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>

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.

SE/FS: Get rid of FULL_SYSTEM in MIPS.

includes: sort all includes

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

go back and fix up MIPS copyright headers

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