diff --git a/.gitignore b/.gitignore
index 00c76a3d41..7df5de28f2 100644
--- a/.gitignore
+++ b/.gitignore
@@ -58,4 +58,5 @@ docs/doxygen/
 # Per-user configuration
 .python-version
 .make_options
+.make_options.mk
 .*env
diff --git a/Makefile b/Makefile
index 6cbd903f7e..5aaf1f69ac 100644
--- a/Makefile
+++ b/Makefile
@@ -1,7 +1,7 @@
 # Build options can be changed by modifying the makefile or by building with 'make SETTING=value'.
-# It is also possible to override the settings in Defaults in a file called .make_options as 'SETTING=value'.
+# It is also possible to override the settings in Defaults in a file called .make_options.mk as 'SETTING=value'.
 
--include .make_options
+-include .make_options.mk
 
 MAKEFLAGS += --no-builtin-rules
 
@@ -433,7 +433,7 @@ assetclean:
 	$(RM) -r $(ASSET_BIN_DIRS)
 	$(RM) -r $(BUILD_DIR)/assets
 	$(RM) -r assets/text/*.h
-	$(RM) -r .extracted-assets.json
+	$(RM) -r $(EXTRACTED_DIR)/.extracted-assets.json
 
 distclean: assetclean clean
 	$(RM) -r asm data extracted
@@ -457,7 +457,7 @@ setup-audio:
 	$(AUDIO_EXTRACT) -o $(EXTRACTED_DIR) -v $(VERSION) --read-xml
 
 assets:
-	$(PYTHON) extract_assets.py $(EXTRACTED_DIR)/baserom assets -j$(N_THREADS) -Z Wno-hardcoded-pointer
+	$(PYTHON) tools/extract_assets.py $(EXTRACTED_DIR)/baserom assets -j$(N_THREADS) -Z Wno-hardcoded-pointer -v $(VERSION)
 	$(AUDIO_EXTRACT) -o $(EXTRACTED_DIR) -v $(VERSION) --read-xml
 
 ## Assembly generation
diff --git a/extract_assets.py b/tools/extract_assets.py
similarity index 93%
rename from extract_assets.py
rename to tools/extract_assets.py
index 7c69c3b4c3..cb8ace7c2f 100755
--- a/extract_assets.py
+++ b/tools/extract_assets.py
@@ -5,8 +5,6 @@ from pathlib import Path
 
 colorama.init()
 
-EXTRACTED_ASSETS_NAMEFILE = ".extracted-assets.json"
-
 dontGenerateCFilesList = [
     "map_grand_static",
     "map_i_static",
@@ -95,6 +93,7 @@ def main():
         type=Path,
         help="Output directory to place files in",
     )
+    parser.add_argument("-v", "--version", help="Which version should be processed", default="n64-us")
     parser.add_argument("-s", "--single", help="asset path relative to assets/, e.g. objects/gameplay_keep")
     parser.add_argument("-f", "--force", help="Force the extraction of every xml instead of checking the touched ones.", action="store_true")
     parser.add_argument("-j", "--jobs", help="Number of cpu cores to extract with.")
@@ -128,9 +127,10 @@ def main():
     manager = multiprocessing.Manager()
     signal.signal(signal.SIGINT, SignalHandler)
 
+    extractedAssetsFile = Path("extracted") / args.version / ".extracted-assets.json"
     extractedAssetsTracker = manager.dict()
-    if not args.force and os.path.exists(EXTRACTED_ASSETS_NAMEFILE):
-        with open(EXTRACTED_ASSETS_NAMEFILE, encoding='utf-8') as f:
+    if not args.force and extractedAssetsFile.exists():
+        with extractedAssetsFile.open(encoding='utf-8') as f:
             extractedAssetsTracker.update(json.load(f, object_hook=manager.dict))
 
     extract_text_path = outputDir / "text/message_data.h"
@@ -139,11 +139,11 @@ def main():
     asset_path = args.single
     if asset_path is not None:
         if "text/" in asset_path:
-            from tools.msg.nes import msgdisNES
+            from msg.nes import msgdisNES
             print("Extracting message_data")
             msgdisNES.main(extract_text_path)
 
-            from tools.msg.staff import msgdisStaff
+            from msg.staff import msgdisStaff
             print("Extracting staff_message_data")
             msgdisStaff.main(extract_staff_text_path)
         else:
@@ -160,12 +160,12 @@ def main():
     else:
         # Only extract text if the header does not already exist, or if --force was passed
         if args.force or not os.path.isfile(extract_text_path):
-            from tools.msg.nes import msgdisNES
+            from msg.nes import msgdisNES
             print("Extracting message_data")
             msgdisNES.main(baseromSegmentsDir, extract_text_path)
 
         if args.force or not os.path.isfile(extract_staff_text_path):
-            from tools.msg.staff import msgdisStaff
+            from msg.staff import msgdisStaff
             print("Extracting staff_message_data")
             msgdisStaff.main(baseromSegmentsDir, extract_staff_text_path)
 
@@ -191,7 +191,7 @@ def main():
             for singlePath in xmlFiles:
                 ExtractFunc(singlePath)
 
-    with open(EXTRACTED_ASSETS_NAMEFILE, 'w', encoding='utf-8') as f:
+    with extractedAssetsFile.open('w', encoding='utf-8') as f:
         serializableDict = dict()
         for xml, data in extractedAssetsTracker.items():
             serializableDict[xml] = dict(data)