Removed .itp files from top level directory.

There is no need for these files, the water models
should be included from the corresponding .ff directory.
Since many users are likely to still use those files,
an error message is printed.

Also re-added ions.itp and treated it similarly.

Also update an integration test that was using a one of the top-level
water .itp files that is now removed.

Change-Id: I599e203329340587afa7fc5efced485d09b9ce1c