Add security hardening, Ghidra, recreate skill, checkpoints, shells, web search and themes

- Sandbox (bubblewrap) for non-admin shell/git, MCP per-user rights, hard budgets and quotas,
  login rate limiting, audit log and backups
- Ghidra headless decompilation (ARM64 natives built from source), binary_info tool,
  clean room / deep workflow per session
- Recreate skill and commands for analysing and re-building old software
- File checkpoints with rewind/restore, background shells (bash_output, kill_shell)
- web_search tool (DuckDuckGo, SearXNG, Brave, Tavily)
- In-app dialogs and toasts instead of browser dialogs
- 15 base themes (trilium-themes palettes plus Nord, VS Code, GitHub, Catppuccin, One,
  Dracula, Rose Pine, Everforest, Kanagawa) with light/dark/auto switcher and license notes

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

web/src/App.tsx

@@ -12,6 +12,7 @@ import { Settings } from "./components/Settings";
 import { Stats } from "./components/Stats";
 import { Images } from "./components/Images";
 import { Spinner, useTitleActivity } from "./components/Activity";
+import { DialogHost } from "./dialogs";
 
 // The file manager (editor, git) is loaded on demand to keep the chat small.
 const Files = lazy(() => import("./components/Files").then((m) => ({ default: m.Files })));
@@ -58,7 +59,13 @@ export function App() {
 
   if (error) return <div className="empty">{error}</div>;
   if (!info) return <div className="empty">{t("common.loading")}</div>;
-  if (!info.user) return <Login info={info} onSuccess={refresh} />;
+  if (!info.user)
+    return (
+      <>
+        <Login info={info} onSuccess={refresh} />
+        <DialogHost />
+      </>
+    );
 
   const [section, arg] = route;
   let content;
@@ -79,6 +86,7 @@ export function App() {
       {menuOpen && <div className="backdrop" onClick={() => setMenuOpen(false)} />}
       <Sidebar open={menuOpen} activeId={section === "s" ? arg : undefined} section={section ?? ""} />
       <main className="main">{content}</main>
+      <DialogHost />
     </div>
   );
 }