[codex] Move instance settings under company settings (#7680)

## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - Operators manage both company-scoped configuration and
instance-level runtime/admin settings from the board UI
> - Instance settings previously lived as their own top-level sidebar
area, separate from the company settings context operators already use
> - That split made settings navigation feel heavier and made instance
configuration less discoverable from the settings tab
> - This pull request moves instance settings under company settings
while preserving the existing instance settings routes and plugin/admin
surfaces
> - The benefit is a smaller primary sidebar and a more coherent
settings hierarchy for operators

## Linked Issues or Issue Description

- Refs #338
- Internal: PAP-10491, PAP-10538

## What Changed

- Moved instance settings navigation under the company settings area.
- Added route helpers and sidebar entries for nested instance settings
paths.
- Updated plugin/admin settings routes to use the company settings
instance scope.
- Preserved legacy instance-settings bookmarks through compatibility
redirects that keep the active company prefix.
- Updated focused UI and plugin tests for the new navigation shape.
- Stabilized the process-loss retry test that was failing the serialized
server shard in CI.
- Rebased the branch onto current `paperclipai/paperclip` `master` and
pushed the current head.

## Verification

- `pnpm exec vitest run
ui/src/components/CompanySettingsSidebar.test.tsx
ui/src/components/access/CompanySettingsNav.test.tsx
ui/src/lib/instance-settings.test.ts
ui/src/components/InstanceSidebar.test.tsx
ui/src/components/Layout.test.tsx
ui/src/components/SidebarAccountMenu.test.tsx
ui/src/pages/PluginPage.test.tsx ui/src/plugins/bridge.test.ts
packages/shared/src/validators/plugin.test.ts`
- `pnpm exec vitest run ui/src/lib/instance-settings.test.ts
ui/src/components/CompanySettingsSidebar.test.tsx
ui/src/components/access/CompanySettingsNav.test.tsx
ui/src/components/Layout.test.tsx ui/src/plugins/bridge.test.ts`
- `pnpm exec vitest run
server/src/__tests__/heartbeat-process-recovery.test.ts -t "queues
exactly one retry when the recorded local pid is dead"`
- `pnpm test:run:serialized -- --shard-index 0 --shard-count 4`
- GitHub PR checks are green on head
`fe7b0955169dcae55cbe10889c1876a70ab0b80c`, including `verify`, `General
tests (server)`, all serialized server shards, build, e2e, policy,
security checks, and Greptile.
- Confirmed the PR diff does not include `pnpm-lock.yaml` or
`.github/workflows` changes.

## Risks

- Medium UI/navigation risk: instance settings links are intentionally
moving under company settings, so stale external bookmarks to legacy
paths rely on the compatibility routing in this branch.
- Low test-only risk from the CI stabilization commit: it makes the
recovery assertion select the actual retry run by `retryOfRunId` instead
of whichever non-original run appears first.
- No database migrations.
- No dependency lockfile or workflow changes.

> For core feature work, check [`ROADMAP.md`](ROADMAP.md) first and
discuss it in `#dev` before opening the PR. Feature PRs that overlap
with planned core work may need to be redirected — check the roadmap
first. See `CONTRIBUTING.md`.

## Model Used

- OpenAI Codex coding agent based on GPT-5, with shell/tool execution in
a local repository worktree. Exact context window was not exposed by the
runtime.

## Checklist

- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with version and capability
details)
- [x] I have checked ROADMAP.md and confirmed this PR does not duplicate
planned core work
- [x] I have searched GitHub for duplicate or related PRs and linked
them above
- [x] I have either (a) linked existing issues with `Fixes: #` / `Closes
#` / `Refs #` OR (b) described the issue in-PR following the relevant
issue template
- [x] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [ ] If this change affects the UI, I have included before/after
screenshots
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] All Paperclip CI gates are green
- [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [x] I will address all Greptile and reviewer comments before
requesting merge

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>

ui/src/components/Layout.tsx

@@ -2,7 +2,6 @@ import { useCallback, useEffect, useMemo, useRef, useState } from "react";
 import { useQuery } from "@tanstack/react-query";
 import { Outlet, useLocation, useNavigate, useNavigationType, useParams } from "@/lib/router";
 import { Sidebar } from "./Sidebar";
-import { InstanceSidebar } from "./InstanceSidebar";
 import { CompanySettingsSidebar } from "./CompanySettingsSidebar";
 import { CompanySettingsNav } from "./access/CompanySettingsNav";
 import { BreadcrumbBar } from "./BreadcrumbBar";
@@ -30,10 +29,6 @@ import { useCompanyPageMemory } from "../hooks/useCompanyPageMemory";
 import { healthApi } from "../api/health";
 import { instanceSettingsApi } from "../api/instanceSettings";
 import { shouldSyncCompanySelectionFromRoute } from "../lib/company-selection";
-import {
-  DEFAULT_INSTANCE_SETTINGS_PATH,
-  normalizeRememberedInstanceSettingsPath,
-} from "../lib/instance-settings";
 import {
   resetNavigationScroll,
   shouldResetScrollOnNavigation,
@@ -44,8 +39,6 @@ import { cn } from "../lib/utils";
 import { NotFoundPage } from "../pages/NotFound";
 import { PluginSlotMount, resolveRouteSidebarSlot, usePluginSlots } from "../plugins/slots";
 
