Document supplementary diagnostics script and tidy repo

- Rename diagnostics_extreme_and_combined.py to supplementary_diagnostics.py
- Reframe its docstring as supplementary analysis referenced in the Discussion
- Add README pointer to it
- Remove stale results/rule_dynamics/discussion_draft.md

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

README.md

@@ -6,12 +6,14 @@ database connection is needed.
 
 ## How to run
 ### Activate a python env and install deps
-`python -m venv .venv`
+`python -m venv .venv` (I used python version 3.13.3)
 `source ./.venv/Scripts/activate`
 `pip install -r requirements.txt`
 
 ### Run all experiments
 `python run_all_experiments.py`
+or when wanting to re run everything from scratch
+`python run_all_experiments.py --start-fresh`
 
 (The Weka JRip baseline additionally needs a Java runtime; it is skipped
 automatically if `java`/`weka.jar` are unavailable.)
@@ -19,3 +21,6 @@ automatically if `java`/`weka.jar` are unavailable.)
 ### Further info
 - `./results` holds all saved data behind the figures, including the learned rules.
 - the results that were used are in the subfolder `/pooled` (pooled over the 5 folds).
+- `supplementary_diagnostics.py` reproduces the secondary analyses referenced in the
+  Discussion (extreme-lambda behaviour and the combined grow+prune+MDL variant). These are
+  exploratory, single-repeat checks and are not part of the primary study.