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/dialogs.tsx

@@ -0,0 +1,142 @@
+// In-app dialogs and toasts instead of the browser's alert/confirm/prompt.
+import { useEffect, useRef, useState, useSyncExternalStore } from "react";
+import { t } from "./i18n";
+
+interface ConfirmOpts {
+  title?: string;
+  message: string;
+  confirmLabel?: string;
+  /** Destructive action: red button. */
+  danger?: boolean;
+}
+
+interface PromptOpts {
+  title?: string;
+  message: string;
+  defaultValue?: string;
+  placeholder?: string;
+  password?: boolean;
+  confirmLabel?: string;
+}
+
+type Dialog =
+  | ({ kind: "confirm"; id: number; resolve: (v: boolean) => void } & ConfirmOpts)
+  | ({ kind: "prompt"; id: number; resolve: (v: string | null) => void } & PromptOpts);
+
+interface Toast {
+  id: number;
+  message: string;
+  kind: "error" | "info" | "success";
+}
+
+let dialogs: Dialog[] = [];
+let toasts: Toast[] = [];
+let seq = 0;
+const listeners = new Set<() => void>();
+const emit = () => listeners.forEach((l) => l());
+const subscribe = (l: () => void) => (listeners.add(l), () => listeners.delete(l));
+
+export function confirmDialog(opts: ConfirmOpts | string): Promise<boolean> {
+  const o = typeof opts === "string" ? { message: opts } : opts;
+  return new Promise((resolve) => {
+    dialogs = [...dialogs, { kind: "confirm", id: ++seq, resolve, ...o }];
+    emit();
+  });
+}
+
+export function promptDialog(opts: PromptOpts | string): Promise<string | null> {
+  const o = typeof opts === "string" ? { message: opts } : opts;
+  return new Promise((resolve) => {
+    dialogs = [...dialogs, { kind: "prompt", id: ++seq, resolve, ...o }];
+    emit();
+  });
+}
+
+export function toast(message: unknown, kind: Toast["kind"] = "error") {
+  const text = message instanceof Error ? message.message : typeof message === "string" ? message : String((message as any)?.message ?? message);
+  const id = ++seq;
+  toasts = [...toasts, { id, message: text, kind }];
+  emit();
+  setTimeout(() => {
+    toasts = toasts.filter((x) => x.id !== id);
+    emit();
+  }, kind === "error" ? 7000 : 3500);
+}
+
+function close(d: Dialog, value: any) {
+  dialogs = dialogs.filter((x) => x.id !== d.id);
+  emit();
+  (d.resolve as (v: any) => void)(value);
+}
+
+function DialogView({ d }: { d: Dialog }) {
+  const [value, setValue] = useState(d.kind === "prompt" ? d.defaultValue ?? "" : "");
+  const input = useRef<HTMLInputElement>(null);
+  const ok = useRef<HTMLButtonElement>(null);
+  const cancelValue = d.kind === "confirm" ? false : null;
+  useEffect(() => {
+    if (d.kind === "prompt") {
+      input.current?.focus();
+      input.current?.select();
+    } else ok.current?.focus();
+    const h = (e: KeyboardEvent) => e.key === "Escape" && close(d, cancelValue);
+    window.addEventListener("keydown", h);
+    return () => window.removeEventListener("keydown", h);
+    // eslint-disable-next-line react-hooks/exhaustive-deps
+  }, []);
+  const submit = () => close(d, d.kind === "confirm" ? true : value);
+  return (
+    <div className="modal-backdrop" onClick={() => close(d, cancelValue)}>
+      <form
+        className="modal dialog"
+        role={d.kind === "confirm" ? "alertdialog" : "dialog"}
+        aria-label={d.title ?? d.message}
+        onClick={(e) => e.stopPropagation()}
+        onSubmit={(e) => (e.preventDefault(), submit())}
+      >
+        {d.title && <h3>{d.title}</h3>}
+        <p className="dialog-message">{d.message}</p>
+        {d.kind === "prompt" && (
+          <input
+            ref={input}
+            type={d.password ? "password" : "text"}
+            value={value}
+            placeholder={d.placeholder}
+            onChange={(e) => setValue(e.target.value)}
+            autoComplete={d.password ? "new-password" : "off"}
+            style={{ width: "100%" }}
+          />
+        )}
+        <div className="row dialog-actions">
+          <button type="button" onClick={() => close(d, cancelValue)}>
+            {t("common.cancel")}
+          </button>
+          <button ref={ok} type="submit" className={d.kind === "confirm" && d.danger ? "danger-solid" : "primary"}>
+            {d.confirmLabel ?? t("common.ok")}
+          </button>
+        </div>
+      </form>
+    </div>
+  );
+}
+
+/** Renders open dialogs and toasts; mounted once in App. */
+export function DialogHost() {
+  const state = useSyncExternalStore(subscribe, () => dialogs);
+  const ts = useSyncExternalStore(subscribe, () => toasts);
+  return (
+    <>
+      {state.map((d) => (
+        <DialogView key={d.id} d={d} />
+      ))}
+      <div className="toasts" role="status" aria-live="polite">
+        {ts.map((x) => (
+          <div key={x.id} className={`toast ${x.kind}`} onClick={() => ((toasts = toasts.filter((y) => y.id !== x.id)), emit())}>
+            {x.kind === "error" ? "⚠ " : x.kind === "success" ? "✓ " : ""}
+            {x.message}
+          </div>
+        ))}
+      </div>
+    </>
+  );
+}