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/01-inventory.md

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+# Inventory
+
+| File | From (archive/installer) | Type (`file`) | Size | Role |
+|---|---|---|---|---|
+
+## Unpacking log
+
+| Source | Tool | Result |
+|---|---|---|
+
+## Not unpacked / open questions

server/resources/skills/recreate/templates/02-overview.md

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+# Overview
+
+- Name, publisher, year, platform, original system requirements:
+- What the program does (from the user's perspective):
+- Executables and how they relate (main program, setup, overlays, drivers):
+- Engines, libraries, compilers detected:

server/resources/skills/recreate/templates/03-architecture.md

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+# Architecture of the original
+
+## Start-up and main loop
+## Modules / subsystems (input, graphics, sound, logic, file I/O, configuration)
+## Important functions (address → purpose)
+## Memory and data structures

server/resources/skills/recreate/templates/04-file-formats.md

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+# File and data formats
+
+For each format: files using it, header/magic, layout (offset, size, meaning), compression,
+how the program reads/writes it (function references), decoding status and tools in analysis/tools/.

server/resources/skills/recreate/templates/05-ui-and-behaviour.md

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+# User interface and behaviour
+
+## Screens / windows / menus
+## Controls and input
+## Rules and logic
+## Timing (frame rate, tick rate, delays)
+## Sound and music

server/resources/skills/recreate/templates/06-assets.md

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+# Assets
+
+Graphics, palettes, fonts, sounds, music, levels/maps, texts: where they are, format, how many,
+how the re-creation will use them.

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

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+# 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