Need better documentation of the usage of submodules

[billsacks]

As discussed last week between @jedwards4b @mvertens @gold2718 @uturuncoglu and myself - we apparently need better documentation of some aspects of the use of submodules with manage_externals. A specific example is that the specification of externals = None (which is needed in order to avoid a recursive clone) appears not to be documented.

Some / all of the needed documentation appears in the top-level comment in #119 ; this documentation should be moved into the --help message for manage_externals.