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

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.

dev: prevent intel 8254 timer counter events firing before startup

This change includes edits to Intel8254Timer to prevent counter events firing
before startup to comply with SimObject initialization call sequence.

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

dev: prevent RTC events firing before startup

This change includes edits to MC146818 timer to prevent RTC events
firing before startup to comply with SimObject initialization call sequence.

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

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: Build the devices in SE mode.

includes: sort all includes

tick: rename Clock namespace to SimClock

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

MIPS: Get MIPS_FS to compile, more style fixes.
Some breakage was from my BitUnion change, some was much older.

Make the Event::description() a const function

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