Rewrite InputGraph's Group

The aim of this patch is to reduce the excessive abstraction from
the InputGraph. We found that even a simple thing, such as sorting
input files (Mach-O) or adding a new file to the input file list
(PE/COFF), is nearly impossible with the InputGraph abstraction,
because it hides too much information behind it. As a result,
we invented complex interactions between components (e.g.
notifyProgress() mechanism) and tricky code to work around that
limitation. There were many occasions that we needed to write
awkward code.

This patch is a first step to make it cleaner. As a first step,
this removes Group class from the InputGraph. The grouping feature
is now directly handled by the Resolver. notifyProgress is removed
since we no longer need that. I could have cleaned it up even more,
but in order to keep the patch minimum, I focused on Group.

SimpleFileNode class, a container of File objects, is now limited
to have only one File. We shold have done this earlier.
We used to allow putting multiple File objects to FileNode.
Although SimpleFileNode usually has only one file, the Driver class
actually used that capability. I modified the Driver class a bit,
so that one FileNode is created for each input File.

We should now probably remove SimpleFileNode and directly store
File objects to the InputGraph in some way, because a container
that can contain only one object is useless. This is a TODO.

Mach-O input files are now sorted before they are passe to the
Resolver. DarwinInputGraph class is no longer needed, so removed.

PECOFF still has hacky code to add a new file to the input file list.
This will be cleaned up in another patch.