Update TODO.md — mark completed items, add plan for σ-reduction blocker and next steps

TODO.md

@@ -1,26 +1,42 @@
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-
-#### `TODO.md`
-```markdown
 # TODO (Prioritised)
 
 ## Immediate (blockers)
-- **Add candidate snapshot to beam logs** (if not already present) so each accepted candidate can be inspected offline.  
-- **Ensure gate values are booleans** in logs (coerce string values).  
-- **Make tile transform nontrivial** (shifted tiling) so transforms can change the field.  
-- **Implement robust fill_enclosed** (dependency‑free BFS hole filler).
+- ~~**Add candidate snapshot to beam logs**~~ ✅ Done — `beam_logging.py` logs candidates; `fix_and_inspect_logs.py` attaches `candidate_array` post‑hoc.
+- ~~**Ensure gate values are booleans**~~ ✅ Done — `coerce_gates()` in `fix_and_inspect_logs.py` and `postprocess_logs.py`.
+- ~~**Make tile transform nontrivial**~~ ⚠️ Partial — `ShiftedTile` exists in `transforms.py` but is **not wired into `default_atomic_factory`**. The beam only sees vanilla `tile_to_target` (idempotent), so σ never decreases. **This is the critical blocker.**
+- ~~**Implement robust fill_enclosed**~~ ✅ Done — BFS implementation in `solver_core.py`.
+
+### ➡️ Next: Fix σ=98 flatline (residue never decreases)
+The beam composes `tile_to_target ∘ tile_to_target` which is idempotent — tiling an already-tiled grid returns the same grid. The atomic library needs transforms that can actually express the input→target mapping.
+
+**Plan:**
+1. **Wire `ShiftedTile` into `default_atomic_factory`** so the beam can explore shifted tilings.
+2. **Add region‑aware placement transforms** — the example1 target is a 3×3 arrangement of sub‑blocks where each 3×3 quadrant is a conditional variant of the input (some reflected, some identity, some zero‑filled). The library needs transforms that place sub‑blocks at specific offsets.
+3. **Add conditional fill / mask‑based composition** — transforms that zero‑out or overwrite specific quadrants based on input symmetry.
+4. **Re‑run sweep** with enriched library and verify σ decreases below 98.
 
 ## Short term
-- Add CLI entrypoint with `--use_wandb` flag (default: false).  
+- ~~Add CLI entrypoint with `--use_wandb` flag~~ ✅ Done — `scripts/entrypoint.py`.
 - Add unit tests for `tile_transform`, `fill_enclosed`, and transform `.apply()` semantics.  
+  - `tests.py` has `run_atomic_effects` and `transform_effect_test` but no proper pytest suite yet.
 - Add small visualization notebook for `phi_best`, diff maps, and Layer‑1 masks.
 
 ## Medium term
-- Improve Layer‑1 mask generation (percentile + min_abs + dilation).  
-- Add a toggle to include/exclude `candidate_array` in logs to control log size.  
-- Create a reproducible benchmark harness for parameter sweeps and CSV aggregation.
+- ~~Improve Layer‑1 mask generation~~ ✅ Done — percentile + min_abs + dilation in `layer_minus_one.py`.
+- Add a toggle to include/exclude `candidate_array` in logs to control log size.
+- ~~Create a reproducible benchmark harness for parameter sweeps and CSV aggregation~~ ✅ Done — `experiment_driver.sweep()` + `results.csv`. Needs more tasks.
 
 ## Long term
-- Integrate a safe external W&B uploader (runs after experiments finish).  
-- Add more ARC tasks and automated evaluation harness.  
+- ~~Integrate a safe external W&B uploader~~ ✅ Done — `wandb_runner.py` runs after experiments finish, decoupled from core.
+- Add more ARC tasks and automated evaluation harness.
 - Document reproducibility steps and expected outputs for each example task.
+
+## Code hygiene (completed)
+- ~~Duplicate `Transform` class in `transforms.py`~~ ✅ Fixed — now imports from `solver_core`.
+- ~~Duplicate imports/paste blocks in `solver_core.py`~~ ✅ Fixed — single clean definition.
+- ~~Lambda closure bug in `default_atomic_factory`~~ ✅ Fixed — captures `target_shape` by value.
+- ~~`wandb_runner.py` `int(generate_id(), 36)` crash~~ ✅ Fixed — uses string ID directly.
+- ~~`minimal_runner.py` TARGET was all‑zeros~~ ✅ Fixed — uses real example1 target.
+- ~~README.md referenced non‑existent paths~~ ✅ Fixed — corrected to actual repo structure.
+- ~~Committed `.pyc` files~~ ✅ Fixed — deleted + `.gitignore` added.
+- ~~`itt_solver/README.md.md` double extension~~ ✅ Fixed — renamed to `README.md`.