chore: update .gitignore to include additional patterns and reorganize entries for clarity

Author: danihae

.gitignore

@@ -1,19 +1,56 @@
+# IDE / editors
 .idea/
-.venv/
-.pytest_cache/
-/build/
-/dist/
-/.DS_Store
-/private/
-/.vscode/
+.vscode/
+*.swp
+*.swo
+*~
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Python
 *.pyc
 *.pyo
 *.pyd
 __pycache__/
 *.egg-info/
+*.egg
+build/
+dist/
+*.whl
+.eggs/
+
+# Virtual environments
+.venv/
+venv/
+env/
+
+# Testing / coverage
+.pytest_cache/
+.coverage
+htmlcov/
+.tox/
+.nox/
+
+# Logs
 *.log
-*.DS_Store
-sarcasm/.DS_Store
-scripts/.DS_Store
+
+# Jupyter
+.ipynb_checkpoints/
+dev.ipynb
+
+# Project-specific
+/private/
 uv.lock
-dev.ipynb
+
+# Test data analysis outputs (generated by running the pipeline on test inputs)
+test_data/_*
+test_data/**/zbands.tif
+test_data/**/mbands.tif
+test_data/**/orientation.tif
+test_data/**/cell_mask.tif
+test_data/**/sarcomere_mask.tif
+test_data/**/flow.tif
+test_data/**/data/
+test_data/**/analysis/