base: Add support for changing output directories

This changeset adds support for changing the simulator output
directory. This can be useful when the simulation goes through several
stages (e.g., a warming phase, a simulation phase, and a verification
phase) since it allows the output from each stage to be located in a
different directory. Relocation is done by calling core.setOutputDir()
from Python or simout.setOutputDirectory() from C++.

This change affects several parts of the design of the gem5's output
subsystem. First, files returned by an OutputDirectory instance (e.g.,
simout) are of the type OutputStream instead of a std::ostream. This
allows us to do some more book keeping and control re-opening of files
when the output directory is changed. Second, new subdirectories are
OutputDirectory instances, which should be used to create files in
that sub-directory.

Signed-off-by: Andreas Sandberg <andreas@sandberg.pp.se>
[sascha.bischoff@arm.com: Rebased patches onto a newer gem5 version]
Signed-off-by: Sascha Bischoff <sascha.bischoff@arm.com>
Signed-off-by: Andreas Sandberg <andreas.sandberg@arm.com>

sim: Disable gzip compression for writefile pseudo instruction

The writefile pseudo instruction uses OutputDirectory::create and
OutputDirectory::openFile to create the output files. However, by
default these will check the file extention for .gz, and create a gzip
compressed stream if the file ending matches. When writing out files,
we want to write them out exactly as they are in the guest simulation,
and never want to compress them with gzio. Additionally, this causes
m5 writefile to fail when checking the error flags for the output
steam.

With this patch we add an additional no_gz argument to
OutputDirectory::create and OutputDirectory::openFile which allows us
to override the gzip compression. Therefore, for m5 writefile we
disable the filename check, and always create a standard ostream.

mem: Add tracing support in the communication monitor

This patch adds packet tracing to the communication monitor using a
protobuf as the mechanism for creating the trace.

If no file is specified, then the tracing is disabled. If a file is
specified, then for every packet that is successfully sent, a protobuf
message is serialized to the file.

util: implements "writefile" gem5 op to export file from guest to host filesystem

Usage: m5 writefile <filename>

File will be created in the gem5 output folder with the identical filename.
Implementation is largely based on the existing "readfile" functionality.
Currently does not support exporting of folders.

Output: Add hierarchical output support and cleanup existing codebase.

Output: Include gzstream package to allow automatically-gzipped output
The gzstream package provides an ostream-interface for writing gzipped files.
The package comes from:
http://www.cs.unc.edu/Research/compgeom/gzstream/
And is distributed under the LGPL license. Both the license and version
information has been preservered, though all other files in the package have
been purged. Minor modifications to the code have been made. The output module
detects when a filename ends in .gz and constructs an ogzstream object instead
of an ofstream object. This works for both the create(...) and find(...)
commands. Additionally, since gzstream objects needs to be closed to ensure
proper file termination, I have the output deconstructor deleting all ostream's
that it manages on behalf of find(...). At the moment, the only output file
that I know this functionality works for is stats, i.e. by specifying
"--stats-file=m5stats.txt.gz" on the command line.

Make sure that output files are always checked success before they're used.
Make OutputDirectory::resolve() private and change the functions using
resolve() to instead use create().

Output: Make OutputDirectory::create() be able to create binary files.

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.