clang: Enable compiling gem5 using clang 2.9 and 3.0

This patch adds the necessary flags to the SConstruct and SConscript
files for compiling using clang 2.9 and later (on Ubuntu et al and OSX
XCode 4.2), and also cleans up a bunch of compiler warnings found by
clang. Most of the warnings are related to hidden virtual functions,
comparisons with unsigneds >= 0, and if-statements with empty
bodies. A number of mismatches between struct and class are also
fixed. clang 2.8 is not working as it has problems with class names
that occur in multiple namespaces (e.g. Statistics in
kernel_stats.hh).

clang has a bug (http://llvm.org/bugs/show_bug.cgi?id=7247) which
causes confusion between the container std::set and the function
Packet::set, and this is currently addressed by not including the
entire namespace std, but rather selecting e.g. "using std::vector" in
the appropriate places.

includes: sort all includes

now O3CPU is totally independent of the ISA... all alpha specific stuff is the cpu/o3/alpha directory

src/cpu/o3/alpha/cpu.cc:
src/cpu/o3/alpha/cpu_impl.hh:
src/cpu/o3/alpha/impl.hh:
filenames
src/cpu/o3/alpha/thread_context.hh:
public
src/cpu/o3/base_dyn_inst.cc:
src/cpu/o3/bpred_unit.cc:
src/cpu/o3/commit.cc:
src/cpu/o3/cpu.cc:
src/cpu/o3/decode.cc:
src/cpu/o3/fetch.cc:
src/cpu/o3/iew.cc:
src/cpu/o3/inst_queue.cc:
src/cpu/o3/lsq.cc:
src/cpu/o3/lsq_unit.cc:
src/cpu/o3/mem_dep_unit.cc:
src/cpu/o3/rename.cc:
src/cpu/o3/rob.cc:
use O3CPUImpl ... not Alpha
src/cpu/o3/checker_builder.cc:
filename

Make O3CPU model independent of the ISA

Use O3CPU when building instead of AlphaO3CPU.

I could use some better python magic in the cpu_models.py file!

AUTHORS:
add middle initial
SConstruct:
change from AlphaO3CPU to O3CPU
src/cpu/SConscript:
edits to build O3CPU instead of AlphaO3CPU
src/cpu/cpu_models.py:
change substitution template to use proper CPU EXEC CONTEXT For O3CPU Model...

Actually, some Python expertise could be used here. The 'env' variable is not
passed to this file, so I had to parse through the ARGV to find the ISA...
src/cpu/o3/base_dyn_inst.cc:
src/cpu/o3/bpred_unit.cc:
src/cpu/o3/commit.cc:
src/cpu/o3/cpu.cc:
src/cpu/o3/cpu.hh:
src/cpu/o3/decode.cc:
src/cpu/o3/fetch.cc:
src/cpu/o3/iew.cc:
src/cpu/o3/inst_queue.cc:
src/cpu/o3/lsq.cc:
src/cpu/o3/lsq_unit.cc:
src/cpu/o3/mem_dep_unit.cc:
src/cpu/o3/rename.cc:
src/cpu/o3/rob.cc:
use isa_specific.hh
src/sim/process.cc:
only initi NextNPC if not ALPHA
src/cpu/o3/alpha/cpu.cc:
alphao3cpu impl
src/cpu/o3/alpha/cpu.hh:
move AlphaTC to it's own file
src/cpu/o3/alpha/cpu_impl.hh:
Move AlphaTC to it's own file ...
src/cpu/o3/alpha/dyn_inst.cc:
src/cpu/o3/alpha/dyn_inst.hh:
src/cpu/o3/alpha/dyn_inst_impl.hh:
include paths
src/cpu/o3/alpha/impl.hh:
include paths, set default MaxThreads to 2 instead of 4
src/cpu/o3/alpha/params.hh:
set Alpha Specific Params here
src/python/m5/objects/O3CPU.py:
add O3CPU class
src/cpu/o3/SConscript:
include isa-specific build files
src/cpu/o3/alpha/thread_context.cc:
NEW HOME of AlphaTC
src/cpu/o3/alpha/thread_context.hh:
new home of AlphaTC
src/cpu/o3/isa_specific.hh:
includes ISA specific files
src/cpu/o3/params.hh:
base o3 params
src/cpu/o3/thread_context.hh:
base o3 thread context
src/cpu/o3/thread_context_impl.hh:
base o3 thead context impl

Fixes to get new CPU model working for simple test case. The CPU does not yet support retrying accesses.

