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/resources/skills/recreate/templates/recreation-plan.md

@@ -0,0 +1,13 @@
+# Recreation proposal
+
+## Summary
+## Technology options
+| Option | Fit | Pros | Cons | Effort |
+|---|---|---|---|---|
+## Recommendation
+## Architecture sketch
+## Milestones
+1. First runnable version:
+## Handling of original assets
+## Comparison tests against the original
+## Risks and open questions