⚡ Bolt: Update journal with CC3D loop safety learnings

.jules/bolt.md

@@ -4,3 +4,6 @@
 ## 2026-08-30 - Pre-calculate nested spatial loops bounds in CC3D
 **Learning:** Checking boundary conditions (e.g., `0 <= x < self.dim.x`) during *every single iteration* inside tightly nested loops degrades performance in operations executed frequently per MCS (like cell removals or checking neighborhood contacts).
 **Action:** When a bounding box is known relative to a central coordinate, use `min` and `max` with grid dimensions *outside* the loop to strictly bound the `range()` generators, completely eliminating conditionally evaluated boundary checks inside the innermost loop body.
+## 2023-10-27 - CC3D Steppable Safety and Semantics
+**Learning:** In CompuCell3D, attempting to optimize `O(N)` loops by combining sequential physics operations (like secretion then degradation) into a single iteration over `self.cell_list` alters the fundamental physics of the simulation by interleaving state updates. Additionally, `self.cell_list` is dynamic; removing dictionary existence checks for `cell.id` on hot paths causes `KeyError` regressions when cells divide.
+**Action:** Do not combine sequential loop operations that compute distinct simulation steps. Never remove `cell.id` initialization checks from state dictionaries in hot paths, as cells are dynamically created during the simulation.