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>

MEM: Make port proxies use references rather than pointers

This patch is adding a clearer design intent to all objects that would
not be complete without a port proxy by making the proxies members
rathen than dynamically allocated. In essence, if NULL would not be a
valid value for the proxy, then we avoid using a pointer to make this
clear.

The same approach is used for the methods using these proxies, such as
loadSections, that now use references rather than pointers to better
reflect the fact that NULL would not be an acceptable value (in fact
the code would break and that is how this patch started out).

Overall the concept of "using a reference to express unconditional
composition where a NULL pointer is never valid" could be done on a
much broader scale throughout the code base, but for now it is only
done in the locations affected by the proxies.

MEM: Add port proxies instead of non-structural ports

Port proxies are used to replace non-structural ports, and thus enable
all ports in the system to correspond to a structural entity. This has
the advantage of accessing memory through the normal memory subsystem
and thus allowing any constellation of distributed memories, address
maps, etc. Most accesses are done through the "system port" that is
used for loading binaries, debugging etc. For the entities that belong
to the CPU, e.g. threads and thread contexts, they wrap the CPU data
port in a port proxy.

The following replacements are made:
FunctionalPort > PortProxy
TranslatingPort > SETranslatingPortProxy
VirtualPort > FSTranslatingPortProxy

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

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

style: This file hugely violated the M5 style.
Remove a bunch of unused cruft from the interface while we're at it

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