getAllWindows()[0]
+
+  if (!prompt || !parent || parent.isDestroyed()) {
+    return false
+  }
+
+  event.preventDefault()
+  quitPromptOpen = true
+
+  void dialog
+    .showMessageBox(parent, {
+      buttons: ['Keep Running', 'Quit Anyway'],
+      cancelId: 0,
+      defaultId: 0,
+      detail: prompt.detail,
+      message: prompt.message,
+      type: 'question'
+    })
+    .then(({ response }) => {
+      quitPromptOpen = false
+
+      if (response === 1) {
+        quitConfirmedWithActiveWork = true
+        app.quit()
+      }
+    })
+    .catch(() => {
+      // A dialog we can't show must not become a quit we can't perform.
+      quitPromptOpen = false
+      quitConfirmedWithActiveWork = true
+      app.quit()
+    })
+
+  return true
+}
+
 app.on('before-quit', event => {
+  // Runs ahead of every teardown below, so "Keep Running" leaves the app
+  // exactly as it was.
+  if (heldQuitForActiveWork(event)) {
+    return
+  }
+
   if ((sshConnections.size > 0 || sshBootstrapCoordinator.promises().length > 0) && !sshQuitTeardownDone) {
     event.preventDefault()
     sshBootstrapCoordinator.cancelAll()
diff --git a/apps/desktop/electron/preload.ts b/apps/desktop/electron/preload.ts
index 99df85abd4c1..059a03986afe 100644
--- a/apps/desktop/electron/preload.ts
+++ b/apps/desktop/electron/preload.ts
@@ -114,6 +114,7 @@ contextBridge.exposeInMainWorld('hermesDesktop', {
   normalizePreviewTarget: (target, baseDir) => ipcRenderer.invoke('hermes:normalizePreviewTarget', target, baseDir),
   watchPreviewFile: url => ipcRenderer.invoke('hermes:watchPreviewFile', url),
   stopPreviewFileWatch: id => ipcRenderer.invoke('hermes:stopPreviewFileWatch', id),
+  setActiveWork: payload => ipcRenderer.send('hermes:active-work', payload),
   setTitleBarTheme: payload => ipcRenderer.send('hermes:titlebar-theme', payload),
   setNativeTheme: mode => ipcRenderer.send('hermes:native-theme', mode),
   setTranslucency: payload => ipcRenderer.send('hermes:translucency', payload),
diff --git a/apps/desktop/electron/quit-guard.test.ts b/apps/desktop/electron/quit-guard.test.ts
new file mode 100644
index 000000000000..8888f99b40f4
--- /dev/null
+++ b/apps/desktop/electron/quit-guard.test.ts
@@ -0,0 +1,62 @@
+import assert from 'node:assert/strict'
+
+import { test } from 'vitest'
+
+import { mergeActiveWork, normalizeActiveWork, quitPromptFor } from './quit-guard'
+
+test('normalizeActiveWork drops junk and keeps the count at least the title count', () => {
+  assert.deepEqual(normalizeActiveWork(null), { count: 0, titles: [] })
+  assert.deepEqual(normalizeActiveWork({ count: 'many', titles: 'nope' }), { count: 0, titles: [] })
+  assert.deepEqual(normalizeActiveWork({ count: -3, titles: ['  Fix login  ', '', 7] }), {
+    count: 1,
+    titles: ['Fix login']
+  })
+})
+
+test('normalizeActiveWork keeps untitled sessions in the count', () => {
+  assert.deepEqual(normalizeActiveWork({ count: 3, titles: ['Fix login'] }), { count: 3, titles: ['Fix login'] })
+})
+
+test('mergeActiveWork de-dupes a session two windows both report', () => {
+  const merged = mergeActiveWork([
+    { count: 2, titles: ['Fix login', 'Ship docs'] },
+    { count: 1, titles: ['Fix login'] }
+  ])
+
+  assert.deepEqual(merged, { count: 2, titles: ['Fix login', 'Ship docs'] })
+})
+
+test('quitPromptFor stays out of the way when nothing is running', () => {
+  assert.equal(quitPromptFor({ count: 0, titles: [] }, false), null)
+})
+
+test('quitPromptFor stays out of the way during an update handoff', () => {
+  assert.equal(quitPromptFor({ count: 2, titles: ['Fix login'] }, true), null)
+})
+
+test('quitPromptFor names the running chats', () => {
+  const prompt = quitPromptFor({ count: 2, titles: ['Fix login', 'Ship docs'] }, false)
+
+  assert.ok(prompt)
+  assert.equal(prompt.message, 'Hermes is still working on 2 chats.')
+  assert.ok(prompt.detail.includes('• Fix login'))
+  assert.ok(prompt.detail.includes('• Ship docs'))
+})
+
+test('quitPromptFor summarizes past the list cap and counts untitled work', () => {
+  const prompt = quitPromptFor({ count: 9, titles: ['a', 'b', 'c', 'd', 'e', 'f'] }, false)
+
+  assert.ok(prompt)
+  assert.equal(prompt.message, 'Hermes is still working on 9 chats.')
+  assert.ok(prompt.detail.includes('• d'))
+  assert.ok(!prompt.detail.includes('• e'))
+  assert.ok(prompt.detail.includes('• 5 more'))
+})
+
+test('quitPromptFor speaks singular for one chat', () => {
+  const prompt = quitPromptFor({ count: 1, titles: [] }, false)
+
+  assert.ok(prompt)
+  assert.equal(prompt.message, 'Hermes is still working on 1 chat.')
+  assert.ok(prompt.detail.includes('mid-turn'))
+})
diff --git a/apps/desktop/electron/quit-guard.ts b/apps/desktop/electron/quit-guard.ts
new file mode 100644
index 000000000000..e2bb40e59da5
--- /dev/null
+++ b/apps/desktop/electron/quit-guard.ts
@@ -0,0 +1,92 @@
+// Quitting with a turn in flight kills the backend mid-tool-call: the work is
+// lost, and anything the agent had half-written to disk stays half-written.
+// Renderers publish what they're running; the main process asks before it lets
+// that go. The decision + copy live here (pure, testable) so main.ts only owns
+// the IPC and the dialog call.
+
+const MAX_LISTED = 4
+
+export interface ActiveWork {
+  /** Titles of sessions running a turn. Untitled sessions contribute a count only. */
+  titles: string[]
+  /** Running turns, including untitled ones — always >= titles.length. */
+  count: number
+}
+
+export const NO_ACTIVE_WORK: ActiveWork = { count: 0, titles: [] }
+
+/** Coerce an IPC payload from an untrusted renderer into an ActiveWork. */
+export function normalizeActiveWork(payload: unknown): ActiveWork {
+  if (!payload || typeof payload !== 'object') {
+    return NO_ACTIVE_WORK
+  }
+
+  const raw = payload as { count?: unknown; titles?: unknown }
+
+  const titles = Array.isArray(raw.titles)
+    ? raw.titles
+        .filter((title): title is string => typeof title === 'string')
+        .map(title => title.trim())
+        .filter(Boolean)
+    : []
+
+  const count = typeof raw.count === 'number' && Number.isFinite(raw.count) ? Math.max(0, Math.floor(raw.count)) : 0
+
+  return { count: Math.max(count, titles.length), titles }
+}
+
+/** Merge every window's report into one. Windows can show the same session. */
+export function mergeActiveWork(reports: Iterable<ActiveWork>): ActiveWork {
+  const titles: string[] = []
+  let count = 0
+
+  for (const report of reports) {
