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>

docker-compose.yml

@@ -30,6 +30,16 @@ services:
     extra_hosts:
       - "host.docker.internal:host-gateway"
     shm_size: "1gb" # Chromium (craft mode)
+    # Shell commands of non-admin users run in a bubblewrap sandbox. It needs
+    # user namespaces: a seccomp profile that adds exactly those syscalls to
+    # Docker's default, AppArmor relaxed for the namespace mounts, and an
+    # unmasked /proc so the sandbox can mount its own (hiding server processes).
+    # Remove these three lines and set [sandbox] mode = "off" if you are the
+    # only user.
+    security_opt:
+      - seccomp=./docker/seccomp-sandbox.json
+      - apparmor=unconfined
+      - systempaths=unconfined
 
 volumes:
   codecraft-data: