Replace direct uses of gmx::File with streams

Replace direct uses of gmx::File with streams

Replace all cases that used gmx::File with a stream-based
implementation.  Only static methods in gmx::File are called from
outside file.cpp (will be removed separately).

This is only direct replacement to remove uses of gmx::File; some
additional refactoring is necessary to support alternative streams for
unit testing.

Change-Id: I5e5905f9f8956909f3396359b18e9660f100bcaa