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/harbor-light.css

@@ -0,0 +1,40 @@
+/*
+ * Harbor Light
+ * Palette: HANCORE-linux/omarchy-harbor-theme (MIT), via zink/trilium-themes (MIT).
+ */
+:root[data-theme="harbor-light"] {
+  color-scheme: light;
+  --theme-color: #dfe4c4;
+
+  --bg0: #dfe4c4;
+  --bg1: #d0d6b4;
+  --bg2: #c3c9a6;
+  --bg3: #b3b994;
+  --fg0: #101c18;
+  --fg1: #1c2d28;
+  --fg2: #2f413b;
+  --fg3: #435650;
+  --muted: #556753;
+
+  --accent: #4c6c94;
+  --accent2: #dc8164;
+  --on-accent: #ffffff;
+  --red: #b14752;
+  --green: #556753;
+  --aqua: #3d727d;
+  --blue: #4c6c94;
+  --purple: #8a5b81;
+
+  --diff-add: rgba(85, 103, 83, 0.16);
+  --diff-del: rgba(177, 71, 82, 0.12);
+  --shadow: 0 6px 24px rgba(40, 40, 40, 0.18);
+
+  --syntax-keyword: #b14752;
+  --syntax-string: #556753;
+  --syntax-number: #8a5b81;
+  --syntax-comment: #6f7d6c;
+  --syntax-function: #3d727d;
+  --syntax-type: #4c6c94;
+  --syntax-variable: #1c2d28;
+  --syntax-meta: #b06247;
+}