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/themes/ash-dark.css

@@ -0,0 +1,40 @@
+/*
+ * Ash Dark
+ * Original Ash palette (Gruvbox-derived) from zink/trilium-themes (MIT).
+ */
+:root[data-theme="ash-dark"] {
+  color-scheme: dark;
+  --theme-color: #1c1b1f;
+
+  --bg0: #1c1b1f;
+  --bg1: #232226;
+  --bg2: #29282c;
+  --bg3: #3a383d;
+  --fg0: #f3ede1;
+  --fg1: #e6dfd1;
+  --fg2: #cfc7b8;
+  --fg3: #b0a89b;
+  --muted: #999187;
+
+  --accent: #e0914f;
+  --accent2: #d6b46a;
+  --on-accent: #1c1b1f;
+  --red: #c15c46;
+  --green: #8f9a5c;
+  --aqua: #8aa89a;
+  --blue: #7c9aa1;
+  --purple: #b47e99;
+
+  --diff-add: rgba(143, 154, 92, 0.16);
+  --diff-del: rgba(193, 92, 70, 0.16);
+  --shadow: 0 6px 24px rgba(0, 0, 0, 0.35);
+
+  --syntax-keyword: #c15c46;
+  --syntax-string: #8f9a5c;
+  --syntax-number: #a585ac;
+  --syntax-comment: #6d6a63;
+  --syntax-function: #7c9aa1;
+  --syntax-type: #d6b46a;
+  --syntax-variable: #e6dfd1;
+  --syntax-meta: #e0914f;
+}