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-light.css

@@ -0,0 +1,40 @@
+/*
+ * VS Code Light Modern
+ * Palette: Visual Studio Code Light Modern / Light+ (microsoft/vscode, MIT).
+ */
+:root[data-theme="vscode-light"] {
+  color-scheme: light;
+  --theme-color: #ffffff;
+
+  --bg0: #ffffff;
+  --bg1: #f8f8f8;
+  --bg2: #e5e5e5;
+  --bg3: #cecece;
+  --fg0: #000000;
+  --fg1: #3b3b3b;
+  --fg2: #444444;
+  --fg3: #616161;
+  --muted: #6e7681;
+
+  --accent: #005fb8;
+  --accent2: #a31515;
+  --on-accent: #ffffff;
+  --red: #cd3131;
+  --green: #388a34;
+  --aqua: #267f99;
+  --blue: #005fb8;
+  --purple: #af00db;
+
+  --diff-add: rgba(56, 138, 52, 0.16);
+  --diff-del: rgba(205, 49, 49, 0.12);
+  --shadow: 0 6px 24px rgba(40, 40, 40, 0.18);
+
+  --syntax-keyword: #0000ff;
+  --syntax-string: #a31515;
+  --syntax-number: #098658;
+  --syntax-comment: #008000;
+  --syntax-function: #795e26;
+  --syntax-type: #267f99;
+  --syntax-variable: #001080;
+  --syntax-meta: #af00db;
+}