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/catppuccin-light.css

@@ -0,0 +1,40 @@
+/*
+ * Catppuccin Latte
+ * Palette: Catppuccin Latte (catppuccin/catppuccin, MIT).
+ */
+:root[data-theme="catppuccin-light"] {
+  color-scheme: light;
+  --theme-color: #eff1f5;
+
+  --bg0: #eff1f5;
+  --bg1: #e6e9ef;
+  --bg2: #ccd0da;
+  --bg3: #bcc0cc;
+  --fg0: #4c4f69;
+  --fg1: #4c4f69;
+  --fg2: #5c5f77;
+  --fg3: #6c6f85;
+  --muted: #6c6f85;
+
+  --accent: #8839ef;
+  --accent2: #fe640b;
+  --on-accent: #ffffff;
+  --red: #d20f39;
+  --green: #40a02b;
+  --aqua: #179299;
+  --blue: #1e66f5;
+  --purple: #ea76cb;
+
+  --diff-add: rgba(64, 160, 43, 0.16);
+  --diff-del: rgba(210, 15, 57, 0.12);
+  --shadow: 0 6px 24px rgba(40, 40, 40, 0.18);
+
+  --syntax-keyword: #8839ef;
+  --syntax-string: #40a02b;
+  --syntax-number: #fe640b;
+  --syntax-comment: #8c8fa1;
+  --syntax-function: #1e66f5;
+  --syntax-type: #df8e1d;
+  --syntax-variable: #4c4f69;
+  --syntax-meta: #ea76cb;
+}