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/vscode-dark.css

@@ -0,0 +1,40 @@
+/*
+ * VS Code Dark Modern
+ * Palette: Visual Studio Code Dark Modern / Dark+ (microsoft/vscode, MIT).
+ */
+:root[data-theme="vscode-dark"] {
+  color-scheme: dark;
+  --theme-color: #1f1f1f;
+
+  --bg0: #1f1f1f;
+  --bg1: #181818;
+  --bg2: #2b2b2b;
+  --bg3: #3c3c3c;
+  --fg0: #ffffff;
+  --fg1: #cccccc;
+  --fg2: #bbbbbb;
+  --fg3: #9d9d9d;
+  --muted: #8b8b8b;
+
+  --accent: #0078d4;
+  --accent2: #ce9178;
+  --on-accent: #ffffff;
+  --red: #f14c4c;
+  --green: #89d185;
+  --aqua: #4ec9b0;
+  --blue: #3794ff;
+  --purple: #c586c0;
+
+  --diff-add: rgba(137, 209, 133, 0.16);
+  --diff-del: rgba(241, 76, 76, 0.16);
+  --shadow: 0 6px 24px rgba(0, 0, 0, 0.35);
+
+  --syntax-keyword: #569cd6;
+  --syntax-string: #ce9178;
+  --syntax-number: #b5cea8;
+  --syntax-comment: #6a9955;
+  --syntax-function: #dcdcaa;
+  --syntax-type: #4ec9b0;
+  --syntax-variable: #9cdcfe;
+  --syntax-meta: #c586c0;
+}