+    count = Math.max(count, report.count)
+
+    for (const title of report.titles) {
+      if (!titles.includes(title)) {
+        titles.push(title)
+      }
+    }
+  }
+
+  return { count: Math.max(count, titles.length), titles }
+}
+
+export interface QuitPrompt {
+  detail: string
+  message: string
+}
+
+/**
+ * The confirmation to show, or null when quitting should just proceed.
+ *
+ * `quittingForHandoff` covers the update / swap / uninstall relaunches: those
+ * are the app replacing itself, not the user walking away, and a modal there
+ * would strand the detached script waiting on a PID that never exits.
+ */
+export function quitPromptFor(work: ActiveWork, quittingForHandoff: boolean): null | QuitPrompt {
+  if (quittingForHandoff || work.count < 1) {
+    return null
+  }
+
+  const listed = work.titles.slice(0, MAX_LISTED)
+  const remaining = work.count - listed.length
+  const lines = listed.map(title => `• ${title}`)
+
+  if (remaining > 0) {
+    lines.push(remaining === 1 ? '• 1 more' : `• ${remaining} more`)
+  }
+
+  return {
+    detail: [
+      lines.join('\n'),
+      lines.length > 0 ? '' : null,
+      'Quitting stops the agent mid-turn. Any work it has not finished writing is lost.'
+    ]
+      .filter(line => line !== null)
+      .join('\n')
+      .trim(),
+    message: work.count === 1 ? 'Hermes is still working on 1 chat.' : `Hermes is still working on ${work.count} chats.`
+  }
+}
diff --git a/apps/desktop/src/app/chat/sidebar/projects/base-branch-picker.tsx b/apps/desktop/src/app/chat/sidebar/projects/base-branch-picker.tsx
index c3870be01357..f07a3c04310b 100644
--- a/apps/desktop/src/app/chat/sidebar/projects/base-branch-picker.tsx
+++ b/apps/desktop/src/app/chat/sidebar/projects/base-branch-picker.tsx
@@ -119,7 +119,7 @@ export function BaseBranchPicker({
             <span className="shrink-0">{parts.after}</span>
           </Button>
         </PopoverTrigger>
-        <PopoverContent align="start" className="z-[140] min-w-(--radix-popover-trigger-width) p-0">
+        <PopoverContent align="start" className="z-(--z-modal-popover) min-w-(--radix-popover-trigger-width) p-0">
           <Command filter={(searchValue, search) => (searchValue.toLowerCase().includes(search.toLowerCase()) ? 1 : 0)}>
             <CommandInput autoFocus placeholder={p.baseBranchPlaceholder} />
             <CommandList className="max-h-64">
diff --git a/apps/desktop/src/app/command-palette/index.tsx b/apps/desktop/src/app/command-palette/index.tsx
index e86bd2415e39..55e19fc9d665 100644
--- a/apps/desktop/src/app/command-palette/index.tsx
+++ b/apps/desktop/src/app/command-palette/index.tsx
@@ -875,13 +875,13 @@ export function CommandPalette() {
     <DialogPrimitive.Root onOpenChange={setCommandPaletteOpen} open={open}>
       <DialogPrimitive.Portal>
         {/* Transparent overlay: keeps click-away + focus trap, but no dim/blur. */}
-        <DialogPrimitive.Overlay className="fixed inset-0 z-[200]" />
+        <DialogPrimitive.Overlay className="fixed inset-0 z-(--z-over-modal)" />
         <DialogPrimitive.Content
           aria-describedby={undefined}
           className={cn(
             HUD_POSITION,
             HUD_SURFACE,
-            'z-[210] w-[min(34rem,calc(100vw-2rem))] overflow-hidden duration-150 data-[state=closed]:animate-out data-[state=closed]:fade-out-0 data-[state=closed]:zoom-out-95 data-[state=open]:animate-in data-[state=open]:fade-in-0 data-[state=open]:slide-in-from-top-2 data-[state=open]:zoom-in-95'
+            'z-(--z-over-modal-content) w-[min(34rem,calc(100vw-2rem))] overflow-hidden duration-150 data-[state=closed]:animate-out data-[state=closed]:fade-out-0 data-[state=closed]:zoom-out-95 data-[state=open]:animate-in data-[state=open]:fade-in-0 data-[state=open]:slide-in-from-top-2 data-[state=open]:zoom-in-95'
           )}
         >
           <DialogPrimitive.Title className="sr-only">{t.commandCenter.paletteTitle}</DialogPrimitive.Title>
diff --git a/apps/desktop/src/app/pet-generate/components/provider-picker.tsx b/apps/desktop/src/app/pet-generate/components/provider-picker.tsx
index 3279d7758aa6..dad76c78d57e 100644
--- a/apps/desktop/src/app/pet-generate/components/provider-picker.tsx
+++ b/apps/desktop/src/app/pet-generate/components/provider-picker.tsx
@@ -31,9 +31,9 @@ export function ProviderPicker() {
           <ChevronDown className="size-3" />
         </button>
       </DropdownMenuTrigger>
-      {/* The picker lives inside the pet-gen Dialog (z-130) and portals to body,
-          so lift its menu above the dialog or it opens behind it. */}
-      <DropdownMenuContent align="start" className="z-[140]">
+      {/* The picker lives inside the pet-gen Dialog and portals to body, so its
+          menu needs the rung above the modal or it opens behind the dialog. */}
+      <DropdownMenuContent align="start" className="z-(--z-modal-popover)">
         {providers.map(provider => (
           <DropdownMenuItem
             className="flex items-center gap-1.5"
diff --git a/apps/desktop/src/app/session-switcher.tsx b/apps/desktop/src/app/session-switcher.tsx
index eb8df9136c1c..e7b2411e78f8 100644
--- a/apps/desktop/src/app/session-switcher.tsx
+++ b/apps/desktop/src/app/session-switcher.tsx
@@ -46,7 +46,7 @@ export function SessionSwitcher() {
     <>
       {/* Transparent click-catcher: click-away closes, but no dim/blur. */}
       <div
-        className="fixed inset-0 z-[219]"
+        className="fixed inset-0 z-(--z-switcher-backdrop)"
         onMouseDown={e => {
           e.preventDefault()
           closeSwitcher()
@@ -56,7 +56,7 @@ export function SessionSwitcher() {
         className={cn(
           HUD_POSITION,
           HUD_SURFACE,
-          'dt-portal-scrollbar z-[220] max-h-[min(22rem,64vh)] w-[min(19rem,calc(100vw-2rem))] select-none overflow-y-auto p-1'
+          'dt-portal-scrollbar z-(--z-switcher) max-h-[min(22rem,64vh)] w-[min(19rem,calc(100vw-2rem))] select-none overflow-y-auto p-1'
         )}
       >
         {sessions.map((session, i) => {
diff --git a/apps/desktop/src/components/assistant-ui/thread/status.tsx b/apps/desktop/src/components/assistant-ui/thread/status.tsx
index b239f0fb8a8f..5b9a5837c265 100644
--- a/apps/desktop/src/components/assistant-ui/thread/status.tsx
+++ b/apps/desktop/src/components/assistant-ui/thread/status.tsx
@@ -142,7 +142,11 @@ export const StreamStallIndicator: FC = () => {
     return `${s.message.content.length}:${textLength}`
   })
 
