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)
 

src/events.py

@@ -102,6 +102,15 @@ class AsyncEventQueue:
   """
   return self._queue.get()
 
+ def empty(self) -> bool:
+  """
+  Checks if the queue is empty.
+  
+  Returns:
+   True if the queue is empty, False otherwise.
+  """
+  return self._queue.empty()
+
  def task_done(self) -> None:
   """Signals that a formerly enqueued task is complete."""
   self._queue.task_done()

src/gui_2.py

@@ -2026,7 +2026,7 @@ def hello():
     if changed:
      if self._track_discussion_active:
       self._flush_disc_entries_to_project()
-      history_strings = project_manager.load_track_history(self.active_track.id, self.ui_files_base_dir)
+      history_strings = project_manager.load_track_history(self.active_track.id, self.active_project_root)
       with self._disc_entries_lock:
        self.disc_entries = models.parse_history_entries(history_strings, self.disc_roles)
       self.ai_status = f"track discussion: {self.active_track.id}"

tests/test_gui_phase3.py

@@ -6,6 +6,7 @@ import os
 import json
 from pathlib import Path
 from unittest.mock import patch
+from src import paths
 
 
 def test_track_proposal_editing(app_instance):
@@ -30,7 +31,7 @@ def test_track_proposal_editing(app_instance):
  assert app_instance.proposed_tracks[0]['title'] == "New Title"
 
 
-def test_conductor_setup_scan(app_instance, tmp_path):
+def test_conductor_setup_scan(app_instance, tmp_path, monkeypatch):
  """
  Verifies that the conductor setup scan properly iterates through the conductor directory,
  counts files and lines, and identifies active tracks.
@@ -44,6 +45,9 @@ def test_conductor_setup_scan(app_instance, tmp_path):
   (cond_dir / "tracks").mkdir(exist_ok=True)
   (cond_dir / "tracks" / "track1").mkdir(exist_ok=True)
   
+  monkeypatch.setenv('SLOP_CONDUCTOR_DIR', str((tmp_path / 'conductor').resolve()))
+  paths.reset_resolved()
+  
   app_instance._cb_run_conductor_setup()
   
   # ANTI-SIMPLIFICATION: Assert that the summary output correctly counts files/lines/tracks

tests/test_gui_updates.py

@@ -58,6 +58,9 @@ def test_gui_updates_on_event(app_instance: App) -> None:
  mock_stats = {"percentage": 50.0, "current": 500, "limit": 1000}
  app_instance.last_md = "mock_md"
  with patch('src.ai_client.get_token_stats', return_value=mock_stats):
+  # Drain the queue
+  while not app_instance.event_queue.empty():
+   app_instance.event_queue.get()
   # Simulate receiving an event from the API client thread
   app_instance._on_api_event(payload={"text": "test"})
   

tests/test_live_gui_integration_v2.py

@@ -37,6 +37,10 @@ def test_user_request_integration_flow(mock_app: App) -> None:
    disc_text="History",
    base_dir="."
   )
+
+  while not app.controller.event_queue.empty():
+   app.controller.event_queue.get()
+
   # 2. Call the handler directly since start_services is mocked (no event loop thread)
   # But _handle_request_event itself puts a 'response' event in the queue.
   # Our mock_app fixture mocks start_services, so _process_event_queue is NOT running.
@@ -87,6 +91,10 @@ def test_user_request_error_handling(mock_app: App) -> None:
    disc_text="",
    base_dir="."
   )
+
+  while not app.controller.event_queue.empty():
+   app.controller.event_queue.get()
+
   app.controller._handle_request_event(event)
   
   # Manually consume from queue

tests/test_mma_dashboard_refresh.py

@@ -54,7 +54,7 @@ def test_mma_dashboard_refresh(app_instance: Any) -> None:
     assert len(app.tracks) == 2
     assert app.tracks[0]["id"] == "track_1"
     assert app.tracks[1]["id"] == "track_2"
-    mock_pm.get_all_tracks.assert_called_with(app.ui_files_base_dir)
+    mock_pm.get_all_tracks.assert_called_with(app.active_project_root)
 
 
 def test_mma_dashboard_initialization_refresh(app_instance: Any) -> None:

tests/test_paths.py

@@ -10,26 +10,31 @@ def reset_paths():
  paths.reset_resolved()
 
