Merge lp:~reg-hugonweb/spods/2.0dev into lp:spods

[Justin]

Adds many 2.0 features:
  Skimming
  Documentation
  Pileup
  Preliminary Atlas config
  tclap command line arguments
  configurable random number seed
  metadata tree
  let TClonesArray handle max number of entries
  jet background subtraction

Adds many 2.0 features:
  Skimming
  Documentation
  Pileup
  Preliminary Atlas config
  tclap command line arguments
  configurable random number seed
  metadata tree
  let TClonesArray handle max number of entries
  jet background subtraction

=== added file '.bzrignore'
--- .bzrignore	1970-01-01 00:00:00 +0000
+++ .bzrignore	2013-05-01 15:50:43 +0000
@@ -0,0 +1,32 @@
+docs/html/genindex.html
+docs/html/_images
+docs/html/index.html
+docs/html/objects.inv
+docs/html/readme.html
+docs/html/search.html
+docs/html/searchindex.js
+docs/html/_sources
+docs/html/spodsConfig.html
+docs/html/_static
+docs/latex/fncychap.sty
+docs/latex/Makefile
+docs/latex/python.ist
+docs/latex/sphinxhowto.cls
+docs/latex/sphinxmanual.cls
+docs/latex/sphinx.sty
+docs/latex/spods.tex
+docs/latex/tabulary.sty
+docs/text/index.txt
+docs/text/readme.txt
+docs/text/spodsConfig.txt
+docs/man/spods.1
+.sconf_temp
+.sconsign.dblite
+config.log
+diff.txt
+texput.log
+docs/html/.doctrees
+docs/html/.buildinfo
+docs/latex/.doctrees
+docs/man/.doctrees
+docs/text/.doctrees

=== modified file 'README'
--- README	2012-07-03 14:52:36 +0000
+++ README	2013-05-01 15:50:43 +0000
@@ -1,6 +1,6 @@
 
 SPODS--Simple Physics Object based Detector Simulation
-Copyright (C) 2011, 2012 Justin Hugon
+Copyright (C) 2011, 2012, 2013 Justin Hugon
 
 SPODS is a detector simulation for particle physics collider experiments.
 It reconstructs muons, electrons, jets, and MET from generator events in

=== modified file 'SConstruct'
--- SConstruct	2012-08-18 11:50:47 +0000
+++ SConstruct	2013-05-01 15:50:43 +0000
@@ -1,18 +1,25 @@
 
 # SPODS--Simple Physics Object based Detector Simulation
-# Copyright (C) 2011, 2012 Justin Hugon
+# Copyright (C) 2011, 2012, 2013 Justin Hugon
 
 # Main SCONS Build Configuration File
 
 import os
 import glob
 
+buildDocs = False
+#buildDocs = True
+AddOption("--gccdebug",action="store_true",dest="gccdebug",default=False,help="turns on the debug flag in GCC")
+
 env = Environment(ENV = {'PATH':os.environ['PATH']} )
 
 includes = ["#include"]
 libpath = ["#lib"]
 libs = []
-env.MergeFlags('-fPIC -O2 -lm')
+if GetOption('gccdebug'):
+  env.MergeFlags('-g -lm -fPIC') # For Debugging
+else:
+  env.MergeFlags('-O2 -lm -fPIC ')
 
 #root
 env.ParseConfig('root-config --cflags')
@@ -48,19 +55,28 @@
 
 #fastjet
 includes.append("#external/fastjet/include")
+includes.append("#external/fastjet/tools")
 libpath.append("#external/fastjet/lib")
+libs.append("fastjettools")
 libs.append("fastjet")
 
+#tclap
+includes.append("#external/tclap/include")
+
 env.Append(CPPPATH=includes)
 env.Append(LIBPATH=libpath)
 env.Append(LIBS=libs)
  
 libSources = glob.glob("src/*")
 
