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

Checkpoint: Make system serialize call children

This patch changes how the serialization of the system works. The base
class had a non-virtual serialize and unserialize, that was hidden by
a function with the same name for a number of subclasses (most likely
not intentional as the base class should have been virtual). A few of
the derived systems had no specialization at all (e.g. Power and x86
that simply called the System::serialize), but MIPS and Alpha adds
additional symbol table entries to the checkpoint.

Instead of overriding the virtual function, the additional entries are
now printed through a virtual function (un)serializeSymtab. The reason
for not calling System::serialize from the two related systems is that
a follow up patch will require the system to also serialize the
PhysicalMemory, and if this is done in the base class if ends up being
between the general parts and the specialized symbol table.

With this patch, the checkpoint is not modified, as the order of the
segments is unchanged.

Merge with the main repo.

SE/FS: Get rid of FULL_SYSTEM in MIPS.

includes: sort all includes

sim: Use forward declarations for ports.

Virtual ports need TLB data which means anything touching a file in the arch
directory rebuilds any file that includes system.hh which in everything.

Loader: Make the load address mask be a parameter of the system rather than a constant.

This allows one two different OS requirements for the same ISA to be handled.
Some OSes are compiled for a virtual address and need to be loaded into physical
memory that starts at address 0, while other bare metal tools generate
images that start at address 0.

More minor gdb-related cleanup.
Found several more stale includes and forward decls.

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

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

alpha: Get rid fo the namespace called EV5.
We're never going to do an alpha platform other than the one we've got.

style: Remove non-leading tabs everywhere they shouldn't be. Developers should configure their editors to not insert tabs

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