fix(server): improve agent session state lifecycle

- Skip stale "done" state from file when detecting agent state, since
  the tmux window may have been reused for a new process
- Ensure hook scripts exist on disk before injecting Claude Code hooks
  (guards against missing scripts if startup write failed)
- Clean up session state directory when closing a session

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: fab-uleuh

nomadflow-rs/crates/nomadflow-core/src/agent_state.rs

@@ -377,7 +377,9 @@ impl AgentStateService {
             self.read_state(&session.session_id).await
         } else {
             // Try hook-driven state file first (works when Claude Code runs
-            // in a legacy 2-part tmux window with auto-discovered session ID)
+            // in a legacy 2-part tmux window with auto-discovered session ID).
+            // Ignore "done" state from file: the tmux window may have been reused
+            // for a new process, so fall through to live process detection.
             if let Some(state) = self.read_state(&session.session_id).await {
                 if state.state != AgentStateKind::Done {
                     return Some(state);

nomadflow-rs/crates/nomadflow-server/src/routes/sessions.rs

@@ -119,6 +119,8 @@ async fn create_session(
 
     // Inject Claude Code hooks if agent type is claude-code (AC #2)
     if agent_type == "claude-code" {
+        // Ensure hook script exists on disk (idempotent, guards against startup failure)
+        let _ = state.agent_state.ensure_hook_scripts().await;
         let worktree_path = std::path::Path::new(&request.worktree_path);
         if let Err(e) = state
             .agent_state
@@ -239,6 +241,18 @@ async fn close_session(
     }
 
     let closed = state.tmux.kill_window(&window_name).await;
+
+    // Clean up session state directory (agent-state.json, worktree-path)
+    let session_state_dir = state.agent_state.sessions_dir().join(&request.session_id);
+    if session_state_dir.is_dir() {
+        if let Err(e) = tokio::fs::remove_dir_all(&session_state_dir).await {
+            tracing::warn!(
+                "Failed to clean up session state dir for {}: {e}",
+                request.session_id
+            );
+        }
+    }
+
     Ok(Json(CloseSessionResponse { closed }))
 }