diff --git a/Makefile b/Makefile
index 33416c6ba..bb7b1a8e9 100644
--- a/Makefile
+++ b/Makefile
@@ -3,8 +3,11 @@ SIM_TOP = SimTop
 FPGATOP = NutShellFPGATop
 
 BUILD_DIR = $(abspath ./build)
-SIM_TOP_V = $(BUILD_DIR)/$(SIM_TOP).v
-TOP_V = $(BUILD_DIR)/$(TOP).v
+
+RTL_DIR = $(BUILD_DIR)/rtl
+SIM_TOP_V = $(RTL_DIR)/$(SIM_TOP).v
+TOP_V = $(RTL_DIR)/$(TOP).v
+
 SCALA_FILE = $(shell find ./src/main/scala -name '*.scala')
 TEST_FILE = $(shell find ./src/test/scala -name '*.scala')
 
@@ -17,7 +20,7 @@ DATAWIDTH ?= 64
 BOARD ?= sim  # sim  pynq  axu3cg
 CORE  ?= inorder  # inorder  ooo  embedded
 
-MILL_ARGS = -td $(@D) BOARD=$(BOARD) CORE=$(CORE)
+MILL_ARGS = -td $(RTL_DIR) BOARD=$(BOARD) CORE=$(CORE)
 FPGA_ARGS =
 
 # If firtool is not specified and not found in PATH, download and cache it.
@@ -40,6 +43,8 @@ ifneq ($(FIRTOOL),)
 MILL_ARGS += --firtool-binary-path $(FIRTOOL)
 endif
 
+EXTRACTOR = $(abspath ./scripts/extract_files.sh)
+
 .DEFAULT_GOAL = verilog
 
 help:
@@ -49,7 +54,7 @@ $(TOP_V): $(SCALA_FILE)
 	mkdir -p $(@D)
 	mill -i generator.test.runMain top.$(TOP) $(MILL_ARGS) $(FPGA_ARGS)
 	@mv $(SIM_TOP_V) $(TOP_V)
-	@cd $(BUILD_DIR) && bash ../scripts/extract_files.sh $(TOP_V)
+	@cd $(RTL_DIR) && bash $(EXTRACTOR) $(TOP_V)
 	sed -i -e 's/_\(aw\|ar\|w\|r\|b\)_\(\|bits_\)/_\1/g' $@
 	@git log -n 1 >> .__head__
 	@git diff >> .__diff__
@@ -74,7 +79,7 @@ $(SIM_TOP_V): $(SCALA_FILE) $(TEST_FILE)
 	mill -i generator.test.runMain $(SIMTOP) $(MILL_ARGS)
 	@sed -i 's/$$fatal/xs_assert(`__LINE__)/g' $(SIM_TOP_V)
 	@sed -i -e "s/\$$error(/\$$fwrite(32\'h80000002, /g" $(SIM_TOP_V)
-	@cd $(BUILD_DIR) && bash ../scripts/extract_files.sh $(SIM_TOP_V)
+	@cd $(RTL_DIR) && bash $(EXTRACTOR) $(SIM_TOP_V)
 
 sim-verilog: $(SIM_TOP_V)
 
diff --git a/difftest b/difftest
index cbcc80169..63d130444 160000
--- a/difftest
+++ b/difftest
@@ -1 +1 @@
-Subproject commit cbcc801699c7b20de84f3bc15f03f3f24c72d400
+Subproject commit 63d130444215b07fa1b2236911699c3b503edd67
diff --git a/scripts/extract_files.sh b/scripts/extract_files.sh
deleted file mode 100644
index 98b19006d..000000000
--- a/scripts/extract_files.sh
+++ /dev/null
@@ -1,52 +0,0 @@
-#!/bin/bash
-
-# Check if input file is provided
-if [ "$#" -ne 1 ]; then
-    echo "Usage: $0 <input-file>"
-    exit 1
-fi
-
-input_file="$1"
-
-# Check if input file exists
-if [ ! -f "$input_file" ]; then
-    echo "Error: File '$input_file' not found!"
-    exit 1
-fi
-
-# Set initial state to false
-extract=false
-output_file=""
-temp_file=$(mktemp)
-
-# Read input file line by line
-while IFS= read -r line; do
-    # Check if line contains the marker
-    if [[ $line == *'// ----- 8< ----- FILE'* ]]; then
-        # Set extract state to true
-        extract=true
-        # Extract filename from the line
-        output_file=$(echo "$line" | grep -o '".*"' | tr -d '"')
-        # Check if output file is not empty
-        if [ -z "$output_file" ]; then
-            echo "Error: Could not extract filename!"
-            exit 1
-        fi
-        # Create/overwrite the output file
-        : > "$output_file"
-    elif [ "$extract" = true ]; then
-        # Write line to output file
-        echo "$line" >> "$output_file"
-    else
-        # Write line to temporary file
-        echo "$line" >> "$temp_file"
-    fi
-
-    # Reset extract flag if endmodule is encountered
-    if [[ $line == "endmodule" ]]; then
-        extract=false
-    fi
-done < "$input_file"
-
-# Replace the original file with the temporary file
-mv "$temp_file" "$input_file"
\ No newline at end of file