diff --git a/data/tool-guides/aesthetic-quality-guide.md b/data/tool-guides/aesthetic-quality-guide.md
index 5c3be39..38c311e 100644
--- a/data/tool-guides/aesthetic-quality-guide.md
+++ b/data/tool-guides/aesthetic-quality-guide.md
@@ -2,7 +2,7 @@
 title: "Aesthetic Quality & Stylistic Coherence Guide"
 category: "scene-design"
 tags: ["aesthetic", "quality", "style", "decorative", "detail", "execute_code", "procedural", "torch", "lantern", "ornament", "medieval", "modern", "furniture"]
-description: "Principles for creating visually convincing, aesthetically rich 3D scenes. Prevents minimalistic primitive-based shortcuts and teaches the agent to match object detail to scene context using execute_code for complex geometry."
+description: "Principles for creating visually convincing, aesthetically rich 3D scenes. Prevents minimalistic primitive-based shortcuts and teaches the agent to match object detail to scene context while preferring direct tools before execute_code fallbacks."
 blender_version: "5.0+"
 ---
 
@@ -35,15 +35,18 @@ Every named object in the scene should have AT LEAST:
 - **Architectural features:** Follow the Architectural Completeness Guide
 - **Organic shapes:** Use subdivision + proportional editing, never raw primitives
 
-### When to Use `execute_code` Instead of Basic Tools
-Use `execute_code` with Python scripting for ANY object that:
+### When to Use Direct Tools First
+
+Use direct tools first for repeatable operations: transforms, materials, lighting, cameras, render settings, collection organization, parenting, modifiers, constraints, mesh validation, and viewport verification.
+
+Use `execute_code` only when direct tools cannot express the required custom geometry, such as an object that:
 1. Has **irregular or organic shapes** (flames, plants, terrain, fabric)
 2. Requires **multi-part assembly** (torch = bracket + handle + flame)
 3. Needs **vertex-level manipulation** (tapering, bending, sculpting)
 4. Benefits from **loop cuts or edge detail** (beveled edges, chamfers)
 5. Involves **array/curve modifiers** for repeated elements (chain links, bricks, spiral stairs)
 
-**Rule:** If you catch yourself making a single `create_cube` or `create_cylinder` call for a decorative object, STOP and use `execute_code` to build it properly.
+**Rule:** If you catch yourself making a single `create_cube` or `create_cylinder` call for a decorative object, STOP and decompose it into a multi-part assembly. Use direct tools for the parts they cover, and use a focused `execute_code` fallback only for the custom geometry that remains.
 
 ## STYLISTIC COHERENCE
 
diff --git a/data/tool-guides/architectural-completeness-guide.md b/data/tool-guides/architectural-completeness-guide.md
index b40cf32..96aabce 100644
--- a/data/tool-guides/architectural-completeness-guide.md
+++ b/data/tool-guides/architectural-completeness-guide.md
@@ -65,17 +65,8 @@ bpy.data.objects.remove(cutter)
 # Glass pane fills the window opening
 glass = create_cube("Window_Glass", 1, (-2.0, 0, 1.4), (0.02, 1.9, 1.1))
 
