Move scripts to better place

Some scripts are moved to better place.
The "scripts" directory is a place for executable. Those scripts in this directory are registered as executables, thus you don't have to put relative path to your script. 
Simply, you don't have to put "./" before submitCrab3.py.

In the same manner, castortools.py is a python library, not an executable script. So I'm moving it to ordinary python directory. (I don't know this is still used or not)