diff --git a/Makefile b/Makefile
index e59647d..175459f 100644
--- a/Makefile
+++ b/Makefile
@@ -35,11 +35,11 @@ $(PROGNAME).hex: $(PROGNAME).elf
 fuse:
 
 flash: $(HEXFILE)
-	./enter_bootloader.sh
-	./wait_then_flash.sh $(CPU) $(HEXFILE)
+	- ./scripts/enter_bootloader.sh
+	./scripts/wait_then_flash.sh $(CPU) $(HEXFILE)
 
 justflash: $(HEXFILE)
-	./wait_then_flash.sh $(CPU) $(HEXFILE)
+	./scripts/wait_then_flash.sh $(CPU) $(HEXFILE)
 
 chip_erase:
 	dfu-programmer atmega32u2 erase
diff --git a/Makefile.stk525 b/Makefile.stk525
index 25caa9a..befe7ad 100644
--- a/Makefile.stk525
+++ b/Makefile.stk525
@@ -39,11 +39,11 @@ clean:
 fuse:
 
 flash: $(HEXFILE)
-	./enter_bootloader.sh
-	./wait_then_flash.sh $(CPU) $(HEXFILE)
+	- ./scripts/enter_bootloader.sh
+	./scripts/wait_then_flash.sh $(CPU) $(HEXFILE)
 
 justflash: $(HEXFILE)
-	./wait_then_flash.sh $(CPU) $(HEXFILE)
+	./scripts/wait_then_flash.sh $(CPU) $(HEXFILE)
 
 chip_erase:
 	dfu-programmer atmega32u2 erase
diff --git a/enter_bootloader.sh b/scripts/enter_bootloader.sh
similarity index 76%
rename from enter_bootloader.sh
rename to scripts/enter_bootloader.sh
index 3b6f80d..36e332b 100755
--- a/enter_bootloader.sh
+++ b/scripts/enter_bootloader.sh
@@ -4,6 +4,7 @@ TOOL=./tool/gcn64ctl
 
 if [ -x $TOOL ]; then
 	$TOOL -f --bootloader
+	exit 0 # The tool fails, but we should continue
 else
 	echo $TOOL not found. Please compile it to enter bootloader automatically.
 fi
diff --git a/wait_then_flash.sh b/scripts/wait_then_flash.sh
similarity index 100%
rename from wait_then_flash.sh
rename to scripts/wait_then_flash.sh