-SConscript([
+sconscripts = [
 	"#test/SConscript",
-	"#external/SConscript"
-	],exports="env")
+	"#external/SConscript",
+	]
+if buildDocs:
+  sconscripts.append("#docs/SConscript")
+
+SConscript(sconscripts,exports="env")
 
 env.StaticLibrary(target="lib/spods", source=libSources)
 #env.SharedLibrary(target="lib/spods", source=libSources)

=== modified file 'build.sh'
--- build.sh	2012-04-25 09:31:26 +0000
+++ build.sh	2013-05-01 15:50:43 +0000
@@ -1,7 +1,7 @@
 #/bin/bash
 
 # SPODS--Simple Physics Object based Detector Simulation
-# Copyright (C) 2011, 2012 Justin Hugon
+# Copyright (C) 2011, 2012, 2013 Justin Hugon
 
 #script to build SPODS, use -jN for multi-processor building, and -c to clean up
 

=== added directory 'docs'
=== added file 'docs/SConscript'
--- docs/SConscript	1970-01-01 00:00:00 +0000
+++ docs/SConscript	2013-05-01 15:50:43 +0000
@@ -0,0 +1,76 @@
+
+## SPODS--Simple Physics Object based Detector Simulation
+## Copyright (C) 2011, 2012, 2013 Justin Hugon
+
+import os
+import glob
+
+def checkSphinx(context):
+  context.Message("Checking for sphinx-build...")
+  tryBuild = env.Command("","","sphinx-build -h")
+  ret = context.TryAction(tryBuild)
+  context.Result(ret[0])
+  return ret[0]
+
+def checkLatex(context):
+  context.Message("Checking for latex...")
+  tryBuild = env.Command("","","latex --help")
+  ret = context.TryAction(tryBuild)
+  context.Result(ret[0])
+  return ret[0]
+
+def checkPdfLatex(context):
+  context.Message("Checking for pdflatex...")
+  tryBuild = env.Command("","","pdflatex --help")
+  ret = context.TryAction(tryBuild)
+  context.Result(ret[0])
+  return ret[0]
+
+
+def checkDviPng(context):
+  context.Message("Checking for dvipng...")
+  tryBuild = env.Command("","","dvipng --help")
+  ret = context.TryAction(tryBuild)
+  context.Result(ret[0])
+  return ret[0]
+
+tests = {
+  "CheckSphinx":checkSphinx,
+  "CheckLatex":checkLatex,
+  "CheckPdfLatex":checkPdfLatex,
+  "CheckDviPng":checkDviPng
+}
+
+###################
+#For Particle Gun
+env = Environment(ENV = {'PATH':os.environ['PATH']} )
+
+doSphinx = False
+doSphinxHtml = False
+doSphinxPdf = False
+
+if not env.GetOption("clean"):
+ conf = Configure(env, custom_tests = tests)
+ if conf.CheckSphinx():
+   doSphinx = True
+ if conf.CheckLatex() and conf.CheckDviPng():
+   doSphinxHtml = True
+ #if conf.CheckPdfLatex():
+ #  doSphinxPdf = True
+ env = conf.Finish()
+
+sphinxOutputs = ["latex","text","man"]
+if doSphinxHtml:
+  sphinxOutputs.append("html")
+
+if doSphinx:
+  for outputFormat in sphinxOutputs:
+    name = Dir(outputFormat)
+    source = Dir("src")
+    targets = env.Command(name,source,"sphinx-build -b {0} $SOURCE $TARGET".format(outputFormat))
+    env.Depends(targets, source)
+    env.AlwaysBuild(name)
+    if outputFormat == "latex" and doSphinxPdf:
+      pdfTarget = env.Command("latex/spods.pdf","latex/spods.tex","pdflatex spods.tex",chdir=True)
+      env.Depends(pdfTarget,"latex/spods.tex")
+      

