diff --git a/.jules/superintendent.md b/.jules/superintendent.md
new file mode 100644
index 000000000..626777bb1
--- /dev/null
+++ b/.jules/superintendent.md
@@ -0,0 +1,2 @@
+Instability: Root directory hallway trash (.py scripts dumped without structure).
+Fortification: Swept all stray python utility scripts into a dedicated scripts/ directory to maintain strict root hygiene.
diff --git a/.phpunit.cache/test-results b/.phpunit.cache/test-results
deleted file mode 100644
index b5eb77a67..000000000
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\ No newline at end of file
diff --git a/ARCHITECTURE.md b/ARCHITECTURE.md
index e19e094db..497609769 100644
--- a/ARCHITECTURE.md
+++ b/ARCHITECTURE.md
@@ -603,4 +603,7 @@ The Sovereign Agent Blueprint for the Next.js Frontend RAG Agent is documented t
 This project integrates the Progressive Disclosure Level 2 schema from [LEXICON.md](LEXICON.md) (DRP-LEXICON-992). This standard defines core pattern definitions such as Isomorphic Bridges, Paraconsistent Scarring, and Topological Orthogonality Hypotheses. It provides PDL decorators to mitigate pathological decays (like Semantic Saponification and Polyglot Hallucination Resonance) and emergent use cases at orthogonal domain intersections.
 
 ## Metrological Conformance
-The operational workflow incorporates Draft-Conditioned Constrained Decoding and Semantic Metrology via `validate_pdt_specification.py`, ensuring `AGENTS.md` mathematically bounds execution paths and prevents logical deviations during autonomous recursive loops.
+The operational workflow incorporates Draft-Conditioned Constrained Decoding and Semantic Metrology via `scripts/validate_pdt_specification.py`, ensuring `AGENTS.md` mathematically bounds execution paths and prevents logical deviations during autonomous recursive loops.
+
+## Infrastructure and Tooling
+- `scripts/`: Centralized directory for utility scripts.
diff --git a/mcp_server.py b/scripts/mcp_server.py
similarity index 100%
rename from mcp_server.py
rename to scripts/mcp_server.py
diff --git a/pdl_extractor.py b/scripts/pdl_extractor.py
similarity index 100%
rename from pdl_extractor.py
rename to scripts/pdl_extractor.py
diff --git a/validate_pdt_specification.py b/scripts/validate_pdt_specification.py
similarity index 100%
rename from validate_pdt_specification.py
rename to scripts/validate_pdt_specification.py