src/cpu/base_dyn_inst.cc:
Delete the allocated data in destructor.
src/cpu/base_dyn_inst.hh:
Only copy the addresses if the translation succeeded.
src/cpu/o3/alpha_cpu.hh:
Return actual translating port.
Don't panic on setNextNPC() as it's always called, regardless of the architecture, when the process initializes.
src/cpu/o3/alpha_cpu_impl.hh:
Pass in memobject to the thread state in SE mode.
src/cpu/o3/commit_impl.hh:
Initialize all variables.
src/cpu/o3/decode_impl.hh:
Handle early resolution of branches properly.
src/cpu/o3/fetch.hh:
Switch structure back to requests.
src/cpu/o3/fetch_impl.hh:
Initialize all variables, create/delete requests properly.
src/cpu/o3/lsq_unit.hh:
Include sender state along with the packet. Also include a more generic writeback event that's only used for stores forwarding data to loads.
src/cpu/o3/lsq_unit_impl.hh:
Redo writeback code to support the response path of the memory system.
src/cpu/o3/mem_dep_unit.cc:
src/cpu/o3/mem_dep_unit_impl.hh:
Wrap variables in #ifdefs.
src/cpu/o3/store_set.cc:
Include to get panic() function.
src/cpu/o3/thread_state.hh:
Create with MemObject as well.
src/cpu/thread_state.hh:
Have a translating port in the thread state object.
src/python/m5/objects/AlphaFullCPU.py:
Mem parameter no longer needed.

Merge ktlim@zizzer:/bk/newmem
into zizzer.eecs.umich.edu:/.automount/zamp/z/ktlim2/clean/newmem

Updated Authors from bk prs info

Merge ktlim@zizzer:/bk/m5
into zamp.eecs.umich.edu:/z/ktlim2/clean/newmem

SConstruct:
src/SConscript:
src/arch/SConscript:
src/arch/alpha/faults.cc:
src/arch/alpha/tlb.cc:
src/base/traceflags.py:
src/cpu/SConscript:
src/cpu/base.cc:
src/cpu/base.hh:
src/cpu/base_dyn_inst.cc:
src/cpu/cpu_exec_context.cc:
src/cpu/cpu_exec_context.hh:
src/cpu/exec_context.hh:
src/cpu/o3/alpha_cpu.hh:
src/cpu/o3/alpha_cpu_impl.hh:
src/cpu/o3/alpha_dyn_inst.hh:
src/cpu/o3/cpu.cc:
src/cpu/o3/cpu.hh:
src/cpu/o3/regfile.hh:
src/cpu/ozone/cpu.hh:
src/cpu/simple/base.cc:
src/cpu/base_dyn_inst.hh:
src/cpu/o3/2bit_local_pred.cc:
src/cpu/o3/2bit_local_pred.hh:
src/cpu/o3/alpha_cpu.cc:
src/cpu/o3/alpha_cpu_builder.cc:
src/cpu/o3/alpha_dyn_inst.cc:
src/cpu/o3/alpha_dyn_inst_impl.hh:
src/cpu/o3/alpha_impl.hh:
src/cpu/o3/alpha_params.hh:
src/cpu/o3/bpred_unit.cc:
src/cpu/o3/bpred_unit.hh:
src/cpu/o3/bpred_unit_impl.hh:
src/cpu/o3/btb.cc:
src/cpu/o3/btb.hh:
src/cpu/o3/comm.hh:
src/cpu/o3/commit.cc:
src/cpu/o3/commit.hh:
src/cpu/o3/commit_impl.hh:
src/cpu/o3/cpu_policy.hh:
src/cpu/o3/decode.cc:
src/cpu/o3/decode.hh:
src/cpu/o3/decode_impl.hh:
src/cpu/o3/fetch.cc:
src/cpu/o3/fetch.hh:
src/cpu/o3/fetch_impl.hh:
src/cpu/o3/free_list.cc:
src/cpu/o3/free_list.hh:
src/cpu/o3/iew.cc:
src/cpu/o3/iew.hh:
src/cpu/o3/iew_impl.hh:
src/cpu/o3/inst_queue.cc:
src/cpu/o3/inst_queue.hh:
src/cpu/o3/inst_queue_impl.hh:
src/cpu/o3/mem_dep_unit.cc:
src/cpu/o3/mem_dep_unit.hh:
src/cpu/o3/mem_dep_unit_impl.hh:
src/cpu/o3/ras.cc:
src/cpu/o3/ras.hh:
src/cpu/o3/rename.cc:
src/cpu/o3/rename.hh:
src/cpu/o3/rename_impl.hh:
src/cpu/o3/rename_map.cc:
src/cpu/o3/rename_map.hh:
src/cpu/o3/rob.cc:
src/cpu/o3/rob.hh:
src/cpu/o3/rob_impl.hh:
src/cpu/o3/sat_counter.cc:
src/cpu/o3/sat_counter.hh:
src/cpu/o3/store_set.cc:
src/cpu/o3/store_set.hh:
src/cpu/o3/tournament_pred.cc:
src/cpu/o3/tournament_pred.hh:
Hand merges.

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.