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/src/tools/craft.rs

@@ -100,6 +100,12 @@ impl Tool for BrowserSnapshot {
     }
     async fn run(&self, input: Value, ctx: &ToolCtx) -> Result<ToolOutput> {
         let url = arg_str(&input, "url")?.to_string();
+        // Local files only from the user's own folders.
+        if let Some(path) = url.strip_prefix("file://") {
+            ctx.resolve(path)?;
+        } else if !(url.starts_with("http://") || url.starts_with("https://")) {
+            bail!("only http(s) and file:// URLs are supported");
+        }
         let label = slug(input["label"].as_str().unwrap_or(&url));
         let widths: Vec<u32> = input["widths"]
             .as_array()