Implement background exclusion and refactor folder structure

- Added configurable background exclusion (#1f2937) with tolerance
- Implemented alpha thresholding (>= 128) to eliminate edge artifacts
- Refactored folder structure into analyses/[slug]/images, settings, and results
- Updated pattern puller to skip existing images and handle network errors
- Updated .gitignore and automated tests for path integrity

tests/test_file_paths.py

@@ -0,0 +1,72 @@
+import pytest
+from pathlib import Path
+from unittest.mock import MagicMock, patch
+
+from PySide6 import QtWidgets
+from app.qt.main_window import MainWindow
+from app.qt.pattern_puller import PatternDownloadWorker
+
+
+@pytest.fixture
+def qt_app():
+    from PySide6.QtWidgets import QApplication
+    import sys
+    app = QApplication.instance()
+    if app is None:
+        app = QApplication(sys.argv)
+    yield app
+
+
+def test_export_settings_path_generation(qt_app, tmp_path):
+    mock_widget = QtWidgets.QWidget()
+    mock_widget.title_label = MagicMock()
+    mock_widget.apply_theme = MagicMock()
+    with patch('app.qt.main_window.TitleBar', return_value=mock_widget):
+        window = MainWindow(language="en", defaults={}, reset_exclusions=False)
+    
+    with patch("PySide6.QtWidgets.QFileDialog.getSaveFileName", return_value=("", "")) as mock_get_save:
+        
+        # Test case 1: New subfolder structure (analyses/m4a1-s/images/1.png)
+        root = tmp_path / "analyses" / "m4a1_s"
+        img_dir = root / "images"
+        img_dir.mkdir(parents=True)
+        img_path = img_dir / "1.png"
+        
+        window._current_image_path = img_path
+        window.export_settings()
+        
+        # Verify settings directory was created
+        assert (root / "settings").exists()
+        
+        # Verify default path given to QFileDialog
+        args, kwargs = mock_get_save.call_args
+        # args[2] is the default path string
+        expected_path = str(root / "settings" / "icra_settings_m4a1_s.json")
+        assert args[2] == expected_path
+
+
+def test_export_folder_path_generation(qt_app, tmp_path):
+    mock_widget = QtWidgets.QWidget()
+    mock_widget.title_label = MagicMock()
+    mock_widget.apply_theme = MagicMock()
+    with patch('app.qt.main_window.TitleBar', return_value=mock_widget):
+        window = MainWindow(language="en", defaults={}, reset_exclusions=False)
+
+    with patch("PySide6.QtWidgets.QFileDialog.getSaveFileName", return_value=("", "")) as mock_get_save:
+        # Mock processor paths
+        root = tmp_path / "analyses" / "m4a1_s"
+        img_dir = root / "images"
+        img_dir.mkdir(parents=True)
+        window.processor.preview_paths = [img_dir / "1.png"]
+        
+        window.export_folder()
+        
+        assert (root / "results").exists()
+        args, kwargs = mock_get_save.call_args
+        expected_path = str(root / "results" / "icra_results_m4a1_s.csv")
+        assert args[2] == expected_path
+
+
+def test_pattern_download_worker_dir(tmp_path):
+    worker = PatternDownloadWorker(slug="test-slug", save_dir=tmp_path / "analyses" / "test-slug" / "images")
+    assert worker.save_dir == tmp_path / "analyses" / "test-slug" / "images"