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>

web/src/themes/one-dark.css

@@ -0,0 +1,40 @@
+/*
+ * One Dark
+ * Palette: Atom One Dark (atom/atom, MIT).
+ */
+:root[data-theme="one-dark"] {
+  color-scheme: dark;
+  --theme-color: #282c34;
+
+  --bg0: #282c34;
+  --bg1: #21252b;
+  --bg2: #2c313a;
+  --bg3: #3e4451;
+  --fg0: #d7dae0;
+  --fg1: #abb2bf;
+  --fg2: #9da5b4;
+  --fg3: #8b929e;
+  --muted: #7f848e;
+
+  --accent: #61afef;
+  --accent2: #d19a66;
+  --on-accent: #282c34;
+  --red: #e06c75;
+  --green: #98c379;
+  --aqua: #56b6c2;
+  --blue: #61afef;
+  --purple: #c678dd;
+
+  --diff-add: rgba(152, 195, 121, 0.16);
+  --diff-del: rgba(224, 108, 117, 0.16);
+  --shadow: 0 6px 24px rgba(0, 0, 0, 0.35);
+
+  --syntax-keyword: #c678dd;
+  --syntax-string: #98c379;
+  --syntax-number: #d19a66;
+  --syntax-comment: #7f848e;
+  --syntax-function: #61afef;
+  --syntax-type: #e5c07b;
+  --syntax-variable: #e06c75;
+  --syntax-meta: #56b6c2;
+}