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/tokyonight-light.css

@@ -0,0 +1,40 @@
+/*
+ * Tokyo Night Day
+ * Palette: folke/tokyonight.nvim (Apache-2.0), via zink/trilium-themes (MIT).
+ */
+:root[data-theme="tokyonight-light"] {
+  color-scheme: light;
+  --theme-color: #e1e2e7;
+
+  --bg0: #e1e2e7;
+  --bg1: #d0d5e3;
+  --bg2: #c4c8da;
+  --bg3: #a8aecb;
+  --fg0: #273463;
+  --fg1: #3760bf;
+  --fg2: #4b5a99;
+  --fg3: #6172b0;
+  --muted: #6c74a0;
+
+  --accent: #2e7de9;
+  --accent2: #b15c00;
+  --on-accent: #ffffff;
+  --red: #f52a65;
+  --green: #587539;
+  --aqua: #118c74;
+  --blue: #2e7de9;
+  --purple: #9854f1;
+
+  --diff-add: rgba(88, 117, 57, 0.16);
+  --diff-del: rgba(245, 42, 101, 0.12);
+  --shadow: 0 6px 24px rgba(40, 40, 40, 0.18);
+
+  --syntax-keyword: #9854f1;
+  --syntax-string: #587539;
+  --syntax-number: #b15c00;
+  --syntax-comment: #848cb5;
+  --syntax-function: #2e7de9;
+  --syntax-type: #007197;
+  --syntax-variable: #3760bf;
+  --syntax-meta: #8c6c3e;
+}