Polish scripts

News:
- Suppress the error message from Rake which is useless for users and I!
- Remove the duplicate lib in CodeBuilder.
- Collect the objects for the final linking stage in fortran_rakefile_base.
- Add the forgotten rspec_system_tools.rb.
Fix unnecessary rebuild

Bugs:
- Due to the always rebuilding of external library task, the codes that
  depend on libraries will also be rebuilt. So we will link the libraries
  in the project no matter they are required by all the executables.