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

ruby: perfect switch: refactor code
Refactored the code in operateVnet(), moved partly to a new function
operateMessageBuffer(). This is required since a later patch moves to having a
wakeup event per MessageBuffer instead of one event for the entire Switch.

ruby: simple network: store Switch* in PerfectSwitch and Throttle
There are two reasons for doing so:

a. provide a source of clock to PerfectSwitch. A follow on patch removes sender
and receiver pointers from MessageBuffer means that the object owning the
buffer should have some way of providing timing info.

b. schedule events. A follow on patch removes the consumer class. So the
PerfectSwitch needs some EventManager object to schedule events on its own.

ruby: reverts to changeset: bf82f1f7b040

ruby: simple network: store Switch* in PerfectSwitch and Throttle

ruby: perfect switch: refactor code

Refactored the code in operateVnet(), moved partly to a new function
operateMessageBuffer().

ruby: network: revert some of the changes from ad9c042dce54
The changeset ad9c042dce54 made changes to the structures under the network
directory to use a map of buffers instead of vector of buffers.
The reasoning was that not all vnets that are created are used and we
needlessly allocate more buffers than required and then iterate over them
while processing network messages. But the move to map resulted in a slow
down which was pointed out by Andreas Hansson. This patch moves things
back to using vector of message buffers.

ruby: PerfectSwitch: moves code to a per vnet helper function
This patch moves code from the wakeup() function to a operateVnet().
The aim is to improve the readiblity of the code.

ruby: message buffers: significant changes

This patch is the final patch in a series of patches. The aim of the series
is to make ruby more configurable than it was. More specifically, the
connections between controllers are not at all possible (unless one is ready
to make significant changes to the coherence protocol). Moreover the buffers
themselves are magically connected to the network inside the slicc code.
These connections are not part of the configuration file.

This patch makes changes so that these connections will now be made in the
python configuration files associated with the protocols. This requires
each state machine to expose the message buffers it uses for input and output.
So, the patch makes these buffers configurable members of the machines.

The patch drops the slicc code that usd to connect these buffers to the
network. Now these buffers are exposed to the python configuration system
as Master and Slave ports. In the configuration files, any master port
can be connected any slave port. The file pyobject.cc has been modified to
take care of allocating the actual message buffer. This is inline with how
other port connections work.

ruby: network: convert to gem5 style stats

scons: Add warning for missing declarations

This patch enables warnings for missing declarations. To avoid issues
with SWIG-generated code, the warning is only applied to non-SWIG
code.

ruby: enable multiple clock domains
This patch allows ruby to have multiple clock domains. As I understand
with this patch, controllers can have different frequencies. The entire
network needs to run at a single frequency.

The idea is that with in an object, time is treated in terms of cycles.
But the messages that are passed from one entity to another should contain
the time in Ticks. As of now, this is only true for the message buffers,
but not for the links in the network. As I understand the code, all the
entities in different networks (simple, garnet-fixed, garnet-flexible) should
be clocked at the same frequency.

Another problem is that the directory controller has to operate at the same
frequency as the ruby system. This is because the memory controller does
not make use of the Message Buffer, and instead implements a buffer of its
own. So, it has no idea of the frequency at which the directory controller
is operating and uses ruby system's frequency for scheduling events.

Ruby: use ClockedObject in Consumer class
Many Ruby structures inherit from the Consumer, which is used for scheduling
events. The Consumer used to relay on an Event Manager for scheduling events
and on g_system_ptr for time. With this patch, the Consumer will now use a
ClockedObject to schedule events and to query for current time. This resulted
in several structures being converted from SimObjects to ClockedObjects. Also,
the MessageBuffer class now requires a pointer to a ClockedObject so as to
query for time.

ruby: changes to simple network
This patch makes the Switch structure inherit from BasicRouter, as is
done in two other networks.

Ruby: remove config information from ruby.stats
This patch removes printConfig() functions from all structures in Ruby.
Most of the information is already part of config.ini, and where ever it
is not, it would become in due course.

Ruby: Remove some unused typedefs
This patch removes some of the unused typedefs. It also moves
some of the typedefs from Global.hh to TypeDefines.hh. The patch
also eliminates the file NodeID.hh.

includes: sort all includes

ruby: cleaning up RubyQueue and RubyNetwork dprintfs
Overall, continue to progress Ruby debug messages to more of the normal M5
debug message style
- add a name() to the Ruby Throttle & PerfectSwitch objects so that the debug output
isn't littered w/"global:" everywhere.
- clean up messages that print over multiple lines when possible
- clean up duplicate prints in the message buffer

Ruby: Improve Change PerfectSwitch's wakeup function
Currently the wakeup function for the PerfectSwitch contains three loops -

loop on number of virtual networks
loop on number of incoming links
loop till all messages for this (link, network) have been routed

With an 8 processor mesh network and Hammer protocol, about 11-12% of the
was observed to have been spent in this function, which is the highest
amongst all the functions. It was found that the innermost loop is executed
about 45 times per invocation of the wakeup function, when each invocation
of the wakeup function processes just about one message.

The patch tries to do away with the redundant executions of the innermost
loop. Counters have been added for each virtual network that record the
number of messages that need to be routed for that virtual network. The
inner loops are only executed when the number of messages for that particular
virtual network > 0. This does away with almost 80% of the executions of the
innermost loop. The function now consumes about 5-6% of the total execution
time.

ruby: get rid of Vector and use STL
add a couple of helper functions to base for deleteing all pointers in
a container and outputting containers to a stream

style: another ruby style pass

ruby: get rid of std-includes.hh
Do not use "using namespace std;" in headers
Include header files as needed

ruby: Make ruby #includes use full paths to the files they're including.
This basically means changing all #include statements and changing
autogenerated code so that it generates the correct paths. Because
slicc generates #includes, I had to hard code the include paths to
mem/protocol.

ruby: Import ruby and slicc from GEMS

We eventually plan to replace the m5 cache hierarchy with the GEMS
hierarchy, but for now we will make both live alongside eachother.