-  const [stalled, setStalled] = useState(false)
+  // Timestamp of the activity that preceded the current quiet spell, set once
+  // the spell qualifies as a stall. Holding the timestamp (not a boolean) is
+  // what lets the timer read "quiet for 12s" rather than the age of this
+  // component, which is the whole turn so far.
+  const [quietSince, setQuietSince] = useState<number | undefined>(undefined)
   const compacting = useStore($compactionActive)
   const turnTimerKey = useActiveTurnTimerKey()
   // A pending clarify / approval / sudo / secret means the turn is paused on the
@@ -151,14 +155,18 @@ export const StreamStallIndicator: FC = () => {
   const awaitingInput = useStore($activeSessionAwaitingInput)
 
   useEffect(() => {
-    setStalled(false)
-    const id = window.setTimeout(() => setStalled(true), STREAM_STALL_S * 1000)
+    setQuietSince(undefined)
+    const seenAt = Date.now()
+    const id = window.setTimeout(() => setQuietSince(seenAt), STREAM_STALL_S * 1000)
 
     return () => window.clearTimeout(id)
   }, [activity])
 
-  const active = (stalled || compacting) && !awaitingInput
-  const elapsed = useElapsedSeconds(active, compacting ? turnTimerKey : undefined)
+  const active = (quietSince !== undefined || compacting) && !awaitingInput
+
+  // Compaction owns the whole turn, so it keeps counting from the turn's start;
+  // a plain stall counts from the last thing the stream produced.
+  const elapsed = useElapsedSeconds(active, compacting ? turnTimerKey : undefined, compacting ? undefined : quietSince)
 
   if (!active) {
     return null
diff --git a/apps/desktop/src/components/boot-failure-overlay.tsx b/apps/desktop/src/components/boot-failure-overlay.tsx
index ea5ca27a1066..f07366f2898a 100644
--- a/apps/desktop/src/components/boot-failure-overlay.tsx
+++ b/apps/desktop/src/components/boot-failure-overlay.tsx
@@ -284,7 +284,7 @@ export function BootFailureOverlay() {
 
   if (view === 'connect') {
     return (
-      <div className="fixed inset-0 z-[1400] flex items-center justify-center bg-(--ui-chat-surface-background) p-6">
+      <div className="fixed inset-0 z-(--z-setup) flex items-center justify-center bg-(--ui-chat-surface-background) p-6">
         <div className="flex max-h-[86vh] w-full max-w-[46rem] flex-col overflow-hidden rounded-xl border border-(--stroke-nous) bg-(--ui-chat-bubble-background) shadow-nous">
           {/* Subtle back affordance (projects/overlay idiom): muted → foreground
               on hover, no divider. */}
@@ -307,7 +307,7 @@ export function BootFailureOverlay() {
   }
 
   return (
-    <div className="fixed inset-0 z-[1400] flex items-center justify-center bg-(--ui-chat-surface-background) p-6">
+    <div className="fixed inset-0 z-(--z-setup) flex items-center justify-center bg-(--ui-chat-surface-background) p-6">
       <div className="w-full max-w-[40rem] overflow-hidden rounded-xl border border-(--stroke-nous) bg-(--ui-chat-bubble-background) shadow-nous">
         <div className="flex items-start gap-3 px-5 py-4">
           <ErrorIcon className="mt-0.5" size="1.25rem" />
diff --git a/apps/desktop/src/components/chat/activity-timer.test.tsx b/apps/desktop/src/components/chat/activity-timer.test.tsx
index acc70a99ed06..4768f60c56ef 100644
--- a/apps/desktop/src/components/chat/activity-timer.test.tsx
+++ b/apps/desktop/src/components/chat/activity-timer.test.tsx
@@ -3,8 +3,8 @@ import { afterEach, beforeEach, describe, expect, it, vi } from 'vitest'
 
 import { __resetElapsedTimerRegistryForTests, useElapsedSeconds } from './activity-timer'
 
-function Probe({ active, timerKey }: { active: boolean; timerKey?: string }) {
-  const elapsed = useElapsedSeconds(active, timerKey)
+function Probe({ active, since, timerKey }: { active: boolean; since?: number; timerKey?: string }) {
+  const elapsed = useElapsedSeconds(active, timerKey, since)
 
   return <span data-testid="elapsed">{elapsed}</span>
 }
@@ -40,4 +40,30 @@ describe('useElapsedSeconds', () => {
 
     expect(screen.getByTestId('elapsed').textContent).toBe('8')
   })
+
+  it('counts from an explicit epoch rather than mount time', () => {
+    const mountedAt = Date.now()
+
+    act(() => {
+      vi.advanceTimersByTime(30_000)
+    })
+
+    render(<Probe active since={mountedAt + 28_000} />)
+
+    expect(screen.getByTestId('elapsed').textContent).toBe('2')
+  })
+
+  it('re-anchors when the epoch moves', () => {
+    const { rerender } = render(<Probe active since={Date.now()} />)
+
+    act(() => {
+      vi.advanceTimersByTime(10_000)
+    })
+
+    expect(screen.getByTestId('elapsed').textContent).toBe('10')
+
+    rerender(<Probe active since={Date.now()} />)
+
+    expect(screen.getByTestId('elapsed').textContent).toBe('0')
+  })
 })
diff --git a/apps/desktop/src/components/chat/activity-timer.ts b/apps/desktop/src/components/chat/activity-timer.ts
index afb27fb02f3b..9fe67642239d 100644
--- a/apps/desktop/src/components/chat/activity-timer.ts
+++ b/apps/desktop/src/components/chat/activity-timer.ts
@@ -30,13 +30,22 @@ export function formatElapsed(seconds: number): string {
   return `${Math.floor(seconds / 60)}:${String(seconds % 60).padStart(2, '0')}`
 }
 
-export function useElapsedSeconds(active = true, timerKey?: string): number {
-  const start = useRef(startedAt(timerKey))
+/**
+ * Seconds since the timer's origin, reported once a second while `active`.
+ *
+ * Origin, in order: an explicit `since` timestamp, else the `timerKey`'s
+ * registry entry (survives unmount/remount), else mount time. Pass `since` when
+ * the thing being measured started at a moment the caller knows and that moment
+ * isn't the mount — otherwise an anonymous timer reports the component's age,
+ * which is only the same number by accident.
+ */
+export function useElapsedSeconds(active = true, timerKey?: string, since?: number): number {
+  const start = useRef(since ?? startedAt(timerKey))
   const lastKey = useRef(timerKey)
   const [elapsed, setElapsed] = useState(() => Math.max(0, Math.floor((Date.now() - start.current) / 1000)))
 
   if (lastKey.current !== timerKey) {
-    start.current = startedAt(timerKey)
+    start.current = since ?? startedAt(timerKey)
     lastKey.current = timerKey
   }
 
@@ -46,7 +55,9 @@ export function useElapsedSeconds(active = true, timerKey?: string): number {
       return
     }
 
-    if (timerKey) {
+    if (since !== undefined) {
+      start.current = since
+    } else if (timerKey) {
       start.current = startedAt(timerKey)
     }
 