-# EEVEE glass material via execute_code
-mat = bpy.data.materials.new("Glass_Mat")
-mat.use_nodes = True
-mat.blend_method = 'BLEND'  # Required for transparency in 5.x
-nodes = mat.node_tree.nodes
-bsdf = nodes["Principled BSDF"]
-bsdf.inputs["Transmission Weight"].default_value = 0.95
-bsdf.inputs["IOR"].default_value = 1.5
-bsdf.inputs["Roughness"].default_value = 0.0
-bsdf.inputs["Base Color"].default_value = (0.9, 0.95, 1.0, 1.0)
-glass.data.materials.append(mat)
+# Then call create_material_preset with preset "glass" and object_name "Window_Glass".
+# Follow with inspect_material_node_graph to verify Transmission Weight, IOR, and assignment.
 ```
 
 **EEVEE Note:** For interior scenes, using a Transparent shader instead of Glass may prevent light bleed artifacts if exact refraction isn't needed.
diff --git a/data/tool-guides/local-asset-guide.md b/data/tool-guides/local-asset-guide.md
index 311846d..d53c186 100644
--- a/data/tool-guides/local-asset-guide.md
+++ b/data/tool-guides/local-asset-guide.md
@@ -41,7 +41,8 @@ Choose PolyHaven when:
 - the local library does not contain a suitable match
 
 Keep the workflow hybrid:
-- use direct tools and `execute_code` for room structure, spatial layout, cameras, lights, and custom hero forms
+- use direct tools for room structure, spatial layout, cameras, lights, transforms, and render setup
+- reserve `execute_code` for unsupported custom hero forms or procedural geometry that direct tools cannot express
 - use local curated assets for commodity props that benefit from a prepared silhouette
 - after import, always treat scale and orientation as suspect until checked in scene context
 
diff --git a/data/tool-guides/object-assembly-guide.md b/data/tool-guides/object-assembly-guide.md
index 23015a1..6757197 100644
--- a/data/tool-guides/object-assembly-guide.md
+++ b/data/tool-guides/object-assembly-guide.md
@@ -209,26 +209,9 @@ wheel_positions = [
 ### When to Parent
 - **Always parent** when the object should move/rotate as one unit
 - **Use an Empty as root** for easy manipulation of the whole assembly
-- **Parent in Python** using `parent_set` tool or `execute_code`
+- **Prefer direct tools**: use `parent_set` for parent-child links and `organize_collection_hierarchy` when grouping, collection movement, parenting, and visibility changes belong in one batch
 
-### Parenting in execute_code
-```python
-import bpy
-
-# Create root empty
-bpy.ops.object.empty_add(type='PLAIN_AXES', location=(0, 0, 0))
-root = bpy.context.active_object
-root.name = "Lamp_Root"
-
-# Parent all parts to root (keep visual position)
-for part_name in ["Lamp_Pole", "Lamp_Arm", "Lamp_Head", "Lamp_Base"]:
-    part = bpy.data.objects.get(part_name)
-    if part:
-        part.parent = root
-        part.matrix_parent_inverse = root.matrix_world.inverted()
-```
-
-**Key:** Setting `matrix_parent_inverse` to the parent's inverted world matrix prevents the child from "jumping" to a new position when parented.
+`parent_set` and `organize_collection_hierarchy` preserve world transforms so child objects do not visually jump when parented. Use `execute_code` only if the root helper object itself must be procedurally generated and no direct creation tool covers it.
 
 ### Using parent_set MCP Tool
 ```
@@ -252,5 +235,5 @@ After assembling a compound object, verify:
 3. ❌ **Forgetting that cylinder depth is FULL height, not half** — A `depth=3.5` cylinder extends 1.75m above and below its origin
 4. ❌ **Not accounting for object radius in side attachments** — An arm touching a pole must offset by `pole_radius + arm_radius`, not just `arm_length/2`
 5. ❌ **Hardcoding heights instead of calculating from connected parts** — If you change the pole height later, all attachment points break
-6. ❌ **Parenting without setting `matrix_parent_inverse`** — Child objects will visually jump to unexpected positions
+6. ❌ **Hand-writing parenting logic when direct tools cover it** — Use `parent_set` or `organize_collection_hierarchy` so world transforms are preserved and child objects do not visually jump
 7. ❌ **Building top-down** — Always start from the ground up to prevent accumulated positioning errors
diff --git a/scripts/test/test-direct-tool-guide-cleanup-secondary.ts b/scripts/test/test-direct-tool-guide-cleanup-secondary.ts
new file mode 100644
index 0000000..ee5f477
--- /dev/null
+++ b/scripts/test/test-direct-tool-guide-cleanup-secondary.ts
@@ -0,0 +1,28 @@
+import assert from "node:assert/strict"
+import { readFileSync } from "node:fs"
+
+const guides = {
+    architecturalCompleteness: readFileSync("data/tool-guides/architectural-completeness-guide.md", "utf8"),
+    localAsset: readFileSync("data/tool-guides/local-asset-guide.md", "utf8"),
+    objectAssembly: readFileSync("data/tool-guides/object-assembly-guide.md", "utf8"),
+    aestheticQuality: readFileSync("data/tool-guides/aesthetic-quality-guide.md", "utf8"),
+}
+
+assert.doesNotMatch(guides.architecturalCompleteness, /glass material via execute_code/i)
+assert.match(guides.architecturalCompleteness, /create_material_preset/)
+assert.match(guides.architecturalCompleteness, /inspect_material_node_graph/)
+
+assert.doesNotMatch(guides.localAsset, /use direct tools and `execute_code` for room structure, spatial layout, cameras, lights/)
+assert.match(guides.localAsset, /direct tools for room structure, spatial layout, cameras, lights/)
+
+assert.doesNotMatch(guides.objectAssembly, /Parent in Python/)
+assert.doesNotMatch(guides.objectAssembly, /Parenting in execute_code/)
+assert.doesNotMatch(guides.objectAssembly, /matrix_parent_inverse/)
+assert.match(guides.objectAssembly, /parent_set/)
+assert.match(guides.objectAssembly, /organize_collection_hierarchy/)
+
+assert.doesNotMatch(guides.aestheticQuality, /using execute_code for complex geometry/)
+assert.doesNotMatch(guides.aestheticQuality, /Use `execute_code` with Python scripting for ANY object/)
+assert.match(guides.aestheticQuality, /Use direct tools first/)
+
+console.log("Secondary direct tool guide cleanup tests passed")