Use dedicated -mrelax linker option in the Atmel Studio integration toolchain configurations, rather than a freeform linker switch.

LUFA/StudioIntegration/lufa_toolchain.xml

@@ -22,7 +22,7 @@
 				<toolchain-config name="avrgcc.compiler.warnings.AllWarnings" value="True" toolchain="avrgcc"/>
 				<toolchain-config name="avrgcc.compiler.miscellaneous.OtherFlags" value="-std=gnu99 -fno-strict-aliasing" toolchain="avrgcc"/>
 				<toolchain-config name="avrgcc.linker.optimization.GarbageCollectUnusedSections" value="True" toolchain="avrgcc"/>
-				<toolchain-config name="avrgcc.linker.miscellaneous.LinkerFlags" value="-Wl,--relax" toolchain="avrgcc"/>
+				<toolchain-config name="avrgcc.linker.optimization.RelaxBranches" value="True" toolchain="avrgcc"/>
 			</module>
 		</select-by-device>
 
@@ -37,7 +37,7 @@
 			<toolchain-config name="avr32gcc.compiler.warnings.AllWarnings" value="True" toolchain="avr32gcc"/>
 			<toolchain-config name="avr32gcc.compiler.miscellaneous.OtherFlags" value="-std=gnu99 -fno-strict-aliasing -mno-cond-exec-before-reload" toolchain="avr32gcc"/>
 			<toolchain-config name="avr32gcc.linker.optimization.GarbageCollectUnusedSections" value="True" toolchain="avr32gcc"/>
-			<toolchain-config name="avr32gcc.linker.miscellaneous.LinkerFlags" value="-Wl,--relax" toolchain="avr32gcc"/>
+			<toolchain-config name="avr32gcc.linker.optimization.RelaxBranches" value="True" toolchain="avr32gcc"/>
 		</module>
 	</asf>
 </lufa>

LUFA/StudioIntegration/makefile

@@ -21,7 +21,7 @@ EXT_VERSION_NUM      := $(shell date +"%y.%m.%d").$(LUFA_VERSION_NUM)
 all: generate_xml check_filenames generate_vsix
 
 clean:
-	@rm $(TEMP_MANIFEST_XML) $(MODULE_OUTPUT_XML) $(EXTENSION_OUTPUT_XML)
+	@rm -f $(TEMP_MANIFEST_XML) $(MODULE_OUTPUT_XML) $(EXTENSION_OUTPUT_XML)
 
 $(DOXYGEN_TAG_FILE_XML):
 	$(MAKE) -C ../ doxygen