=== added directory 'docs/html'
=== added directory 'docs/latex'
=== added directory 'docs/man'
=== added directory 'docs/src'
=== added file 'docs/src/conf.py'
--- docs/src/conf.py	1970-01-01 00:00:00 +0000
+++ docs/src/conf.py	2013-05-01 15:50:43 +0000
@@ -0,0 +1,244 @@
+# -*- coding: utf-8 -*-
+#
+# SPODS documentation build configuration file, created by
+# sphinx-quickstart on Sat Aug 18 09:24:05 2012.
+#
+# This file is execfile()d with the current directory set to its containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import sys, os
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#sys.path.insert(0, os.path.abspath('.'))
+
+# -- General configuration -----------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be extensions
+# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+extensions = ["sphinx.ext.pngmath"]
+
+# Add any paths that contain templates here, relative to this directory.
+#templates_path = ['_templates']
+
+# The suffix of source filenames.
+source_suffix = '.rst'
+
+# The encoding of source files.
+#source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'SPODS'
+copyright = u'2011, 2012, Justin Hugon'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = '1.0'
+# The full version, including alpha/beta/rc tags.
+release = '1.0'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+#today_fmt = '%B %d, %Y'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+#exclude_patterns = ['_build']
+
+# The reST default role (used for this markup: `text`) to use for all documents.
+#default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+#modindex_common_prefix = []
+
+
+# -- Options for HTML output ---------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#html_theme = 'default'
+#html_theme = 'haiku'
+html_theme = 'agogo'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#html_theme_options = {}
+
+# Add any paths that contain custom themes here, relative to this directory.
+#html_theme_path = []
+
+# The name for this set of Sphinx documents.  If None, it defaults to
+# "<project> v<release> documentation".
+#html_title = None
+
+# A shorter title for the navigation bar.  Default is the same as html_title.
+#html_short_title = None
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#html_logo = None
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#html_favicon = None
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+#html_static_path = ['_static']
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+#html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+
+# If false, no module index is generated.
+#html_domain_indices = True
+
+# If false, no index is generated.
+#html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+#html_show_sourcelink = True
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+#html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+#html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it.  The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = None
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'spodsdoc'
+
+
+# -- Options for LaTeX output --------------------------------------------------
+
+latex_elements = {
+# The paper size ('letterpaper' or 'a4paper').
+#'papersize': 'letterpaper',
+
+# The font size ('10pt', '11pt' or '12pt').
+#'pointsize': '10pt',
+
+# Additional stuff for the LaTeX preamble.
+#'preamble': '',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title, author, documentclass [howto/manual]).
+latex_documents = [
+  ('index', 'spods.tex', u'SPODS Documentation',
+   u'Justin Hugon', 'howto'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+#latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#latex_use_parts = False
+
+# If true, show page references after internal links.
+#latex_show_pagerefs = False
+
+# If true, show URL addresses after external links.
+#latex_show_urls = False
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_domain_indices = True
+
+
+# -- Options for manual page output --------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    ('index', 'spods', u'SPODS Documentation',
+     [u'Justin Hugon'], 1)
+]
+
+# If true, show URL addresses after external links.
+#man_show_urls = False
+
+
+# -- Options for Texinfo output ------------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+  ('index', 'SPODS', u'SPODS Documentation',
+   u'Justin Hugon', 'SPODS', 'One line description of project.',
+   'Miscellaneous'),
+]
+
+# Documents to append as an appendix to all manuals.
+#texinfo_appendices = []
+
+# If false, no module index is generated.
+#texinfo_domain_indices = True
+
+# How to display URL addresses: 'footnote', 'no', or 'inline'.
+#texinfo_show_urls = 'footnote'

=== added file 'docs/src/index.rst'
--- docs/src/index.rst	1970-01-01 00:00:00 +0000
+++ docs/src/index.rst	2013-05-01 15:50:43 +0000
@@ -0,0 +1,22 @@
+.. SPODS documentation master file, created by
+   sphinx-quickstart on Sat Aug 18 09:24:05 2012.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to SPODS's documentation!
+=================================
+
+Contents:
+
+.. toctree::
+   :maxdepth: 2
+
+   readme
+   spodsConfig
+
+..  Indices and tables
+    ==================
+
+..  * :ref:`genindex`
+    * :ref:`modindex`
+    * :ref:`search`

