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

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

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.

tick: rename Clock namespace to SimClock

Processes: Make getting and setting system call arguments part of a process object.

style: Make a style pass over the whole arch/alpha directory.

X86: Fix argument register indexing.
Code was assuming that all argument registers followed in order from ArgumentReg0. There is now an ArgumentReg array which is indexed to find the right index. There is a constant, NumArgumentRegs, which can be used to protect against using an invalid ArgumentReg.

Major changes to how SimObjects are created and initialized. Almost all
creation and initialization now happens in python. Parameter objects
are generated and initialized by python. The .ini file is now solely for
debugging purposes and is not used in construction of the objects in any
way.

Merge ktlim@zamp:./local/clean/o3-merge/m5
into zamp.eecs.umich.edu:/z/ktlim2/clean/o3-merge/newmem

configs/boot/micro_memlat.rcS:
configs/boot/micro_tlblat.rcS:
src/arch/alpha/ev5.cc:
src/arch/alpha/isa/decoder.isa:
src/arch/alpha/isa_traits.hh:
src/cpu/base.cc:
src/cpu/base.hh:
src/cpu/base_dyn_inst.hh:
src/cpu/checker/cpu.hh:
src/cpu/checker/cpu_impl.hh:
src/cpu/o3/alpha/cpu_impl.hh:
src/cpu/o3/alpha/params.hh:
src/cpu/o3/checker_builder.cc:
src/cpu/o3/commit_impl.hh:
src/cpu/o3/cpu.cc:
src/cpu/o3/decode_impl.hh:
src/cpu/o3/fetch_impl.hh:
src/cpu/o3/iew.hh:
src/cpu/o3/iew_impl.hh:
src/cpu/o3/inst_queue.hh:
src/cpu/o3/lsq.hh:
src/cpu/o3/lsq_impl.hh:
src/cpu/o3/lsq_unit.hh:
src/cpu/o3/lsq_unit_impl.hh:
src/cpu/o3/regfile.hh:
src/cpu/o3/rename_impl.hh:
src/cpu/o3/thread_state.hh:
src/cpu/ozone/checker_builder.cc:
src/cpu/ozone/cpu.hh:
src/cpu/ozone/cpu_impl.hh:
src/cpu/ozone/front_end.hh:
src/cpu/ozone/front_end_impl.hh:
src/cpu/ozone/lw_back_end.hh:
src/cpu/ozone/lw_back_end_impl.hh:
src/cpu/ozone/lw_lsq.hh:
src/cpu/ozone/lw_lsq_impl.hh:
src/cpu/ozone/thread_state.hh:
src/cpu/simple/base.cc:
src/cpu/simple_thread.cc:
src/cpu/simple_thread.hh:
src/cpu/thread_state.hh:
src/dev/ide_disk.cc:
src/python/m5/objects/O3CPU.py:
src/python/m5/objects/Root.py:
src/python/m5/objects/System.py:
src/sim/pseudo_inst.cc:
src/sim/pseudo_inst.hh:
src/sim/system.hh:
util/m5/m5.c:
Hand merge.

add system.mem_mode = ['timing', 'atomic']
update scripts acordingly

configs/test/SysPaths.py:
new syspaths from nate, this one allows you to set script, binary, and disk paths like
system.dir = 'aouaou' in your script
configs/test/fs.py:
update for system mem_mode
Put small checkpoint example
Make clock 1THz
configs/test/test.py:
src/arch/alpha/freebsd/system.cc:
src/arch/alpha/linux/system.cc:
src/arch/alpha/system.cc:
src/arch/alpha/tru64/system.cc:
src/arch/sparc/system.cc:
src/python/m5/objects/System.py:
src/sim/system.cc:
src/sim/system.hh:
update for system mem_mode
src/dev/io_device.cc:
Use time returned from sendAtomic to delay

Merge iceaxe.:/Volumes/work/research/m5/head
into iceaxe.:/Volumes/work/research/m5/merge

src/cpu/simple/base.cc:
src/kern/kernel_stats.cc:
src/kern/kernel_stats.hh:
src/kern/system_events.cc:
src/kern/system_events.hh:
src/python/m5/objects/System.py:
src/sim/system.cc:
src/sim/system.hh:
hand merge

Change ExecContext to ThreadContext. This is being renamed to differentiate between the interface used objects outside of the CPU, and the interface used by the ISA. ThreadContext is used by objects outside of the CPU and is specifically defined in thread_context.hh. ExecContext is more implicit, and is defined by files such as base_dyn_inst.hh or cpu/simple/base.hh.

Further renames/reorganization will be coming shortly; what is currently CPUExecContext (the old ExecContext from m5) will be renamed to SimpleThread or something similar.