@@ -55,7 +66,7 @@ export function useElapsedSeconds(active = true, timerKey?: string): number {
     const id = window.setInterval(tick, 1000)
 
     return () => window.clearInterval(id)
-  }, [active, timerKey])
+  }, [active, since, timerKey])
 
   return elapsed
 }
diff --git a/apps/desktop/src/components/chat/diff-lines.tsx b/apps/desktop/src/components/chat/diff-lines.tsx
index edcf08e38f70..d7155bef2884 100644
--- a/apps/desktop/src/components/chat/diff-lines.tsx
+++ b/apps/desktop/src/components/chat/diff-lines.tsx
@@ -41,15 +41,15 @@ interface ParsedHunk {
 // plain renderer; the Shiki path omits it so syntax colors win, layering only
 // the background + border.
 const DIFF_KIND_TINT: Record<DiffKind, string> = {
-  add: 'border-emerald-500 bg-emerald-500/12',
+  add: 'border-(--ui-diff-add-border) bg-(--ui-diff-add-background)',
   context: 'border-transparent',
-  remove: 'border-rose-500 bg-rose-500/12'
+  remove: 'border-(--ui-diff-remove-border) bg-(--ui-diff-remove-background)'
 }
 
 const DIFF_KIND_TEXT: Record<DiffKind, string> = {
-  add: 'text-emerald-800 dark:text-emerald-200',
+  add: 'text-(--ui-diff-add-foreground)',
   context: '',
-  remove: 'text-rose-800 dark:text-rose-200'
+  remove: 'text-(--ui-diff-remove-foreground)'
 }
 
 const DIFF_LINE_BASE = 'block min-w-max whitespace-pre border-l-2 px-2.5 py-px'
@@ -537,7 +537,10 @@ function DiffOverviewRuler({ lines }: { lines: DiffLine[] }) {
       <div className="relative w-full" style={{ height: `min(100%, ${lines.length * PREVIEW_LINE_PX}px)` }}>
         {runs.map((run, index) => (
           <div
-            className={cn('absolute inset-x-0', run.kind === 'add' ? 'bg-(--ui-green)' : 'bg-(--ui-red)')}
+            className={cn(
+              'absolute inset-x-0',
+              run.kind === 'add' ? 'bg-(--ui-diff-add-border)' : 'bg-(--ui-diff-remove-border)'
+            )}
             key={index}
             style={{ height: `max(0.125rem, ${run.sizePct}%)`, top: `${run.startPct}%` }}
           />
diff --git a/apps/desktop/src/components/desktop-install-overlay.tsx b/apps/desktop/src/components/desktop-install-overlay.tsx
index 4941f6dd6bc4..4f814832395a 100644
--- a/apps/desktop/src/components/desktop-install-overlay.tsx
+++ b/apps/desktop/src/components/desktop-install-overlay.tsx
@@ -398,7 +398,7 @@ export function DesktopInstallOverlay({ enabled = true }: DesktopInstallOverlayP
 
   if (state.setupChoice) {
     return (
-      <div className="fixed inset-0 z-[1400] flex items-center justify-center bg-background/90 p-4 backdrop-blur-md">
+      <div className="fixed inset-0 z-(--z-setup) flex items-center justify-center bg-background/90 p-4 backdrop-blur-md">
         <div className="w-full max-w-2xl rounded-xl border border-(--stroke-nous) bg-card p-8 shadow-nous">
           <div className="flex items-start gap-4">
             <BrandMark className="size-11 shrink-0" />
@@ -478,7 +478,7 @@ export function DesktopInstallOverlay({ enabled = true }: DesktopInstallOverlayP
     const platformLabel = ups.platform === 'darwin' ? 'macOS' : ups.platform === 'linux' ? 'Linux' : ups.platform
 
     return (
-      <div className="fixed inset-0 z-[1400] flex items-center justify-center bg-background/90 backdrop-blur-md">
+      <div className="fixed inset-0 z-(--z-setup) flex items-center justify-center bg-background/90 backdrop-blur-md">
         <div className="w-full max-w-xl rounded-xl border border-(--stroke-nous) bg-card p-8 shadow-nous">
           <h2 className="text-xl font-semibold tracking-tight">{copy.oneTimeTitle}</h2>
           <p className="mt-2 text-sm text-muted-foreground">{copy.unsupportedDesc(platformLabel)}</p>
@@ -547,7 +547,7 @@ export function DesktopInstallOverlay({ enabled = true }: DesktopInstallOverlayP
   const currentElapsed = typeof currentStartedAt === 'number' ? formatElapsed(now - currentStartedAt) : ''
 
   return (
-    <div className="fixed inset-0 z-[1400] flex items-center justify-center bg-background/90 backdrop-blur-md p-4">
+    <div className="fixed inset-0 z-(--z-setup) flex items-center justify-center bg-background/90 backdrop-blur-md p-4">
       <div className="flex w-full max-w-2xl max-h-[90vh] flex-col rounded-xl border border-(--stroke-nous) bg-card shadow-nous">
         {/* Header -- always visible, never scrolls */}
         <div className="flex flex-shrink-0 items-start gap-4 p-8 pb-4">
diff --git a/apps/desktop/src/components/error-boundary.tsx b/apps/desktop/src/components/error-boundary.tsx
index 87b6b7743c51..f89f1d50673b 100644
--- a/apps/desktop/src/components/error-boundary.tsx
+++ b/apps/desktop/src/components/error-boundary.tsx
@@ -56,7 +56,7 @@ function RootErrorFallback({ error, reset }: ErrorBoundaryFallbackProps) {
   const { t } = useI18n()
 
   return (
-    <div className="fixed inset-0 z-[1500] grid place-items-center bg-(--ui-chat-surface-background) p-6">
+    <div className="fixed inset-0 z-(--z-crash) grid place-items-center bg-(--ui-chat-surface-background) p-6">
       <ErrorState
         className="w-full max-w-[28rem]"
         description={error.message || t.errors.boundaryDesc}
diff --git a/apps/desktop/src/components/first-run-remote-form.tsx b/apps/desktop/src/components/first-run-remote-form.tsx
index ced31acdd444..1bd6bf45b403 100644
--- a/apps/desktop/src/components/first-run-remote-form.tsx
+++ b/apps/desktop/src/components/first-run-remote-form.tsx
@@ -222,7 +222,7 @@ export function FirstRunRemoteForm({ onBack }: FirstRunRemoteFormProps) {
   }
 
   return (
-    <div className="fixed inset-0 z-[1400] flex items-center justify-center bg-background/90 p-4 backdrop-blur-md">
+    <div className="fixed inset-0 z-(--z-setup) flex items-center justify-center bg-background/90 p-4 backdrop-blur-md">
       <div className="flex w-full max-w-xl flex-col rounded-xl border border-(--stroke-nous) bg-card p-8 shadow-nous">
         <div className="flex items-start gap-4">
           <BrandMark className="size-11 shrink-0" />
diff --git a/apps/desktop/src/components/gateway-connecting-overlay.test.tsx b/apps/desktop/src/components/gateway-connecting-overlay.test.tsx
index 508dfb27f335..a63fd1c72b3c 100644
--- a/apps/desktop/src/components/gateway-connecting-overlay.test.tsx
+++ b/apps/desktop/src/components/gateway-connecting-overlay.test.tsx
@@ -10,7 +10,7 @@ import { BootFailureOverlay } from './boot-failure-overlay'
 import { GatewayConnectingOverlay } from './gateway-connecting-overlay'
 
