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>

server/Cargo.toml

@@ -19,6 +19,8 @@ globset = "0.4"
 html2text = "0.15"
 image = { version = "0.25", default-features = false, features = ["png", "jpeg", "webp"] }
 base64 = "0.22"
+calamine = "0.38"
+zip = { version = "9", default-features = false, features = ["deflate"] }
 shell-words = "1"
 libc = "0.2"
 ignore = "0.4"