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

SE/FS: Get rid of includes of config/full_system.hh.

includes: sort all includes

build: fix compile problems pointed out by gcc 4.4

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.

style: missed space after switch

style: These files didn't even come close to following the M5 style guide.

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

mips import pt. 1

src/arch/mips/SConscript:
"mips import pt.1".