 // Repro for the "remote gateway → stuck on CONNECTING, no way to settings"
-// report. The connecting overlay (z-1200, full-screen, pointer-events on) used
+// report. The connecting overlay (full-screen, pointer-events on) used
 // to be shown whenever `gatewayState !== 'open' && !boot.error`. The ONLY escape
 // hatch — BootFailureOverlay, which has "Use local gateway" / "Sign in" /
 // "Retry" — only renders when `boot.error` is set.
diff --git a/apps/desktop/src/components/gateway-connecting-overlay.tsx b/apps/desktop/src/components/gateway-connecting-overlay.tsx
index 0268755d5632..34303bb52cfc 100644
--- a/apps/desktop/src/components/gateway-connecting-overlay.tsx
+++ b/apps/desktop/src/components/gateway-connecting-overlay.tsx
@@ -141,7 +141,7 @@ export function GatewayConnectingOverlay() {
   return (
     <div
       className={cn(
-        'fixed inset-0 z-[1200] grid place-items-center bg-(--ui-chat-surface-background) transition-opacity duration-500 ease-out',
+        'fixed inset-0 z-(--z-connecting) grid place-items-center bg-(--ui-chat-surface-background) transition-opacity duration-500 ease-out',
         overlayHidden ? 'pointer-events-none opacity-0' : 'opacity-100'
       )}
     >
diff --git a/apps/desktop/src/components/model-picker.tsx b/apps/desktop/src/components/model-picker.tsx
index 65cc79bedf89..b38630d7e9b0 100644
--- a/apps/desktop/src/components/model-picker.tsx
+++ b/apps/desktop/src/components/model-picker.tsx
@@ -28,10 +28,10 @@ interface ModelPickerDialogProps {
   onSelect: (selection: { provider: string; model: string }) => void
   profile?: string
   /**
-   * Optional class to apply to DialogContent. Use to override z-index when
-   * stacking the picker on top of another fixed overlay (e.g. the desktop
-   * onboarding overlay, which sits at z-1300; the default Dialog z-130 ends
-   * up rendering underneath and blocks pointer events).
+   * Optional class for DialogContent. Use it to lift the picker onto a higher
+   * rung of the overlay ladder when it opens over another fixed overlay (the
+   * desktop onboarding overlay, say) — on the default modal rung it renders
+   * underneath and blocks pointer events.
    */
   contentClassName?: string
 }
@@ -85,7 +85,7 @@ export function ModelPickerDialog({
   // Open the full onboarding provider selector to add/switch a provider.
   // Reuses the entire onboarding flow (OAuth rows, API-key form, device-code,
   // model-confirm) instead of duplicating provider UI here. Closes the picker
-  // so the onboarding overlay (z-1300) isn't rendered underneath it.
+  // so the onboarding overlay isn't rendered underneath it.
   const addProvider = () => {
     startManualOnboarding()
     onOpenChange(false)
diff --git a/apps/desktop/src/components/notifications.tsx b/apps/desktop/src/components/notifications.tsx
index 4d4a3c1058fd..640603236494 100644
--- a/apps/desktop/src/components/notifications.tsx
+++ b/apps/desktop/src/components/notifications.tsx
@@ -92,9 +92,9 @@ export function NotificationStack() {
   )
 }
 
-// Portaled to <body> with a z above the Radix dialog layer (overlay z-[120],
-// content z-[130]) — see the top-center variant below for why.
-const REGION_BASE = 'pointer-events-none fixed z-[200] flex gap-2'
+// Portaled to <body> on the over-modal rung so a toast clears an open dialog —
+// see the top-center variant below for why.
+const REGION_BASE = 'pointer-events-none fixed z-(--z-over-modal) flex gap-2'
 
 // Primary stack: top-center, collapsed to the latest toast with a "+N more"
 // expander + clear-all — the noisy/important surface (errors, warnings,
diff --git a/apps/desktop/src/components/onboarding/flow.tsx b/apps/desktop/src/components/onboarding/flow.tsx
index a6499010c1a6..c81419fc847d 100644
--- a/apps/desktop/src/components/onboarding/flow.tsx
+++ b/apps/desktop/src/components/onboarding/flow.tsx
@@ -308,15 +308,14 @@ function ConfirmingModelPanel({
       </div>
 
