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/everforest-light.css

@@ -0,0 +1,40 @@
+/*
+ * Everforest Light
+ * Palette: Everforest by sainnhe (sainnhe/everforest, MIT).
+ */
+:root[data-theme="everforest-light"] {
+  color-scheme: light;
+  --theme-color: #fdf6e3;
+
+  --bg0: #fdf6e3;
+  --bg1: #f4f0d9;
+  --bg2: #efebd4;
+  --bg3: #e0dcc7;
+  --fg0: #4a565c;
+  --fg1: #5c6a72;
+  --fg2: #66757c;
+  --fg3: #748086;
+  --muted: #7a8478;
+
+  --accent: #8da101;
+  --accent2: #f57d26;
+  --on-accent: #2d353b;
+  --red: #f85552;
+  --green: #8da101;
+  --aqua: #35a77c;
+  --blue: #3a94c5;
+  --purple: #df69ba;
+
+  --diff-add: rgba(141, 161, 1, 0.16);
+  --diff-del: rgba(248, 85, 82, 0.12);
+  --shadow: 0 6px 24px rgba(40, 40, 40, 0.18);
+
+  --syntax-keyword: #f85552;
+  --syntax-string: #dfa000;
+  --syntax-number: #df69ba;
+  --syntax-comment: #939f91;
+  --syntax-function: #8da101;
+  --syntax-type: #3a94c5;
+  --syntax-variable: #5c6a72;
+  --syntax-meta: #f57d26;
+}