Removing patches and rudimentary installation scripts in tools directory.

All patches were merged to Kaldi upstream. Installation scripts are being
replaced with a makefile.
Added tools/Makefile.
Updated graphviz header include path.
Barista build mechanism has undergone a major overhaul.

1. Barista now has a configure script which wraps CMake and provides a bare
bones autoconf like build. Supported command line options:

  Build Options:
    --build-dir=DIR             place build files in directory [build]
    --with-compiler=FILE        compiler name (or path)

  Installation Directories:
    --prefix=PREFIX             installation directory         [/usr/local]

  Required Packages in Non-Standard Locations:
    --with-boost=PATH           path to Boost    install root
    --with-graphviz=PATH        path to GraphViz install root
    --with-kaldi=PATH           path to Kaldi    install root  [tools/kaldi]
    --with-libcppa=PATH         path to libcppa  install root  [tools/libcppa]

2. CMakeLists.txt has seen a major overhaul and was moved to barista root.
There is also a new folder named 'cmake' for additional cmake related scripts.
Major changes include:
 - compiler compatibility check
 - searching system folders for Boost and GraphViz [default]
 - accepting paths for Boost, GraphViz, Kaldi and libcppa installations at
 non-standard locations
 - new install and uninstall targets for the generated makefile
 - adding cppa library path to barista executable RPATH to remove the need for
 setting up LD_LIBRARY_PATH (DYLD_LIBRARY_PATH on Mac OS X)
Minor changes on tools/Makefile.
Updates .gitignore to support new build system.
Fix typo in CMakeLists.txt
Added FindAtlas.cmake module.
Improvements to ATLAS configuration.
Fixed portaudio flags.
Updates to README. Details the new build system.
Updated FindGraphviz.cmake script.
Fixes a few typos in README.
Fix a typo in FindGraphviz.cmake.
Another small fix for FindGraphviz.cmake.
Updates tools/Makefile. Adds support for updating already existing installations.
Updates tools/Makefile. Allows compiling kaldi and graphviz with compilers other than g++ >= 4.7. libcppa still requires g++ >= 4.7.
Updates README. Better build instructions. New upgrade instructions.