       {/*
-        ModelPickerDialog defaults to z-130 on its content, which renders
-        UNDER the onboarding overlay (z-1300) and breaks pointer events.
-        Bump it above with z-[1310] so the picker sits on top of the
-        onboarding panel. The dialog's own dim-backdrop layer stays at
-        its default z-120 — the onboarding overlay is already dimming
-        the rest of the screen, so we don't want a second backdrop.
+        ModelPickerDialog's content sits on the modal rung, which is below the
+        onboarding overlay — it would render underneath and swallow pointer
+        events. Lift it to the rung above onboarding. Its own dim-backdrop
+        layer stays on the modal-backdrop rung: onboarding already dims the
+        rest of the screen, so a second backdrop would double up.
       */}
       <ModelPickerDialog
-        contentClassName="z-[1310]"
+        contentClassName="z-(--z-onboarding-popover)"
         currentModel={flow.currentModel}
         currentProvider={flow.providerSlug}
         onOpenChange={setPickerOpen}
diff --git a/apps/desktop/src/components/onboarding/index.tsx b/apps/desktop/src/components/onboarding/index.tsx
index 0acc4c044d8c..6fb2adfd8566 100644
--- a/apps/desktop/src/components/onboarding/index.tsx
+++ b/apps/desktop/src/components/onboarding/index.tsx
@@ -302,7 +302,7 @@ export function DesktopOnboardingOverlay({
   return (
     <div
       className={cn(
-        'fixed inset-0 z-1300 flex items-center justify-center bg-(--ui-chat-surface-background) p-6 transition-opacity duration-[520ms] ease-out',
+        'fixed inset-0 z-(--z-onboarding) flex items-center justify-center bg-(--ui-chat-surface-background) p-6 transition-opacity duration-[520ms] ease-out',
         // On the bare confirm screen, hold the surface (text-out + hold) so the
         // per-element exit plays before it dissolves.
         bare && leaving ? '[transition-delay:660ms]' : '',
diff --git a/apps/desktop/src/components/session-picker.tsx b/apps/desktop/src/components/session-picker.tsx
index 38600532ba15..b5926f39d05b 100644
--- a/apps/desktop/src/components/session-picker.tsx
+++ b/apps/desktop/src/components/session-picker.tsx
@@ -45,10 +45,10 @@ export function SessionPickerDialog({ activeStoredSessionId, onOpenChange, onRes
   return (
     <DialogPrimitive.Root onOpenChange={onOpenChange} open={open}>
       <DialogPrimitive.Portal>
-        <DialogPrimitive.Overlay className="fixed inset-0 z-[200] bg-black/15 backdrop-blur-[1px] data-[state=closed]:animate-out data-[state=closed]:fade-out-0 data-[state=open]:animate-in data-[state=open]:fade-in-0" />
+        <DialogPrimitive.Overlay className="fixed inset-0 z-(--z-over-modal) bg-black/15 backdrop-blur-[1px] data-[state=closed]:animate-out data-[state=closed]:fade-out-0 data-[state=open]:animate-in data-[state=open]:fade-in-0" />
         <DialogPrimitive.Content
           aria-describedby={undefined}
-          className="fixed left-1/2 top-[14vh] z-[210] w-[min(40rem,calc(100vw-2rem))] -translate-x-1/2 overflow-hidden rounded-xl border border-(--ui-stroke-secondary) bg-(--ui-chat-bubble-background) shadow-lg duration-150 data-[state=closed]:animate-out data-[state=closed]:fade-out-0 data-[state=closed]:zoom-out-95 data-[state=open]:animate-in data-[state=open]:fade-in-0 data-[state=open]:slide-in-from-top-2 data-[state=open]:zoom-in-95"
+          className="fixed left-1/2 top-[14vh] z-(--z-over-modal-content) w-[min(40rem,calc(100vw-2rem))] -translate-x-1/2 overflow-hidden rounded-xl border border-(--ui-stroke-secondary) bg-(--ui-chat-bubble-background) shadow-lg duration-150 data-[state=closed]:animate-out data-[state=closed]:fade-out-0 data-[state=closed]:zoom-out-95 data-[state=open]:animate-in data-[state=open]:fade-in-0 data-[state=open]:slide-in-from-top-2 data-[state=open]:zoom-in-95"
         >
           <DialogPrimitive.Title className="sr-only">{t.commandCenter.sections.sessions}</DialogPrimitive.Title>
           <Command className="bg-transparent" loop>
diff --git a/apps/desktop/src/components/ui/dialog.tsx b/apps/desktop/src/components/ui/dialog.tsx
index d84bb30c3453..7c69bdad8c4a 100644
--- a/apps/desktop/src/components/ui/dialog.tsx
+++ b/apps/desktop/src/components/ui/dialog.tsx
@@ -28,7 +28,7 @@ function DialogOverlay({ className, ...props }: React.ComponentProps<typeof Dial
   return (
     <DialogPrimitive.Overlay
       className={cn(
-        'fixed inset-0 z-[120] pointer-events-auto bg-black/22 backdrop-blur-[0.125rem] data-[state=closed]:animate-out data-[state=closed]:fade-out-0 data-[state=open]:animate-in data-[state=open]:fade-in-0',
+        'fixed inset-0 z-(--z-modal-backdrop) pointer-events-auto bg-black/22 backdrop-blur-[0.125rem] data-[state=closed]:animate-out data-[state=closed]:fade-out-0 data-[state=open]:animate-in data-[state=open]:fade-in-0',
         className
       )}
       data-slot="dialog-overlay"
@@ -130,7 +130,7 @@ function DialogContent({
         <DialogOverlay />
         <DialogPrimitive.Content
           className={cn(
-            'fixed left-1/2 top-1/2 z-[130] pointer-events-auto flex max-h-[85vh] -translate-x-1/2 -translate-y-1/2 flex-col overflow-hidden rounded-xl bg-(--ui-chat-bubble-background) text-[length:var(--conversation-text-font-size)] text-foreground shadow-nous duration-200 data-[state=closed]:animate-out data-[state=closed]:fade-out-0 data-[state=closed]:zoom-out-95 data-[state=open]:animate-in data-[state=open]:fade-in-0 data-[state=open]:zoom-in-95',
+            'fixed left-1/2 top-1/2 z-(--z-modal) pointer-events-auto flex max-h-[85vh] -translate-x-1/2 -translate-y-1/2 flex-col overflow-hidden rounded-xl bg-(--ui-chat-bubble-background) text-[length:var(--conversation-text-font-size)] text-foreground shadow-nous duration-200 data-[state=closed]:animate-out data-[state=closed]:fade-out-0 data-[state=closed]:zoom-out-95 data-[state=open]:animate-in data-[state=open]:fade-in-0 data-[state=open]:zoom-in-95',
             widthClass,
             className,
             // Callers often pass `gap-*` for the no-banner grid layout — suppress
@@ -174,7 +174,7 @@ function DialogContent({
           // Cap height at 85vh and let long content scroll inside the dialog
           // instead of overflowing off-screen (long cron titles, tool detail
           // dumps, etc.). Individual dialogs can still override via className.
-          'fixed left-1/2 top-1/2 z-[130] pointer-events-auto grid max-h-[85vh] -translate-x-1/2 -translate-y-1/2 gap-3 overflow-y-auto rounded-xl border border-(--stroke-nous) bg-(--ui-chat-bubble-background) p-4 text-[length:var(--conversation-text-font-size)] text-foreground shadow-nous duration-200 data-[state=closed]:animate-out data-[state=closed]:fade-out-0 data-[state=closed]:zoom-out-95 data-[state=open]:animate-in data-[state=open]:fade-in-0 data-[state=open]:zoom-in-95',
+          'fixed left-1/2 top-1/2 z-(--z-modal) pointer-events-auto grid max-h-[85vh] -translate-x-1/2 -translate-y-1/2 gap-3 overflow-y-auto rounded-xl border border-(--stroke-nous) bg-(--ui-chat-bubble-background) p-4 text-[length:var(--conversation-text-font-size)] text-foreground shadow-nous duration-200 data-[state=closed]:animate-out data-[state=closed]:fade-out-0 data-[state=closed]:zoom-out-95 data-[state=open]:animate-in data-[state=open]:fade-in-0 data-[state=open]:zoom-in-95',
           widthClass,
           className
         )}
diff --git a/apps/desktop/src/components/ui/select.tsx b/apps/desktop/src/components/ui/select.tsx
index 151316eec0c4..059575a1c826 100644
--- a/apps/desktop/src/components/ui/select.tsx
+++ b/apps/desktop/src/components/ui/select.tsx
@@ -53,7 +53,7 @@ function SelectContent({
     <SelectPrimitive.Portal container={container}>
       <SelectPrimitive.Content
         className={cn(
-          'relative z-[140] max-h-72 min-w-32 overflow-hidden rounded-md border border-border bg-popover text-popover-foreground shadow-md data-[state=open]:animate-in data-[state=closed]:animate-out data-[state=closed]:fade-out-0 data-[state=open]:fade-in-0 data-[state=closed]:zoom-out-95 data-[state=open]:zoom-in-95 data-[side=bottom]:slide-in-from-top-2 data-[side=left]:slide-in-from-right-2 data-[side=top]:slide-in-from-bottom-2 data-[side=right]:slide-in-from-left-2',
+          'relative z-(--z-modal-popover) max-h-72 min-w-32 overflow-hidden rounded-md border border-border bg-popover text-popover-foreground shadow-md data-[state=open]:animate-in data-[state=closed]:animate-out data-[state=closed]:fade-out-0 data-[state=open]:fade-in-0 data-[state=closed]:zoom-out-95 data-[state=open]:zoom-in-95 data-[side=bottom]:slide-in-from-top-2 data-[side=left]:slide-in-from-right-2 data-[side=top]:slide-in-from-bottom-2 data-[side=right]:slide-in-from-left-2',
           position === 'popper' &&
             'data-[side=bottom]:translate-y-1 data-[side=left]:-translate-x-1 data-[side=right]:translate-x-1 data-[side=top]:-translate-y-1',
           className
diff --git a/apps/desktop/src/components/ui/tooltip.tsx b/apps/desktop/src/components/ui/tooltip.tsx
index 226bd9472b3f..fc84933294c3 100644
--- a/apps/desktop/src/components/ui/tooltip.tsx
+++ b/apps/desktop/src/components/ui/tooltip.tsx
@@ -82,7 +82,7 @@ function TooltipContent({
         // rectangular dead space). Instant, no transition (delayDuration=0).
         // pointer-events-none: the tip must never steal hover/clicks from the
         // chrome underneath (titlebar tools, adjacent tabs, etc.).
-        className={cn('pointer-events-none z-[200] w-fit max-w-64 select-none', className)}
+        className={cn('pointer-events-none z-(--z-over-modal) w-fit max-w-64 select-none', className)}
         data-slot="tooltip-content"
         sideOffset={sideOffset}
         {...props}
diff --git a/apps/desktop/src/global.d.ts b/apps/desktop/src/global.d.ts
index 1e6225bb2094..03af8c62adf0 100644
--- a/apps/desktop/src/global.d.ts
+++ b/apps/desktop/src/global.d.ts
@@ -124,6 +124,7 @@ declare global {
       normalizePreviewTarget: (target: string, baseDir?: string) => Promise<HermesPreviewTarget | null>
       watchPreviewFile: (url: string) => Promise<HermesPreviewWatch>
       stopPreviewFileWatch: (id: string) => Promise<boolean>
+      setActiveWork?: (payload: HermesActiveWork) => void
       setTitleBarTheme?: (payload: HermesTitleBarTheme) => void
       setNativeTheme?: (mode: 'dark' | 'light' | 'system') => void
       setTranslucency?: (payload: { intensity: number }) => void
@@ -458,6 +459,12 @@ export interface HermesTitleBarTheme {
   foreground: string
 }
 
