mem: Move ruby protocols into a directory called ruby_protocol.

Now that the gem5 protocols are split out, it would be nice to put them
in their own protocol directory. It's also confusing to have files
called *_protocol which are not in the protocol directory.

Change-Id: I7475ee111630050a2421816dfd290921baab9f71
Reviewed-on: https://gem5-review.googlesource.com/c/public/gem5/+/20230
Reviewed-by: Gabe Black <gabeblack@google.com>
Reviewed-by: Andreas Sandberg <andreas.sandberg@arm.com>
Reviewed-by: Jason Lowe-Power <jason@lowepower.com>
Maintainer: Gabe Black <gabeblack@google.com>
Tested-by: kokoro <noreply+kokoro@google.com>

ruby: coherence protocols: remove data block from dirctory entry
This patch removes the data block present in the directory entry structure
of each protocol in gem5's mainline. Firstly, this is required for moving
towards common set of memory controllers for classic and ruby memory systems.
Secondly, the data block was being misused in several places. It was being
used for having free access to the physical memory instead of calling on the
memory controller.

From now on, the directory controller will not have a direct visibility into
the physical memory. The Memory Vector object now resides in the
Memory Controller class. This also means that some significant changes are
being made to the functional accesses in ruby.

Ruby: Shuffle some of the included files
This patch adds and removes included files from some of the files so as to
organize remove some false dependencies and include some files directly
instead of transitively.

Ruby: Remove files and includes not in use

includes: sort all includes

ruby: automate permission setting

This patch integrates permissions with cache and memory states, and then
automates the setting of permissions within the generated code. No longer
does one need to manually set the permissions within the setState funciton.
This patch will faciliate easier functional access support by always correctly
setting permissions for both cache and memory states.

ruby: get "using namespace" out of headers
In addition to obvious changes, this required a slight change to the slicc
grammar to allow types with :: in them. Otherwise slicc barfs on std::string
which we need for the headers that slicc generates.

ruby: style pass

ruby: Ruby changes required to use the python config system
This patch includes the necessary changes to connect ruby objects using
the python configuration system. Mainly it consists of removing
unnecessary ruby object pointers and connecting the necessary object
pointers using the generated param objects. This patch includes the
slicc changes necessary to connect generated ruby objects together using
the python configuraiton system.