clean gitignore

.gitignore

@@ -1,25 +1,88 @@
-# 1. Broad Ignores
-/Data/*
-/attach/*
-/results/*
-/enarcelona/*
-.env
+# =========================
+# Python
+# =========================
 __pycache__/
-*.pyc
-*.csv
-=======
-/reference/
-*.svg
-**/*.csv
-**/*.json*
-**/*.txt*
-**/*.png*
-*.log
->>>>>>> Stashed changes
-# 2. Ignore virtual environments COMPLETELY
-# This must come BEFORE the unignore rule
-env*/
+*.py[cod]
+*$py.class
+.ipynb_checkpoints/
 
-# 3. The "Unignore" rule (Whitelisting)
-# We only unignore .py files that aren't already blocked by the rules above
-!**/*.py
+# =========================
+# Virtual environments
+# =========================
+env/
+env*/
+venv/
+.venv/
+enarcelona/
+
+# =========================
+# Secrets
+# =========================
+.env
+*.env
+
+# =========================
+# Patient data / sensitive data
+# =========================
+Data/
+data/raw/
+data/processed/
+data/ground_truth/
+reference/
+
+# =========================
+# Generated results and logs
+# =========================
+results/
+results_edss_benchmark/
+*.log
+
+# =========================
+# Large/generated file types
+# =========================
+*.csv
+*.tsv
+*.json
+*.jsonl
+*.xlsx
+*.xls
+*.png
+*.PNG
+*.jpg
+*.jpeg
+*.svg
+*.pdf
+
+# =========================
+# Temporary / backup files
+# =========================
+*.tmp
+*.bak
+*.orig
+.DS_Store
+
+# =========================
+# Keep important code/config/docs
+# =========================
+!README.md
+!requirements.txt
+!*.py
+!*.md
+!*.yml
+!*.yaml
+!*.toml
+
+# Keep prompt templates / schemas if safe to publish
+!prompts/
+!prompts/**
+!attach/
+!attach/*.gbnf
+!attach/just_edss_text.txt
+!attach/Komplett.txt
+
+# Keep example/synthetic data only
+!data/
+!data/example/
+!data/example/**
+!Data/example/
+!Data/example/**