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-dark.css

@@ -0,0 +1,40 @@
+/*
+ * Harbor Dark
+ * Palette: HANCORE-linux/omarchy-harbordark-theme (MIT), via zink/trilium-themes (MIT).
+ */
+:root[data-theme="harbor-dark"] {
+  color-scheme: dark;
+  --theme-color: #1b1b1b;
+
+  --bg0: #1b1b1b;
+  --bg1: #232323;
+  --bg2: #2e2e2e;
+  --bg3: #3f3f3f;
+  --fg0: #f7f4ea;
+  --fg1: #efebdc;
+  --fg2: #d6d1c0;
+  --fg3: #c0b79f;
+  --muted: #a99b7a;
+
+  --accent: #e75a50;
+  --accent2: #e1ce98;
+  --on-accent: #1b1b1b;
+  --red: #f44336;
+  --green: #a99b7a;
+  --aqua: #8a9ba6;
+  --blue: #77838a;
+  --purple: #e58980;
+
+  --diff-add: rgba(169, 155, 122, 0.16);
+  --diff-del: rgba(244, 67, 54, 0.16);
+  --shadow: 0 6px 24px rgba(0, 0, 0, 0.35);
+
+  --syntax-keyword: #e75a50;
+  --syntax-string: #e1ce98;
+  --syntax-number: #e58980;
+  --syntax-comment: #77838a;
+  --syntax-function: #a99b7a;
+  --syntax-type: #e1ce98;
+  --syntax-variable: #efebdc;
+  --syntax-meta: #e58980;
+}