src/arch/alpha/arguments.cc:
src/arch/alpha/arguments.hh:
src/arch/alpha/ev5.cc:
src/arch/alpha/faults.cc:
src/arch/alpha/faults.hh:
src/arch/alpha/freebsd/system.cc:
src/arch/alpha/freebsd/system.hh:
src/arch/alpha/isa/branch.isa:
src/arch/alpha/isa/decoder.isa:
src/arch/alpha/isa/main.isa:
src/arch/alpha/linux/process.cc:
src/arch/alpha/linux/system.cc:
src/arch/alpha/linux/system.hh:
src/arch/alpha/linux/threadinfo.hh:
src/arch/alpha/process.cc:
src/arch/alpha/regfile.hh:
src/arch/alpha/stacktrace.cc:
src/arch/alpha/stacktrace.hh:
src/arch/alpha/tlb.cc:
src/arch/alpha/tlb.hh:
src/arch/alpha/tru64/process.cc:
src/arch/alpha/tru64/system.cc:
src/arch/alpha/tru64/system.hh:
src/arch/alpha/utility.hh:
src/arch/alpha/vtophys.cc:
src/arch/alpha/vtophys.hh:
src/arch/mips/faults.cc:
src/arch/mips/faults.hh:
src/arch/mips/isa_traits.cc:
src/arch/mips/isa_traits.hh:
src/arch/mips/linux/process.cc:
src/arch/mips/process.cc:
src/arch/mips/regfile/float_regfile.hh:
src/arch/mips/regfile/int_regfile.hh:
src/arch/mips/regfile/misc_regfile.hh:
src/arch/mips/regfile/regfile.hh:
src/arch/mips/stacktrace.hh:
src/arch/sparc/faults.cc:
src/arch/sparc/faults.hh:
src/arch/sparc/isa_traits.hh:
src/arch/sparc/linux/process.cc:
src/arch/sparc/linux/process.hh:
src/arch/sparc/process.cc:
src/arch/sparc/regfile.hh:
src/arch/sparc/solaris/process.cc:
src/arch/sparc/stacktrace.hh:
src/arch/sparc/ua2005.cc:
src/arch/sparc/utility.hh:
src/arch/sparc/vtophys.cc:
src/arch/sparc/vtophys.hh:
src/base/remote_gdb.cc:
src/base/remote_gdb.hh:
src/cpu/base.cc:
src/cpu/base.hh:
src/cpu/base_dyn_inst.hh:
src/cpu/checker/cpu.cc:
src/cpu/checker/cpu.hh:
src/cpu/checker/exec_context.hh:
src/cpu/cpu_exec_context.cc:
src/cpu/cpu_exec_context.hh:
src/cpu/cpuevent.cc:
src/cpu/cpuevent.hh:
src/cpu/exetrace.hh:
src/cpu/intr_control.cc:
src/cpu/memtest/memtest.hh:
src/cpu/o3/alpha_cpu.hh:
src/cpu/o3/alpha_cpu_impl.hh:
src/cpu/o3/alpha_dyn_inst_impl.hh:
src/cpu/o3/commit.hh:
src/cpu/o3/commit_impl.hh:
src/cpu/o3/cpu.cc:
src/cpu/o3/cpu.hh:
src/cpu/o3/fetch_impl.hh:
src/cpu/o3/regfile.hh:
src/cpu/o3/thread_state.hh:
src/cpu/ozone/back_end.hh:
src/cpu/ozone/cpu.hh:
src/cpu/ozone/cpu_impl.hh:
src/cpu/ozone/front_end.hh:
src/cpu/ozone/front_end_impl.hh:
src/cpu/ozone/inorder_back_end.hh:
src/cpu/ozone/lw_back_end.hh:
src/cpu/ozone/lw_back_end_impl.hh:
src/cpu/ozone/lw_lsq.hh:
src/cpu/ozone/lw_lsq_impl.hh:
src/cpu/ozone/thread_state.hh:
src/cpu/pc_event.cc:
src/cpu/pc_event.hh:
src/cpu/profile.cc:
src/cpu/profile.hh:
src/cpu/quiesce_event.cc:
src/cpu/quiesce_event.hh:
src/cpu/simple/atomic.cc:
src/cpu/simple/base.cc:
src/cpu/simple/base.hh:
src/cpu/simple/timing.cc:
src/cpu/static_inst.cc:
src/cpu/static_inst.hh:
src/cpu/thread_state.hh:
src/dev/alpha_console.cc:
src/dev/ns_gige.cc:
src/dev/sinic.cc:
src/dev/tsunami_cchip.cc:
src/kern/kernel_stats.cc:
src/kern/kernel_stats.hh:
src/kern/linux/events.cc:
src/kern/linux/events.hh:
src/kern/system_events.cc:
src/kern/system_events.hh:
src/kern/tru64/dump_mbuf.cc:
src/kern/tru64/tru64.hh:
src/kern/tru64/tru64_events.cc:
src/kern/tru64/tru64_events.hh:
src/mem/vport.cc:
src/mem/vport.hh:
src/sim/faults.cc:
src/sim/faults.hh:
src/sim/process.cc:
src/sim/process.hh:
src/sim/pseudo_inst.cc:
src/sim/pseudo_inst.hh:
src/sim/syscall_emul.cc:
src/sim/syscall_emul.hh:
src/sim/system.cc:
src/cpu/thread_context.hh:
src/sim/system.hh:
src/sim/vptr.hh:
Change ExecContext to ThreadContext.

Updated Authors from bk prs info

New directory structure:
- simulator source now in 'src' subdirectory
- imported files from 'ext' repository
- support building in arbitrary places, including
outside of the source tree. See comment at top
of SConstruct file for more details.
Regression tests are temporarily disabled; that
syetem needs more extensive revisions.

SConstruct:
Update for new directory structure.
Modify to support build trees that are not subdirectories
of the source tree. See comment at top of file for
more details.
Regression tests are temporarily disabled.
src/arch/SConscript:
src/arch/isa_parser.py:
src/python/SConscript:
Update for new directory structure.