=== added file 'docs/src/readme.rst'
--- docs/src/readme.rst	1970-01-01 00:00:00 +0000
+++ docs/src/readme.rst	2013-05-01 15:50:43 +0000
@@ -0,0 +1,144 @@
+
+SPODS--Simple Physics Object based Detector Simulation
+=========================================================
+
+Copyright (C) 2011, 2012, 2013 Justin Hugon
+
+SPODS is a detector simulation for particle physics collider experiments.
+It reconstructs muons, electrons, jets, and MET from generator events in
+the HepMC event format.  These "physics objects" are then smeared by
+Gaussians parameterized to the response of various detectors, and
+output in a root tree.
+
+Building
+-----------
+
+Executing ./build.sh will build SPODS.  The script will accept the -jN
+option for parallel compilation, and -c to clean up the build.
+
+SPODS only requirements are a C++ compiler, python, and an installation
+of ROOT.  The python version should be between v2.4 and v2.7.  The
+ROOT executable, ``root``, and build configuration lister ``root-config``, 
+should be in the ``$PATH``.
+
+SPODS has been tested with these versions:
+
+======  =======  ========
+gcc     ROOT     python
+======  =======  ========
+4.1.2   5.32     2.4.3
+4.5.2   5.30     2.7.1
+4.6.3   5.32     2.7.3
+4.7.2   5.34     2.7.3
+======  =======  ========
+
+Running
+----------
+
+The executable can be run as: ::
+
+  ./bin/SPODS <configFile.yaml> <inFile.hepmc> <outFile.root>
+
+Example config files are in the test directory.
+
+Analyzing Output
+------------------
+
+A ROOT TTree is written to the output file, named "tree".  Within this
+file, each physics object is represented by a TClonesArray of TParticles.
+The TParticles' momentum magnitudes are smeared.  Other information can be 
+accessed through the functions present in include/PhysicsObjectFunctions.h.  
+Included are functions to get the factor to scale the momentum to return
+it to the generator value, b-tagging variables, and isolation variables.
+
+An example of reading the output is in test/testReader.cc
+
+It is important to note that jets are made out of all particles besides
+muons.  This means that an isolated electron or photon will appear
+in the jet collection if the "jetVeto*" parameters are relaxed too much.
+
+In addition to the arrays of particles, the output root files contain an
+additional tree called "metadata".  This tree contains useful information
+such as the SPODS input and output filenames, a dump of the configuration,
+and the total number of events, sum of weights, and sum of weights squared
+in the processed input file.  These numbers can be useful when computing
+efficiencies or scaling a sample to a specific cross-section and luminosity.
+Functions to easily access them are provided in include/PhysicsObjectFunctions.h.
+
+Making Input Files with Pythia 8
+-------------------------------------
+
+To make HepMC files with PYTHIA 8, follow these steps:
+
+#. Build SPODS
+
+#. Download and untar PYTHIA 8, and cd into its working directory
+
+#. Run::
+
+    ./configure --with-hepmc=<SPODSDIR>/external/HepMC --with-hepmcversion=2
+
+#. ``make``
+
+#. Go into examples/, and run::
+
+    make main42
+
+(main32 in older versions of pythia8!)
+
+#. PYTHIA 8 requires an environmental variable to run::
+
+    export PYTHIA8DATA=<PYTHIADIR>/xmldoc
+
+#. The executable ``./main42.exe`` takes PYTHIA 8 .cmnd input files, and produces
+HepMC event files.  The ``<SPODSDIR>/test/\*.cmnd`` are further examples.
+Run like::
+
+  ./main42.exe <infile.cmnd> <outfilename.hepmc>
+
+#. To make a SPODS ROOT file out of the HepMC file without detector smearing,
+go back to the SPODS directory and run::
+
+  ./bin/SPODS test/noSmearingConfig.yaml <filename.hepmc> <outfilename.root>
+
+It is faster and takes less space to avoid writing the intermediate .hepmc 
+file to disk.  You can write it to a named pipe and direct it into SPODS::
+
+  mkfifo tmpPipe.hepmc
+  <PYTHIADIR>/examples/main42.exe <config.cmnd> tmpPipe.hepmc &
+  <SPODSDIR>/bin/SPODS <config.yaml> tmpPipe.hepmc <outfile.root>
+  rm tmpPipe.hepmc
+
+Pileup Usage
+-------------------------------------
+
+SPODS can simulate the effects of pileup, extra collisions happening at the 
+same time as a collision of interest.  The distribution of the number of 
+pileup collisions is configurable in the config file.
+
+The more efficient mode of pileup involves first running SPODS on a 
+minbias sample of a few thousand events, making sure the option 
+``keepGenParticles`` is set to true.  Then, SPODS is run on the 
+sample of interest, and random events are selected from the 
+minbias sample for pileup.  The commands required are: ::
+
+   ./bin/SPODS config.yaml minbias.hepmc minbias.root
+   ./bin/SPODS config.yaml -p minbias.root input.hepmc output.root
+
+The same minbias file can be used for many different samples of interest.
+
+The other mode of operation is to have a sufficiently large sample of 
+minbias in HepMC format (or a named pipe of minbias as discussed in the last
+section).  These events will be piled up in-order on top of the sample of
+interest.  For example, with PYTHIA 8 using named pipes, run: ::
+
+  mkfifo tmpPipe.hepmc 
+  mkfifo minbiasPipe.hepmc
+  <PYTHIADIR>/examples/main42.exe <config.cmnd> tmpPipe.hepmc &
+  <PYTHIADIR>/examples/main42.exe <minbias.cmnd> minbiasPipe.hepmc &
+  <SPODSDIR>/bin/SPODS <config.yaml> -p minbiasPipe.hepmc tmpPipe.hepmc <outfile.root>
+  rm tmpPipe.hepmc
+  rm minbiasPipe.hepmc
+
+This method will take much more time than the first method.
+

