dev: Remove a bunch of Alpha code from MIPS, and unnecessary TheISAs.

There was a bunch of commented out code in the MIPS malta
implementation which originally came from Alpha. That code is now
deleted. Also, the MIPS code pulled in the TheISA namespace which it
didn't use.

Change-Id: I8470cc2fecb302f4399e52de4de9daf79c00a711
Reviewed-on: https://gem5-review.googlesource.com/9405
Reviewed-by: Andreas Sandberg <andreas.sandberg@arm.com>
Maintainer: Gabe Black <gabeblack@google.com>

style: change C/C++ source permissions to noexec

Several files in the repository were tracked with execute permissions
even though the files are just normal C/C++ files (and the one .isa).

Change-Id: I976b096acab4a1fc74c5699ef1f9b222c1e635c2
Reviewed-on: https://gem5-review.googlesource.com/7241
Reviewed-by: Gabe Black <gabeblack@google.com>
Reviewed-by: Nikos Nikoleris <nikos.nikoleris@arm.com>
Reviewed-by: Andreas Sandberg <andreas.sandberg@arm.com>
Maintainer: Andreas Sandberg <andreas.sandberg@arm.com>

style: [patch 1/22] use /r/3648/ to reorganize includes

style: fix missing spaces in control statements

Result of running 'hg m5style --skip-all --fix-control -a'.

sim: Refactor the serialization base class

Objects that are can be serialized are supposed to inherit from the
Serializable class. This class is meant to provide a unified API for
such objects. However, so far it has mainly been used by SimObjects
due to some fundamental design limitations. This changeset redesigns
to the serialization interface to make it more generic and hide the
underlying checkpoint storage. Specifically:

* Add a set of APIs to serialize into a subsection of the current
object. Previously, objects that needed this functionality would
use ad-hoc solutions using nameOut() and section name
generation. In the new world, an object that implements the
interface has the methods serializeSection() and
unserializeSection() that serialize into a named /subsection/ of
the current object. Calling serialize() serializes an object into
the current section.

* Move the name() method from Serializable to SimObject as it is no
longer needed for serialization. The fully qualified section name
is generated by the main serialization code on the fly as objects
serialize sub-objects.

* Add a scoped ScopedCheckpointSection helper class. Some objects
need to serialize data structures, that are not deriving from
Serializable, into subsections. Previously, this was done using
nameOut() and manual section name generation. To simplify this,
this changeset introduces a ScopedCheckpointSection() helper
class. When this class is instantiated, it adds a new /subsection/
and subsequent serialization calls during the lifetime of this
helper class happen inside this section (or a subsection in case
of nested sections).

* The serialize() call is now const which prevents accidental state
manipulation during serialization. Objects that rely on modifying
state can use the serializeOld() call instead. The default
implementation simply calls serialize(). Note: The old-style calls
need to be explicitly called using the
serializeOld()/serializeSectionOld() style APIs. These are used by
default when serializing SimObjects.

* Both the input and output checkpoints now use their own named
types. This hides underlying checkpoint implementation from
objects that need checkpointing and makes it easier to change the
underlying checkpoint storage code.

mem: Remove redundant Packet::allocate calls

This patch cleans up the packet memory allocation confusion. The data
is always allocated at the requesting side, when a packet is created
(or copied), and there is never a need for any device to allocate any
space if it is merely responding to a paket. This behaviour is in line
with how SystemC and TLM works as well, thus increasing
interoperability, and matching established conventions.

The redundant calls to Packet::allocate are removed, and the checks in
the function are tightened up to make sure data is only ever allocated
once. There are still some oddities in the packet copy constructor
where we copy the data pointer if it is static (without ownership),
and allocate new space if the data is dynamic (with ownership). The
latter is being worked on further in a follow-on patch.

dev: make BasicPioDevice take size in constructor

Instead of relying on derived classes explicitly assigning
to the BasicPioDevice pioSize field, require them to pass
a size value in to the constructor.

Committed by: Nilay Vaish <nilay@cs.wisc.edu>

SE/FS: Get rid of FULL_SYSTEM in MIPS.

SE/FS: Build the devices in SE mode.

arch: nuke arch/isa_specific.hh and move stuff to generated config/the_isa.hh

Add in Context IDs to the simulator. From now on, cpuId is almost never used,
the primary identifier for a hardware context should be contextId(). The
concept of threads within a CPU remains, in the form of threadId() because
sometimes you need to know which context within a cpu to manipulate.

Add in files from merge-bare-iron, get them compiling in FS and SE mode