misc: Rename misc.(hh|cc) to logging.(hh|cc)

These files aren't a collection of miscellaneous stuff, they're the
definition of the Logger interface, and a few utility macros for
calling into that interface (panic, warn, etc.).

Change-Id: I84267ac3f45896a83c0ef027f8f19c5e9a5667d1
Reviewed-on: https://gem5-review.googlesource.com/6226
Reviewed-by: Brandon Potter <Brandon.Potter@amd.com>
Maintainer: Gabe Black <gabeblack@google.com>

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

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>

ext: Replace gzstream with iostream3 from zlib to avoid LGPL

This patch replaces the gzstream zlib wrapper with the iostream3
wrapper provided as part of zlib contributions. The main reason for
the switch is to avoid including LGPL in the default gem5
build. iostream3 is provided under a more permissive license:

The code is provided "as is", with the permission to use, copy,
modify, distribute and sell it for any purpose without fee.

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.

arch, base, dev, kern, sym: FreeBSD support

This adds support for FreeBSD/aarch64 FS and SE mode (basic set of syscalls only)

Committed by: Nilay Vaish <nilay@cs.wisc.edu>

misc: Fix a bunch of minor issues identified by static analysis

Add some missing initialisation, and fix a handful benign resource
leaks (including some false positives).

scons: Fix up numerous warnings about name shadowing

This patch address the most important name shadowing warnings (as
produced when using gcc/clang with -Wshadow). There are many
locations where constructor parameters and function parameters shadow
local variables, but these are left unchanged.

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.

base: fix a invalid ?: operator

Output: Add hierarchical output support and cleanup existing codebase.

includes: sort all includes

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.

Add -r/-e options to redirect stdout/stderr.
Better than using shell since it automatically uses -d directory
for output files (creating it as needed).

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.