+/** Turns in flight, so the main process can confirm before a quit kills them. */
+export interface HermesActiveWork {
+  count: number
+  titles: string[]
+}
+
 export interface HermesWindowState {
   isFullscreen: boolean
   isMinimized?: boolean
diff --git a/apps/desktop/src/main.tsx b/apps/desktop/src/main.tsx
index 9aec2131073c..9a14e26e457e 100644
--- a/apps/desktop/src/main.tsx
+++ b/apps/desktop/src/main.tsx
@@ -1,4 +1,6 @@
 import './styles.css'
+// Side-effect: reports in-flight turns to the main process for the quit guard.
+import './store/active-work'
 // Side-effect: applies the persisted window translucency on load.
 import './store/translucency'
 // Dev-only render/state churn counters. MUST precede the `react-dom` import
diff --git a/apps/desktop/src/store/active-work.test.ts b/apps/desktop/src/store/active-work.test.ts
new file mode 100644
index 000000000000..fbff83737399
--- /dev/null
+++ b/apps/desktop/src/store/active-work.test.ts
@@ -0,0 +1,60 @@
+import { beforeAll, beforeEach, describe, expect, it, vi } from 'vitest'
+
+import type { ClientSessionState } from '@/app/types'
+
+import { $sessions } from './session'
+import { clearAllSessionStates, publishSessionState } from './session-states'
+
+const desktopWindow = window as unknown as { hermesDesktop?: Window['hermesDesktop'] }
+const setActiveWork = vi.fn()
+
+const busy = (storedSessionId: string, isBusy: boolean) =>
+  ({ busy: isBusy, needsInput: false, storedSessionId }) as ClientSessionState
+
+const session = (id: string, title: null | string) => ({ id, title }) as (typeof $sessions.value)[number]
+
+beforeAll(async () => {
+  desktopWindow.hermesDesktop = { setActiveWork } as unknown as Window['hermesDesktop']
+  // Subscribes at import time, so the bridge has to exist first.
+  await import('./active-work')
+})
+
+beforeEach(() => {
+  clearAllSessionStates()
+  $sessions.set([])
+  setActiveWork.mockClear()
+})
+
+describe('active work bridge', () => {
+  it('reports a busy session by title', () => {
+    $sessions.set([session('s1', 'Fix login'), session('s2', 'Idle chat')])
+    publishSessionState('runtime-1', busy('s1', true))
+
+    expect(setActiveWork).toHaveBeenLastCalledWith({ count: 1, titles: ['Fix login'] })
+  })
+
+  it('counts an untitled busy session without inventing a title', () => {
+    $sessions.set([session('s1', null)])
+    publishSessionState('runtime-1', busy('s1', true))
+
+    expect(setActiveWork).toHaveBeenLastCalledWith({ count: 1, titles: [] })
+  })
+
+  it('drops back to nothing when the turn ends', () => {
+    $sessions.set([session('s1', 'Fix login')])
+    publishSessionState('runtime-1', busy('s1', true))
+    publishSessionState('runtime-1', busy('s1', false))
+
+    expect(setActiveWork).toHaveBeenLastCalledWith({ count: 0, titles: [] })
+  })
+
+  it('does not re-send an unchanged summary', () => {
+    $sessions.set([session('s1', 'Fix login')])
+    publishSessionState('runtime-1', busy('s1', true))
+    setActiveWork.mockClear()
+
+    $sessions.set([session('s1', 'Fix login'), session('s2', 'Something else')])
+
+    expect(setActiveWork).not.toHaveBeenCalled()
+  })
+})
diff --git a/apps/desktop/src/store/active-work.ts b/apps/desktop/src/store/active-work.ts
new file mode 100644
index 000000000000..4d22916ff487
--- /dev/null
+++ b/apps/desktop/src/store/active-work.ts
@@ -0,0 +1,42 @@
+/**
+ * Mirror of "which chats are mid-turn" to the main process.
+ *
+ * The renderer is the only side that knows a turn is in flight, and the main
+ * process is the only side that can intercept a quit. This module bridges the
+ * two: it publishes a small summary on every membership change, and
+ * `electron/quit-guard.ts` turns that into the confirmation dialog.
+ *
+ * Imported for its side effect from `main.tsx`, alongside `store/translucency`.
+ */
+
+import { computed } from 'nanostores'
+
+import type { HermesActiveWork } from '@/global'
+import { $sessions } from '@/store/session'
+import { $workingSessionIds } from '@/store/session-states'
+
+const $activeWork = computed([$workingSessionIds, $sessions], (workingIds, sessions): HermesActiveWork => {
+  const titleById = new Map(sessions.map(session => [session.id, session.title?.trim() ?? '']))
+
+  return {
+    count: workingIds.length,
+    titles: workingIds.map(id => titleById.get(id) ?? '').filter(Boolean)
+  }
+})
+
+if (typeof window !== 'undefined') {
+  // `$sessions` republishes on unrelated churn (previews, heartbeats), so only
+  // send when the summary itself moved — this crosses a process boundary.
+  let lastSent = ''
+
+  $activeWork.subscribe(work => {
+    const next = JSON.stringify(work)
+
+    if (next === lastSent) {
+      return
+    }
+
+    lastSent = next
+    window.hermesDesktop?.setActiveWork?.(work)
+  })
+}
diff --git a/apps/desktop/src/store/gateway.ts b/apps/desktop/src/store/gateway.ts
index 61b6f46abcc7..f9e89ca434d9 100644
--- a/apps/desktop/src/store/gateway.ts
+++ b/apps/desktop/src/store/gateway.ts
@@ -2,6 +2,7 @@ import { type ConnectionState, type GatewayEvent, resolveGatewayWsUrl } from '@h
 import { atom } from 'nanostores'
 
 import { HermesGateway } from '@/hermes'
+import { markNativeNotifyBaseline } from '@/store/notify-baseline'
 import { setGatewayState } from '@/store/session'
 
 // ── Multi-profile gateway routing ──────────────────────────────────────────
@@ -136,6 +137,12 @@ export function activeGateway(): HermesGateway | null {
 // composer reflect the active profile's socket without a background reconnect
 // flipping the foreground enabled/disabled state.
 function reportGatewayState(profile: string, state: ConnectionState): void {
+  // Any socket opening replays parked prompts; hold OS notifications so a
+  // launch/reconnect doesn't alert about state that already existed.
+  if (state === 'open') {
+    markNativeNotifyBaseline()
+  }
+
   if (normKey(profile) === g.activeKey) {
     setGatewayState(state)
   }
diff --git a/apps/desktop/src/store/native-notifications.test.ts b/apps/desktop/src/store/native-notifications.test.ts
index de0bf8765426..4ebfd95a88e9 100644
--- a/apps/desktop/src/store/native-notifications.test.ts
+++ b/apps/desktop/src/store/native-notifications.test.ts
@@ -9,6 +9,7 @@ import {
   setNativeNotifyEnabled,
   setNativeNotifyKind
 } from './native-notifications'
+import { __resetNativeNotifyBaselineForTests, markNativeNotifyBaseline } from './notify-baseline'
 import { $approvalRequest, setApprovalRequest } from './prompts'
 import { $activeSessionId, setActiveSessionId } from './session'
 
