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/package.json

@@ -18,15 +18,18 @@
     "@codemirror/view": "^6.43.15",
     "@lezer/highlight": "^1.2.5",
     "codemirror": "^6.0.2",
+    "occt-import-js": "^0.0.23",
     "react": "^19.3.1",
     "react-dom": "^19.3.1",
     "react-markdown": "^10.1.0",
     "rehype-highlight": "^7.0.2",
-    "remark-gfm": "^4.0.1"
+    "remark-gfm": "^4.0.1",
+    "three": "^0.187.0"
   },
   "devDependencies": {
     "@types/react": "^19.3.0",
     "@types/react-dom": "^19.3.0",
+    "@types/three": "^0.187.0",
     "@vitejs/plugin-react": "^6.2.1",
     "typescript": "^7.0.2",
     "vite": "^8.3.6",