[build system] clean up makefiles and fix dependencies, parallel build with make -j 8 seems to work now

conf/Makefile.sim

@@ -1,6 +1,5 @@
 # Hey Emacs, this is a -*- makefile -*-
 #
-#   $Id$
 #   Copyright (C) 2006 Pascal Brisset, Antoine Drouin
 #
 # This file is part of paparazzi.
@@ -132,6 +131,7 @@ $(OBJDIR)/%.o: %.cpp $(OBJDIR)/../Makefile.ac
 	$(Q)test -d $(dir $@) || mkdir -p $(dir $@)
 	$(Q)$(CC) $(CFLAGS) -c -o $@ $<
 
+.PHONY: all compile check_jsbsim
 
 #
 # Dependencies