 def test_default_paths():
- assert paths.get_conductor_dir() == Path("conductor")
- assert paths.get_logs_dir() == Path("logs/sessions")
- assert paths.get_scripts_dir() == Path("scripts/generated")
- # config path should now be an absolute path relative to src/paths.py
  root_dir = Path(paths.__file__).resolve().parent.parent
+ assert paths.get_conductor_dir() == root_dir / "conductor"
+ assert paths.get_logs_dir() == root_dir / "logs/sessions"
+ assert paths.get_scripts_dir() == root_dir / "scripts/generated"
+ # config path should now be an absolute path relative to src/paths.py
  assert paths.get_config_path() == root_dir / "config.toml"
- assert paths.get_tracks_dir() == Path("conductor/tracks")
+ assert paths.get_tracks_dir() == root_dir / "conductor/tracks"
- assert paths.get_archive_dir() == Path("conductor/archive")
+ assert paths.get_archive_dir() == root_dir / "conductor/archive"
 
-def test_env_var_overrides(monkeypatch):
+def test_env_var_overrides(tmp_path, monkeypatch):
- monkeypatch.setenv("SLOP_CONDUCTOR_DIR", "custom_conductor")
+ root_dir = Path(paths.__file__).resolve().parent.parent
- monkeypatch.setenv("SLOP_LOGS_DIR", "custom_logs")
- monkeypatch.setenv("SLOP_SCRIPTS_DIR", "custom_scripts")
  
- assert paths.get_conductor_dir() == Path("custom_conductor")
+ # Relative env var (resolved against root_dir)
- assert paths.get_logs_dir() == Path("custom_logs")
+ monkeypatch.setenv("SLOP_CONDUCTOR_DIR", "custom_conductor")
- assert paths.get_scripts_dir() == Path("custom_scripts")
+ assert paths.get_conductor_dir() == (root_dir / "custom_conductor").resolve()
- assert paths.get_tracks_dir() == Path("custom_conductor/tracks")
+ 
+ paths.reset_resolved()
+ 
+ # Absolute env var
+ abs_logs = (tmp_path / "abs_logs").resolve()
+ monkeypatch.setenv("SLOP_LOGS_DIR", str(abs_logs))
+ assert paths.get_logs_dir() == abs_logs
 
 def test_config_overrides(tmp_path, monkeypatch):
+ root_dir = Path(paths.__file__).resolve().parent.parent
  config_file = tmp_path / "custom_config.toml"
  content = """
 [paths]
@@ -40,20 +45,12 @@ scripts_dir = "cfg_scripts"
  config_file.write_text(content)
  monkeypatch.setenv("SLOP_CONFIG", str(config_file))
  
- # Need to update the _CONFIG_PATH in paths.py since it's set at import
+ assert paths.get_conductor_dir() == (root_dir / "cfg_conductor").resolve()
- # Actually, the get_config_path() uses _CONFIG_PATH which is Path(os.environ.get("SLOP_CONFIG", "config.toml"))
+ assert paths.get_logs_dir() == root_dir / "cfg_logs"
- # But it's defined at module level. Let's see if we can reload it or if monkeypatching early enough works.
+ assert paths.get_scripts_dir() == root_dir / "cfg_scripts"
- # In src/paths.py: _CONFIG_PATH: Path = Path(os.environ.get("SLOP_CONFIG", "config.toml"))
- # This is set when src.paths is first imported.
- 
- # For the test to work, we might need to manually set paths._CONFIG_PATH or reload the module.
- # paths._CONFIG_PATH = config_file # No longer needed
- 
- assert paths.get_conductor_dir() == Path("cfg_conductor")
- assert paths.get_logs_dir() == Path("cfg_logs")
- assert paths.get_scripts_dir() == Path("cfg_scripts")
 
 def test_precedence(tmp_path, monkeypatch):
+ root_dir = Path(paths.__file__).resolve().parent.parent
  config_file = tmp_path / "custom_config.toml"
  content = """
 [paths]
@@ -63,7 +60,5 @@ conductor_dir = "cfg_conductor"
  monkeypatch.setenv("SLOP_CONFIG", str(config_file))
  monkeypatch.setenv("SLOP_CONDUCTOR_DIR", "env_conductor")
  
- # paths._CONFIG_PATH = config_file # No longer needed
- 
  # Env var should take precedence over config
- assert paths.get_conductor_dir() == Path("env_conductor")
+ assert paths.get_conductor_dir() == (root_dir / "env_conductor").resolve()