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>

misc: Rename misc.(hh|cc) to logging.(hh|cc)

These files aren't a collection of miscellaneous stuff, they're the
definition of the Logger interface, and a few utility macros for
calling into that interface (panic, warn, etc.).

Change-Id: I84267ac3f45896a83c0ef027f8f19c5e9a5667d1
Reviewed-on: https://gem5-review.googlesource.com/6226
Reviewed-by: Brandon Potter <Brandon.Potter@amd.com>
Maintainer: Gabe Black <gabeblack@google.com>

style: remove trailing whitespace

Result of running 'hg m5style --skip-all --fix-white -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: Page Table map api modification

This patch adds uncacheable/cacheable and read-only/read-write attributes to
the map method of PageTableBase. It also modifies the constructor of TlbEntry
structs for all architectures to consider the new attributes.

SE/FS: Turn on the page table class in FS.

MIPS: Many style fixes.
White space, commented out code, some other minor fixes.

gcc: Add extra parens to quell warnings.
Even though we're not incorrect about operator precedence, let's add
some parens in some particularly confusing places to placate GCC 4.3
so that we don't have to turn the warning off. Agreed that this is a
bit of a pain for those users who get the order of operations correct,
but it is likely to prevent bugs in certain cases.

go back and fix up MIPS copyright headers

fix MIPS headers

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