=== added file 'docs/src/spodsConfig.rst'
--- docs/src/spodsConfig.rst	1970-01-01 00:00:00 +0000
+++ docs/src/spodsConfig.rst	2013-05-01 15:50:43 +0000
@@ -0,0 +1,500 @@
+SPODS Configuration File Syntax
+==================================
+
+Copyright (C) 2011, 2012, 2013 Justin Hugon
+
+The SPODS configuration file defines parameters related to cuts on generator
+objects, as well as how those objects are smeared.  Each option must be in
+the config file for SPODS to run correctly.  All options are described below.  
+
+The configuration file syntax is `YAML <http://www.yaml.org/>`_
+
+Run Parameters
+------------------
+
+.. describe:: maxEvents: <integer>
+
+  The maximum number of events to process from the input file.
+
+.. describe:: keepGenParticles: <bool>
+
+  Set true to keep the original particles from the generator, false otherwise.
+
+.. describe:: keepNonFinalStateGenParticles: <bool>
+
+  If keepGenParticles is true, controls whether particles with states != 1 are kept.  Set true to keep them, false otherwise.
+
+Max Particle Parameters
+----------------------------
+
+.. describe:: maxGenParticles: <integer>
+
+  The maximum number of generator particles to read in (per event).
+
+.. describe:: maxElectrons: <integer>
+
+  The maximum number of electrons to write out to the ROOT tree.
+
+.. describe:: maxMuons: <integer>
+
+  The maximum number of muons to write out to the ROOT tree.
+
+.. describe:: maxPhotons: <integer>
+
+  The maximum number of photons to write out to the ROOT tree.
+
+.. describe:: maxJets: <integer>
+
+  The maximum number of jets to write out to the ROOT tree.
+
+Particle Cut Parameters
+--------------------------
+
+.. describe:: etaElectronMax: <float>
+
+  Max \|eta\| Cut
+
+.. describe:: etaMuonMax: <float>
+
+  Max \|eta\| Cut
+
+.. describe:: etaPhotonMax: <float>
+
+  Max \|eta\| Cut
+
+.. describe:: etaJetMax: <float>
+
+  Max \|eta\| cut for particles clustered into jets.
+
+.. describe:: etaMetMax: <float>
+
+  Max \|eta\| cut for particles included in the MET calculation.
+
+
+.. describe:: ptElectronMin: <float>
+
+  Min pt Cut
+
+.. describe:: ptMuonMin: <float>
+
+  Min pt Cut
+
+.. describe:: ptPhotonMin: <float>
+
+  Min pt Cut
+
+.. describe:: ptJetMin: <float>
+
+  Min pt cut for jets.
+
+Jet Configuration
+--------------------
+
+.. describe:: jetAlg: <kt|ca|antikt>
+
+  Jet Algorithm name for `FastJet <http://fastjet.fr>`_ to cluster with.
+
+  kt
+    Longitudinally invariant kt algorithm
+
+  ca
+    Longitudinally invariant inclusive Cambridge/Aachen algorithm
+
+  antikt
+    anti-kt algorithm
+
+.. describe:: jetAlgR: <float>
+
+  Radius parameter for the jet algorithm
+
+.. describe:: jetVetoNPartMin: <int>
+
+  Minimum number of particles in a jet (for jet-ID)
+
+.. describe:: jetVetoNChargMin: <int>
+
+  Minimum number of charged particles in a jet (for jet-ID)
+
+.. describe:: jetVetoNHadMin: <int>
+
+  Minimum number of hadron particles in a jet (for jet-ID)
+
+Isolation Configuration
+-------------------------
+
+.. describe:: muonIsoType: <trk|calo|comb>
+
+  Type of Isolation
+
+  trk
+    Sum all charged particle pt in the isolation cone
+  calo
+    Sum all non-neutrino non-muon particle pt in the isolation cone
