Fixed PLUMED_ROOT in command line tools

Now command line shortcuts such as plumed-patch
follow the same rule as plumed executable to set PLUMED_ROOT
as it was implemented in 1b20cb90

Namely, they have an hard coded value that can be replaced
setting the PLUMED_ROOT variable before launching the tool

src/lib/Makefile

@@ -168,7 +168,7 @@ lib-shared: $(PLUMED_KERNEL) $(PLUMED_SHARED_OBJ) $(PLUMED_MAIN_SHARED) $(PLUMED
 $(PLUMED_SCRIPTS_EXE):
 	@echo "#! /bin/bash" > $@
 	@echo "echo 'NOTE: shell only version, useful when plumed is cross compiled' >&2" >> $@
-	@echo "export PLUMED_ROOT=\"$(PLUMED_ROOT)\"" >> $@
+	@echo "export PLUMED_ROOT=\"\$${PLUMED_ROOT-$(PLUMED_ROOT)}\"" >> $@
 	@echo "source \"\$$PLUMED_ROOT\"/scripts/$(subst plumed-,,$(@F)).sh" >> $@
 	chmod a+x $@