BaseTools: Update BaseTools top GNUMakefile with the clear dependency

BaseTools: Update BaseTools top GNUMakefile with the clear dependency

https://bugzilla.tianocore.org/show_bug.cgi?id=786

After GNUmakefile dependency is fixed up, it can make with -j N to enable
multiple thread build in base tools C source and save build time.

In my linux host machine, make -j 4 to compile BaseTools and save ~60% time.

Contributed-under: TianoCore Contribution Agreement 1.1
Signed-off-by: Liming Gao <liming.gao@intel.com>
Reviewed-by: Yonghong Zhu <yonghong.zhu@intel.com>