+  combined
+    Sum all non-neutrino particle pt in the isolation cone
+
+.. describe:: muonIsoConeSize: <float>
+
+  Radius of isolation cone in 
+  :math:`\Delta R = \sqrt{(\Delta \phi)^2 + (\Delta \eta)^2}`
+
+.. describe:: muonIsoMinPt: <float>
+
+  Min particle pt to include in the isolation calculation
+
+.. describe:: electronIsoType: <trk|calo|comb>
+
+  Type of Isolation
+
+  trk
+    Sum all charged particle pt in the isolation cone
+  calo
+    Sum all non-neutrino non-muon particle pt in the isolation cone
+  combined
+    Sum all non-neutrino particle pt in the isolation cone
+
+.. describe:: electronIsoConeSize: <float>
+
+  Radius of isolation cone in 
+  :math:`\Delta R = \sqrt{(\Delta \phi)^2 + (\Delta \eta)^2}`
+
+.. describe:: electronIsoMinPt: <float>
+
+  Min particle pt to include in the isolation calculation
+
+.. describe:: photonIsoType: <trk|calo|comb>
+
+  Type of Isolation
+
+  trk
+    Sum all charged particle pt in the isolation cone
+  calo
+    Sum all non-neutrino non-muon particle pt in the isolation cone
+  combined
+    Sum all non-neutrino particle pt in the isolation cone
+
+.. describe:: photonIsoConeSize: <float>
+
+  Radius of isolation cone in 
+  :math:`\Delta R = \sqrt((\Delta \phi)^2 + (\Delta \eta)^2)`
+
+.. describe:: photonIsoMinPt: <float>
+
+  Min particle pt to include in the isolation calculation
+
+b-Tagging Parameters
+---------------------
+
+.. describe:: bTagEff: <float>
+
+  b-Tagging Efficiency on Jets Identified to contain b-particles
+
+.. describe:: bTagMistagRate: <float>
+
+  b-Tagging Mistagging Rate on jets not containing b-particles
+
+Skimming Parameters
+---------------------
+
+The skimming parameters control whether an event is written to the output file or not, based on the physics objects in the event.  **All** skim cuts must
+be passed for an event to be written out (put together through a logical AND).
+
+The syntax for skimming is to have::
+
+  skim:
+    xxx: X
+    yyyy: Y
+
+Each statement after ``skim:`` must be indented by the same amount.
+
+All of these cuts are applied after pt smearing and after the detector
+pt and eta cuts are applied.
+
+.. describe:: minPO: <integer>
+
+  Require a minimum number of physics objects in the event.  If
+  nMuons + nElectrons + nJets + nPhotons < minPO, then the event
+  will not be written to the output file.  To be included in the
+  count, each of the physics objects will have to pass the pt*Min
+  cuts described below, after smearing.
+
+.. describe:: minLeptons: <integer>
+
+  Require a minimum number of leptons in the event.  If
+  nMuons + nElectrons < minLeptons, then the event
+  will not be written to the output file.  To be included in the
+  count, each of the leptons will have to pass the pt*Min
+  cuts described below, after smearing.
+
+.. describe:: minMuons: <integer>
+
+  Require a minimum number of muons in the event.  If
+  nMuons < minMuons, then the event
+  will not be written to the output file.  To be included in the
+  count, each of the muons will have to pass the ``ptMuonMin``
+  cut described below, after smearing.
+
+.. describe:: minElectrons: <integer>
+
+  Require a minimum number of electrons in the event.  If
