fixes

src/app_controller.py

@@ -443,7 +443,7 @@ class AppController:
    return
   target_path = self._inject_file_path
   if not os.path.isabs(target_path):
-   target_path = os.path.join(self.ui_files_base_dir, target_path)
+   target_path = os.path.join(self.active_project_root, target_path)
   if not os.path.exists(target_path):
    self._inject_preview = ""
    return
@@ -1679,7 +1679,7 @@ class AppController:
     except Exception as e:
      raise HTTPException(status_code=500, detail=f"Context aggregation failure: {e}")
     user_msg = req.prompt
-    base_dir = self.ui_files_base_dir
+    base_dir = self.active_project_root
     csp = filter(bool, [self.ui_global_system_prompt.strip(), self.ui_project_system_prompt.strip()])
     ai_client.set_custom_system_prompt("\n\n".join(csp))
     temp = req.temperature if req.temperature is not None else self.temperature
@@ -1787,7 +1787,7 @@ class AppController:
     return {
      "files": [f.get("path") if isinstance(f, dict) else str(f) for f in file_items],
      "screenshots": screenshots,
-     "files_base_dir": self.ui_files_base_dir,
+     "files_base_dir": self.active_project_root,
      "markdown": md,
      "discussion": disc_text
     }
@@ -1904,9 +1904,9 @@ class AppController:
     with self._disc_entries_lock:
      self.disc_entries = models.parse_history_entries(track_history, self.disc_roles)
   
-  self.preset_manager.project_root = Path(self.ui_files_base_dir)
+  self.preset_manager.project_root = Path(self.active_project_root)
   self.presets = self.preset_manager.load_all()
-  self.tool_preset_manager.project_root = Path(self.ui_files_base_dir)
+  self.tool_preset_manager.project_root = Path(self.active_project_root)
   self.tool_presets = self.tool_preset_manager.load_all_presets()
   self.bias_profiles = self.tool_preset_manager.load_all_bias_profiles()
 
@@ -2032,7 +2032,7 @@ class AppController:
  def _flush_disc_entries_to_project(self) -> None:
   history_strings = [project_manager.entry_to_str(e) for e in self.disc_entries]
   if self.active_track and self._track_discussion_active:
-   project_manager.save_track_history(self.active_track.id, history_strings, self.ui_files_base_dir)
+   project_manager.save_track_history(self.active_track.id, history_strings, self.active_project_root)
    return
   disc_sec = self.project.setdefault("discussion", {})
   discussions = disc_sec.setdefault("discussions", {})
@@ -2202,7 +2202,7 @@ class AppController:
       file_path, definition, line = res
       user_msg += f'\n\n[Definition: {symbol} from {file_path} (line {line})]\n```python\n{definition}\n```'
 
-    base_dir = self.ui_files_base_dir
+    base_dir = self.active_project_root
     sys.stderr.write(f"[DEBUG] _do_generate success. Prompt: {user_msg[:50]}...\n")
     sys.stderr.flush()
     # Prepare event payload
@@ -2383,7 +2383,7 @@ class AppController:
     sys.stderr.flush()
     proj = project_manager.load_project(self.active_project_path)
     flat = project_manager.flat_config(self.project)
-    file_items = aggregate.build_file_items(Path(self.ui_files_base_dir), flat.get("files", {}).get("paths", []))
+    file_items = aggregate.build_file_items(Path(self.active_project_root), flat.get("files", {}).get("paths", []))
 
     _t1_baseline = len(ai_client.get_comms_log())
     tracks = orchestrator_pm.generate_tracks(self.ui_epic_input, flat, file_items, history_summary=history)
@@ -2435,7 +2435,7 @@ class AppController:
     for i, file_path in enumerate(files_to_scan):
      try:
       self._set_status(f"Phase 2: Scanning files ({i+1}/{len(files_to_scan)})...")
-      abs_path = Path(self.ui_files_base_dir) / file_path
+      abs_path = Path(self.active_project_root) / file_path
       if abs_path.exists() and abs_path.suffix == ".py":
        with open(abs_path, "r", encoding="utf-8") as f:
         code = f.read()
@@ -2537,7 +2537,7 @@ class AppController:
    # Initialize track state in the filesystem
    meta = models.Metadata(id=track_id, name=title, status="todo", created_at=datetime.now(), updated_at=datetime.now())
    state = models.TrackState(metadata=meta, discussion=[], tasks=tickets)
-   project_manager.save_track_state(track_id, state, self.ui_files_base_dir)
+   project_manager.save_track_state(track_id, state, self.active_project_root)
    # Add to memory and notify UI
    self.tracks.append({"id": track_id, "title": title, "status": "todo"})
    with self._pending_gui_tasks_lock:
@@ -2602,7 +2602,7 @@ class AppController:
   file_path = data.get("file_path")
   if file_path:
    if not os.path.isabs(file_path):
-    file_path = os.path.relpath(file_path, self.ui_files_base_dir)
+    file_path = os.path.relpath(file_path, self.active_project_root)
    existing = next((f for f in self.files if (f.path if hasattr(f, "path") else str(f)) == file_path), None)
    if not existing:
     item = models.FileItem(path=file_path)
@@ -2630,7 +2630,7 @@ class AppController:
    self._push_mma_state_update()
 
  def _cb_run_conductor_setup(self) -> None:
-  base = paths.get_conductor_dir()
+  base = paths.get_conductor_dir(project_path=self.active_project_root)
   if not base.exists():
    self.ui_conductor_setup_summary = f"Error: {base}/ directory not found."
    return
@@ -2687,7 +2687,7 @@ class AppController:
    # Sync active_tickets (list of dicts) back to active_track.tickets (list of models.Ticket objects)
   self.active_track.tickets = [models.Ticket.from_dict(t) for t in self.active_tickets]
   # Save the state to disk
-  existing = project_manager.load_track_state(self.active_track.id, self.ui_files_base_dir)
+  existing = project_manager.load_track_state(self.active_track.id, self.active_project_root)
   meta = models.Metadata(
    id=self.active_track.id,
    name=self.active_track.description,
@@ -2700,5 +2700,5 @@ class AppController:
    discussion=existing.discussion if existing else [],
    tasks=self.active_track.tickets
   )
-  project_manager.save_track_state(self.active_track.id, state, self.ui_files_base_dir)
+  project_manager.save_track_state(self.active_track.id, state, self.active_project_root)