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/bash.rs

@@ -24,7 +24,9 @@ impl Tool for Bash {
         "Run a shell command (bash) in the session working directory. stdout and stderr are \
          combined. Default timeout 2 minutes, max 10 minutes (timeout_ms). The working directory \
          does not persist between calls – use absolute paths or `cd dir && ...`. Prefer the \
-         dedicated read/edit/glob/grep tools over cat/sed/find/grep."
+         dedicated read/edit/glob/grep tools over cat/sed/find/grep. For long-running processes \
+         (dev servers, watchers, long builds) set run_in_background=true: you get a shell id, \
+         read new output with bash_output and stop it with kill_shell."
             .into()
     }
     fn schema(&self) -> Value {
@@ -33,7 +35,8 @@ impl Tool for Bash {
             "properties": {
                 "command": {"type": "string"},
                 "description": {"type": "string", "description": "5-10 word description of what the command does"},
-                "timeout_ms": {"type": "integer"}
+                "timeout_ms": {"type": "integer"},
+                "run_in_background": {"type": "boolean", "description": "Keep running; read output with bash_output"}
             },
             "required": ["command"]
         })
@@ -49,17 +52,18 @@ impl Tool for Bash {
         let timeout = Duration::from_millis(
             input["timeout_ms"].as_u64().unwrap_or(DEFAULT_TIMEOUT_MS).min(MAX_TIMEOUT_MS),
         );
-        let mut cmd = Command::new("bash");
-        cmd.arg("-c")
-            .arg(format!("{command} 2>&1"))
-            .current_dir(&ctx.cwd)
-            .stdin(Stdio::null())
-            .stdout(Stdio::piped())
-            .stderr(Stdio::null())
-            .env("CODECRAFT", "1")
-            .env("GIT_TERMINAL_PROMPT", "0")
-            .env("PAGER", "cat")
-            .kill_on_drop(true);
+        let mut cmd = match shell_command(ctx, command) {
+            Ok(c) => c,
+            Err(e) => return Ok(e),
+        };
+        if input["run_in_background"].as_bool().unwrap_or(false) {
+            let id = crate::shells::spawn(&ctx.app, &ctx.session_id, command, cmd)?;
+            return Ok(ToolOutput::text(format!(
+                "Started in the background with shell id {id}. Read its output with bash_output (shell_id \"{id}\") and stop it with kill_shell."
+            ))
+            .with_meta(json!({"shell_id": id})));
+        }
+        cmd.stdin(Stdio::null()).stdout(Stdio::piped()).stderr(Stdio::null()).kill_on_drop(true);
         // Own process group so the whole tree can be killed on abort/timeout.
         cmd.process_group(0);
         let mut child = cmd.spawn()?;
@@ -128,6 +132,27 @@ impl Tool for Bash {
     }
 }
 
+/// The bash command for a script, sandboxed for non-admin users.
+pub fn shell_command(ctx: &ToolCtx, command: &str) -> std::result::Result<Command, ToolOutput> {
+    // stderr of every command (not just the last one) goes into the output.
+    let script = format!("exec 2>&1\n{command}");
+    Ok(match &ctx.sandbox {
+        Some(spec) => {
+            if !crate::sandbox::available() {
+                return Err(ToolOutput::error(
+                    "Shell commands are disabled for this account: the server's sandbox (bubblewrap) is not available. Ask an admin.",
+                ));
+            }
+            crate::sandbox::command(spec, &ctx.cwd, "bash", &["-c", &script])
+        }
+        None => {
+            let mut c = Command::new("bash");
+            c.arg("-c").arg(&script).current_dir(&ctx.cwd).env("CODECRAFT", "1").env("GIT_TERMINAL_PROMPT", "0").env("PAGER", "cat");
+            c
+        }
+    })
+}
+
 fn tail(s: &str, max: usize) -> String {
     if s.len() <= max {
         return s.to_string();