+  nElectrons < minElectrons, then the event
+  will not be written to the output file.  To be included in the
+  count, each of the electrons will have to pass the ``ptElectronMin``
+  cut described below, after smearing.
+
+.. describe:: minPhotons: <integer>
+
+  Require a minimum number of photons in the event.  If
+  nPhotons < minPhotons, then the event
+  will not be written to the output file.  To be included in the
+  count, each of the photons will have to pass the ``ptPhotonMin``
+  cut described below, after smearing.
+
+.. describe:: minJets: <integer>
+
+  Require a minimum number of jets in the event.  If
+  nJets < minJets, then the event
+  will not be written to the output file.  To be included in the
+  count, each of the jets will have to pass the ``ptJetMin``
+  cut described below, after smearing.
+
+.. describe:: ptMuonMin: <float>
+
+  To be included in the above counts, a muon must pass this
+  pt cut, after smearing.
+
+.. describe:: ptElectronMin: <float>
+
+  To be included in the above counts, an electron must pass this
+  pt cut, after smearing.
+
+.. describe:: ptPhotonMin: <float>
+
+  To be included in the above counts, a photon must pass this
+  pt cut, after smearing.
+
+.. describe:: ptJetMin: <float>
+
+  To be included in the above counts, a jet must pass this
+  pt cut, after smearing.  This cut is also applied before a jet
+  is included in the :math:`H_T` sum.
+
+.. describe:: metMin: <float>
+
+  The minimum amount of missing transverse energy 
+  (transverse energy imbalance).
+
+.. describe:: htMin: <float>
+
+  The minimum amount of :math:`H_T`, defined as the scalar sum
+  of jet pt.  Jets are only considered if the pass the minimum 
+  jet pt threshold ``ptJetMin``, above.
+
+Pileup Parameters
+-------------------------------
+
+.. describe:: pileupN: <integer>
+
+  The desired amount of pileup.  Behavior differs depending on 
+  pileupType parameter.
+
+.. describe:: pileupType: <poisson|flat|pileupN>
+
+  Choose the distribution of pileup events.  
+
+  poisson
+    Take the number of pileup interactions from the Poisson distribution
+    with mean "pileupN".
+
+  flat
+    Take the number of pileup interactions from a uniform distribution
+    from [0,pileupN].
+
+  pileupN
+    All events will have "pileupN" pileup events.
+
+Jet Background Subtraction (Pileup Subtraction)
+-------------------------------------------------
+
+Jet area pileup subtraction using the `FastJet <http://fastjet.fr>`_ 
+package may be performed.  See the fastjet documentation for details.
+
+.. describe:: jetBakOn: <bool>
+
+  Set true to enable jet background subtraction, false to disable.
+
+.. describe:: jetBakAlg: <kt|ca|antikt>
+
+  The jet algorithm to use for background estimation.  These options are
+  the same as the ones for "jetAlg".  "antikt" is not recommended.
+
+.. describe:: jetBakAlgR: <float>
+
+  The size parameter for the background estimation jet algorithm.  The 
+  fastjet documentation recommends sizes from 0.4 to 0.6, favoring
+  smaller values for busy events.
+
+.. describe:: jetBakAreaType: <active_area_explicit_ghosts|active_area|passive_area|one_ghost_passive_area>
+
+  The type of jet area.  See fastjet documentation for details.
+
