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>

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

includes: sort all includes

Make commenting on close namespace brackets consistent.

Ran all the source files through 'perl -pi' with this script:

s|\s*(};?\s*)?/\*\s*(end\s*)?namespace\s*(\S+)\s*\*/(\s*})?|} // namespace $3|;
s|\s*};?\s*//\s*(end\s*)?namespace\s*(\S+)\s*|} // namespace $2\n|;
s|\s*};?\s*//\s*(\S+)\s*namespace\s*|} // namespace $1\n|;

Also did a little manual editing on some of the arch/*/isa_traits.hh files
and src/SConscript.

includes: sort includes again

types: Move stuff for global types into src/base/types.hh

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

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

mips import pt. 1

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