diff --git a/.gitmodules b/.gitmodules
index ea797ad4b1..746dc80584 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -7,6 +7,7 @@
 [submodule "tools/decomp-permuter"]
 	path = tools/decomp-permuter
 	url = https://github.com/simonlindholm/decomp-permuter
+	branch = main
 [submodule "ZAPD"]
 	path = tools/ZAPD
 	url = https://github.com/zeldaret/ZAPD.git
diff --git a/Makefile b/Makefile
index 01dcc77d08..cdb2997f92 100644
--- a/Makefile
+++ b/Makefile
@@ -212,7 +212,10 @@ distclean: assetclean clean
 
 ## Extraction step
 setup:
-	git submodule update --init --recursive
+	# Initialize submodules, fetching commit in case it is not on the default branch
+	-git submodule update --init --recursive
+	git submodule foreach --recursive 'git fetch origin $$sha1'
+	git submodule update --recursive
 	python3 -m pip install -r requirements.txt
 	$(MAKE) -C tools
 	./tools/extract_rom.py $(MM_BASEROM)
diff --git a/tools/gen_mips_to_c_context.py b/tools/gen_mips_to_c_context.py
index 5d89bc6c5d..2767457f4f 100755
--- a/tools/gen_mips_to_c_context.py
+++ b/tools/gen_mips_to_c_context.py
@@ -1,4 +1,4 @@
-#!/usr/bin/python3
+#!/usr/bin/env python3
 
 import os
 import sys
diff --git a/tools/m2ctx.py b/tools/m2ctx.py
index a3dad5974f..c3f06cc7c2 100755
--- a/tools/m2ctx.py
+++ b/tools/m2ctx.py
@@ -1,4 +1,4 @@
-#!/usr/bin/python3
+#!/usr/bin/env python3
 
 import os
 import sys
diff --git a/tools/overlayhelpers/ichaindis.py b/tools/overlayhelpers/ichaindis.py
index d899bde77c..1bacff1972 100755
--- a/tools/overlayhelpers/ichaindis.py
+++ b/tools/overlayhelpers/ichaindis.py
@@ -1,4 +1,4 @@
-#!/usr/bin/python3
+#!/usr/bin/env python3
 
 import os
 import sys