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

ISA: generic Linux thread info support

This patch takes the Linux thread info support scattered across
different ISA implementations (currently in ARM, ALPHA, and MIPS), and
unifies them into a single file.

Adds a few more helper functions to read out TGID, mm, etc.

ISA-specific information (e.g., ALPHA PCBB register) is now moved to
the corresponding isa_traits.hh files.

Merge with the main repo.

SE/FS: Get rid of FULL_SYSTEM in MIPS.

SE/FS: Remove System::platform and Platform::intrFrequency.

In order for a system object to work in SE mode and FS mode, it has to either
always require a platform object even in SE mode, or get rid of the
requirement all together. Making SE mode carry around unnecessary/unused bits
of FS seems less than ideal, so I decided to go with the second option. The
platform pointer in the System class was used for exactly one purpose, a path
for the Alpha Linux system object to get to the real time clock and read its
frequency so that it could short cut the loops_per_jiffy calculation. There
was also a copy and pasted implementation in MIPS, but since it was only there
because it was there in Alpha I still count that as one use.

This change reverses the mechanism that communicates the RTC frequency so that
the Tsunami platform object pushes it up to the AlphaSystem object. This is
slightly less specific than it could be because really only the
AlphaLinuxSystem uses it. Because the intrFrequency function on the Platform
class was no longer necessary (and unimplemented on anything but Alpha) it was
eliminated.

After this change, a platform will need to have a system, but a system won't
have to have a platform.

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

includes: sort all includes

tick: rename Clock namespace to SimClock

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

Remove delVirtPort() and make getVirtPort() only return cached version.

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