@@ -43,6 +44,7 @@ beforeEach(() => {
 
   setActiveSessionId(null)
   setWindowState({ focused: false, hidden: true })
+  __resetNativeNotifyBaselineForTests()
 })
 
 afterEach(() => {
@@ -139,6 +141,35 @@ describe('dispatchNativeNotification preferences', () => {
   })
 })
 
+describe('dispatchNativeNotification post-connect baseline', () => {
+  it('suppresses a prompt replayed right after a socket opens', () => {
+    markNativeNotifyBaseline()
+    dispatchNativeNotification({ kind: 'approval', sessionId: freshSession(), title: 'approve' })
+    expect(notify).not.toHaveBeenCalled()
+  })
+
+  it('suppresses a completion replayed right after a socket opens', () => {
+    const sessionId = freshSession()
+    setActiveSessionId(sessionId)
+    markNativeNotifyBaseline()
+    dispatchNativeNotification({ kind: 'turnDone', sessionId, title: 'done' })
+    expect(notify).not.toHaveBeenCalled()
+  })
+
+  it('fires again once the window has passed', () => {
+    vi.useFakeTimers()
+
+    try {
+      markNativeNotifyBaseline()
+      vi.advanceTimersByTime(5000)
+      dispatchNativeNotification({ kind: 'approval', sessionId: freshSession(), title: 'approve' })
+      expect(notify).toHaveBeenCalledTimes(1)
+    } finally {
+      vi.useRealTimers()
+    }
+  })
+})
+
 describe('dispatchNativeNotification throttle', () => {
   it('collapses duplicate kind+session within the throttle window', () => {
     const sessionId = freshSession()
diff --git a/apps/desktop/src/store/native-notifications.ts b/apps/desktop/src/store/native-notifications.ts
index db56d94a3fa4..450360b7666c 100644
--- a/apps/desktop/src/store/native-notifications.ts
+++ b/apps/desktop/src/store/native-notifications.ts
@@ -3,6 +3,7 @@ import { atom } from 'nanostores'
 import { persistString, storedString } from '@/lib/storage'
 
 import { $gateway } from './gateway'
+import { withinNativeNotifyBaseline } from './notify-baseline'
 import { clearApprovalRequest } from './prompts'
 import { $activeSessionId } from './session'
 
@@ -160,6 +161,10 @@ export function dispatchNativeNotification(input: NativeNotificationInput): void
     return
   }
 
+  if (withinNativeNotifyBaseline()) {
+    return
+  }
+
   if (!shouldFire(input.kind, input.sessionId, input.global)) {
     return
   }
diff --git a/apps/desktop/src/store/notify-baseline.ts b/apps/desktop/src/store/notify-baseline.ts
new file mode 100644
index 000000000000..e48fde8ba138
--- /dev/null
+++ b/apps/desktop/src/store/notify-baseline.ts
@@ -0,0 +1,30 @@
+// Post-connect quiet window for native (OS) notifications.
+//
+// A socket opening replays state that already existed: a session parked on an
+// approval re-emits its request so the UI can render the prompt. Those are not
+// things that just happened, so launching Hermes — or any reconnect, profile
+// switch, or gateway-mode apply — would otherwise fire an OS notification for a
+// prompt the user has known about for an hour. The in-app surfaces (sidebar
+// row, inline approval bar) still show the prompt immediately; only the OS
+// notification is held.
+//
+// Lives in its own leaf module so `store/gateway` (which marks the baseline)
+// and `store/native-notifications` (which reads it) don't import each other.
+
+const SEED_QUIET_MS = 4000
+
+let quietUntil = 0
+
+/** Called on every gateway `open`. Opens the quiet window. */
+export function markNativeNotifyBaseline(): void {
+  quietUntil = Date.now() + SEED_QUIET_MS
+}
+
+/** True while replayed post-connect state should not raise an OS notification. */
+export function withinNativeNotifyBaseline(): boolean {
+  return Date.now() < quietUntil
+}
+
+export function __resetNativeNotifyBaselineForTests(): void {
+  quietUntil = 0
+}
diff --git a/apps/desktop/src/styles.css b/apps/desktop/src/styles.css
index 0f7fdbdd3b47..9fb935bbe088 100644
--- a/apps/desktop/src/styles.css
+++ b/apps/desktop/src/styles.css
@@ -188,6 +188,38 @@
     --context-usage-subagents: color-mix(in srgb, var(--ui-blue) 70%, var(--ui-cyan));
     --context-usage-memory: color-mix(in srgb, var(--ui-orange) 80%, var(--ui-yellow));
     --context-usage-conversation: var(--ui-cyan);
+    /* Diff add/remove, derived from the semantic palette so every diff surface
+       (tool cards, preview, review pane) tracks the theme's green/red. Only the
+       foregrounds need a dark override — they mix toward the page instead of
+       away from it. */
+    --ui-diff-add-border: var(--ui-green);
+    --ui-diff-add-background: color-mix(in srgb, var(--ui-green) 12%, transparent);
+    --ui-diff-add-foreground: color-mix(in srgb, var(--ui-green) 70%, #000);
+    --ui-diff-remove-border: var(--ui-red);
+    --ui-diff-remove-background: color-mix(in srgb, var(--ui-red) 12%, transparent);
+    --ui-diff-remove-foreground: color-mix(in srgb, var(--ui-red) 70%, #000);
+
+    /* Overlay ladder. DESIGN.md: app-wide surfaces must not compete through
+       ad-hoc z-index literals — pick the rung that describes the surface.
+       Values are deliberately sparse so a one-off can slot between two rungs
+       without a renumber. Local stacking inside a component (a sticky header
+       over its own scroll area) stays on plain `z-10`/`z-20`; these rungs are
+       only for surfaces that float over the app. */
+    --z-modal-backdrop: 120;
+    --z-modal: 130;
+    /* A select/dropdown/popover opened from inside a modal, portaled to body. */
+    --z-modal-popover: 140;
+    /* Must clear any open modal: toasts, tooltips, command-surface backdrops. */
+    --z-over-modal: 200;
+    --z-over-modal-content: 210;
+    --z-switcher-backdrop: 219;
+    --z-switcher: 220;
+    /* Boot and blocking states, in the order they can stack. */
+    --z-connecting: 1200;
+    --z-onboarding: 1300;
+    --z-onboarding-popover: 1310;
+    --z-setup: 1400;
+    --z-crash: 1500;
     --ui-bg-chrome: color-mix(
       in srgb,
       var(--theme-background-seed) var(--theme-mix-chrome),
@@ -444,6 +476,8 @@
     --ui-red: #e75e78;
     --ui-green: #55a583;
     --ui-cyan: #6f9ba6;
+    --ui-diff-add-foreground: color-mix(in srgb, var(--ui-green) 62%, #fff);
+    --ui-diff-remove-foreground: color-mix(in srgb, var(--ui-red) 62%, #fff);
 
     --sidebar-edge-border: color-mix(in srgb, var(--ui-base) 12%, transparent);
     --composer-ring-strength: 1.3;