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/commands/recreate-init.md

@@ -0,0 +1,15 @@
+---
+description: Set up a project for re-creating existing software (folders, templates, .gitignore)
+---
+Load the skill "recreate" with the skill tool and set up the project layout it describes in the
+current working directory:
+
+1. Create the folders original/, original/extracted/, analysis/, docs/, spec/, proposal/, src/, tests/
+   (keep empty ones with a .gitkeep).
+2. Copy the templates from the skill's templates/ folder: 01–06 into docs/, recreation-plan.md into proposal/.
+3. Create or extend .gitignore with `original/`, `analysis/` and `.codecraft/`.
+4. Create README.md (in English) describing the project's purpose and the layout, if it does not exist.
+5. Do not commit. Finish with a short message telling the user to put the program, its
+   libraries, archives or installers into original/ and then run /recreate-start.
+
+$ARGUMENTS

server/resources/commands/recreate-start.md

@@ -0,0 +1,10 @@
+---
+description: Analyse the software in original/, document it and propose how to re-create it
+agent: craft
+clean_room: false
+---
+Load the skill "recreate" with the skill tool and carry out phases 1–4 for the software in
+original/ (inventory and unpacking, analysis, documentation and specification, proposal).
+Track the phases with todo_write. Stop after the proposal and ask the user how to proceed.
+
+Additional notes from the user: $ARGUMENTS