-const INSTANCE_SETTINGS_MEMORY_KEY = "paperclip.lastInstanceSettingsPath";
-
 function getCompanyRouteSegment(pathname: string, companyPrefix: string | undefined): string | null {
   if (!companyPrefix) return null;
   const segments = pathname.split("/").filter(Boolean);
@@ -54,15 +47,6 @@ function getCompanyRouteSegment(pathname: string, companyPrefix: string | undefi
   return segments[1]?.toLowerCase() ?? null;
 }
 
-function readRememberedInstanceSettingsPath(): string {
-  if (typeof window === "undefined") return DEFAULT_INSTANCE_SETTINGS_PATH;
-  try {
-    return normalizeRememberedInstanceSettingsPath(window.localStorage.getItem(INSTANCE_SETTINGS_MEMORY_KEY));
-  } catch {
-    return DEFAULT_INSTANCE_SETTINGS_PATH;
-  }
-}
-
 export function Layout() {
   const { sidebarOpen, setSidebarOpen, toggleSidebar, isMobile } = useSidebar();
   const { openNewIssue, openOnboarding } = useDialogActions();
@@ -82,14 +66,12 @@ export function Layout() {
   const navigate = useNavigate();
   const location = useLocation();
   const navigationType = useNavigationType();
-  const isInstanceSettingsRoute = location.pathname.startsWith("/instance/");
   const isCompanySettingsRoute = location.pathname.includes("/company/settings");
   const onboardingTriggered = useRef(false);
   const lastMainScrollTop = useRef(0);
   const previousPathname = useRef<string | null>(null);
   const mainContentRef = useRef<HTMLElement | null>(null);
   const [mobileNavVisible, setMobileNavVisible] = useState(true);
-  const [instanceSettingsTarget, setInstanceSettingsTarget] = useState<string>(() => readRememberedInstanceSettingsPath());
   const [shortcutsOpen, setShortcutsOpen] = useState(false);
   const matchedCompany = useMemo(() => {
     if (!companyPrefix) return null;
@@ -313,21 +295,6 @@ export function Layout() {
     };
   }, [isMobile]);
 
-  useEffect(() => {
-    if (!location.pathname.startsWith("/instance/settings/")) return;
-
-    const nextPath = normalizeRememberedInstanceSettingsPath(
-      `${location.pathname}${location.search}${location.hash}`,
-    );
-    setInstanceSettingsTarget(nextPath);
-
-    try {
-      window.localStorage.setItem(INSTANCE_SETTINGS_MEMORY_KEY, nextPath);
-    } catch {
-      // Ignore storage failures in restricted environments.
-    }
-  }, [location.hash, location.pathname, location.search]);
-
   useEffect(() => {
     if (typeof document === "undefined") return;
     const mainContent = mainContentRef.current;
@@ -383,9 +350,7 @@ export function Layout() {
           >
             <div className="flex flex-1 min-h-0 overflow-hidden">
               <div className="w-60 shrink-0 overflow-hidden">
-                {isInstanceSettingsRoute ? (
-                  <InstanceSidebar />
-                ) : isCompanySettingsRoute ? (
+                {isCompanySettingsRoute ? (
                   <CompanySettingsSidebar />
                 ) : (
                   companySidebar
@@ -394,7 +359,6 @@ export function Layout() {
             </div>
             <SidebarAccountMenu
               deploymentMode={health?.deploymentMode}
-              instanceSettingsTarget={instanceSettingsTarget}
               version={health?.version}
             />
           </div>
@@ -402,9 +366,7 @@ export function Layout() {
           <div className="flex h-full flex-col shrink-0">
             <div className="flex flex-1 min-h-0">
               <ResizableSidebarPane open={sidebarOpen} resizable className="h-full shrink-0">
-                {isInstanceSettingsRoute ? (
-                  <InstanceSidebar />
-                ) : isCompanySettingsRoute ? (
+                {isCompanySettingsRoute ? (
                   <CompanySettingsSidebar />
                 ) : (
                   companySidebar
@@ -413,7 +375,6 @@ export function Layout() {
             </div>
             <SidebarAccountMenu
               deploymentMode={health?.deploymentMode}
-              instanceSettingsTarget={instanceSettingsTarget}
               version={health?.version}
             />
           </div>