From d5fabf77757240d2b98e5ce1381f4e76e8e0e515 Mon Sep 17 00:00:00 2001
From: "google-labs-jules[bot]"
 <161369871+google-labs-jules[bot]@users.noreply.github.com>
Date: Wed, 2 Sep 2026 16:05:00 +0000
Subject: [PATCH] Docs: update bolt.md with CC3D semantics learnings

Co-authored-by: NoWon1 <126711057+NoWon1@users.noreply.github.com>
---
 .jules/bolt.md | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.jules/bolt.md b/.jules/bolt.md
index 133dfbf..d1b5d22 100644
--- a/.jules/bolt.md
+++ b/.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.