syscall_emul: factor out flag tables into common file

The openFlagTable and mmapFlagTables for emulated Linux
platforms are basically identical, but are specified
repetitively for every platform. Use a common file
that gets included for each platform so that we only
have one copy, making them more consistent and simplifying
changes (like adding #ifdefs).

In the process, made some minor fixes that slipped through
due to previous inconsistencies, and added more #ifdefs
to try to fix building on alternative hosts.

syscall_emul: extend mmap system call to support file backed mmaps

For O3, which has a stat that counts reg reads, there is an additional
reg read per mmap() call since there's an arg we no longer ignore.
Otherwise, stats should not be affected.

syscall_emul: add many Linux kernel flags

syscall_emul: rename OpenFlagTransTable struct

The structure definition only had the open system call flag set in mind when
it was named, so we rename it here with the intention of using it to define
additional tables to translate flags for other system calls in the future.

includes: sort all includes

MIPS: Many style fixes.
White space, commented out code, some other minor fixes.

style: Remove non-leading tabs everywhere they shouldn't be. Developers should configure their editors to not insert tabs

fix MIPS headers

Add in files from merge-bare-iron, get them compiling in FS and SE mode

mips import pt. 1

src/arch/mips/SConscript:
"mips import pt.1".

Cleaned up include files and got rid of many using directives in header files.

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.