+Muon Resolution Parameters
+-------------------------------
+
+.. describe:: muonResEtaRanges;
+
+  A list of \|eta\| Ranges.  This list allows for different resolutions in
+  different \|eta\| regions.  Each range is itself a two element list. 
+  ::
+
+    muonResEtaRanges:
+     - [minEta, MaxEta] #first eta range
+     - [minEta, MaxEta] #second eta range
+
+.. describe:: muonResConstTerm:
+
+  A list of muon resolution constant terms.  This must be the same length as 
+  muonResEtaRanges
+
+.. describe:: muonResSqrtTerm:
+
+  A list of muon resolution coefficients for Sqrt(momentum) terms, 
+  for momentum in TeV.
+  This must be the same length as muonResEtaRanges
+
+.. describe:: muonResHighPtCut:
+
+  A list of muon resolution HighPtCuts, for momentum in GeV.
+  Above this cut, the following HighPt parameters are used.
+  This must be the same length as muonResEtaRanges
+
+.. describe:: muonResHighPtConstTerm:
+
+  A list of muon resolution constant terms, for use above the 
+  muonResHighPtCut.  
+  This must be the same length as muonResEtaRanges.
+
+.. describe:: muonResHighPtConstTerm:
+
+  A list of muon resolution constant terms, for use above the 
+  muonResHighPtCut.  
+  This must be the same length as muonResEtaRanges.
+
+.. describe:: muonResHighPtSqrtTerm:
+
+  A list of muon resolution coefficients for Sqrt(momentum) terms, 
+  for momentum in TeV,
+  for use above the muonResHighPtCut.  
+  This must be the same length as muonResEtaRanges.
+
+Photon and Electron Resolution Parameters
+-------------------------------------------
+
+Photon Resolution is given by the equation:
+
+.. math::
+
+  \sigma = \sqrt{(a/E)^2+(b/Sqrt(E))^2+(c)^2}
+
+Below, these options are described as
+
+a
+  1/E Term
+
+b
+  1/Sqrt(E) Term
+
+c
+  Constant Term
+
+Electron resolution is treated the same, except at low pt, where the tracker
+makes the resolution better.  Below a given pt cut, the electron resolution
+is considered constant.
+
+.. describe:: photonResEtaRanges;
+
+  A list of \|eta\| Ranges.  This list allows for different resolutions in
+  different \|eta\| regions.  Each range is itself a two element list. 
+  ::
+
+    photonResEtaRanges:
+     - [minEta, MaxEta] #first eta range
+     - [minEta, MaxEta] #second eta range
+
+.. describe:: photonResConstTerm:
+
+  A list of photon resolution constant terms.  This must be the same length as 
+  photonResEtaRanges
+
+.. describe:: photonResOneOverETerm:
+
+  A list of photon coefficients to 1/E terms.  This must be the same length as 
+  photonResEtaRanges
+
+.. describe:: photonResOneOverSqrtETerm:
+
+  A list of photon coefficients to 1/Sqrt(E) terms.  
+  This must be the same length as 
+  photonResEtaRanges
+
+.. describe:: electronResPtCut: <float>
+
+  Below this pt, electrons will have a constant resolution, given below.
+  Above this pt, electrons will be smeared the same as photons.
+
+.. describe:: electronResConstantTerm: <float>
+  
+  Below the electronResPtCut, this constant resolution is applied.
+
+
+Jet Resolution Parameters
+-------------------------------
+
+Jet Resolution is given by the equation:
+
+.. math::
+
+  \sigma = \sqrt{(a/E)^2+(b/Sqrt(E))^2+(c)^2}
+
+Below, these options are described as
+
+a
+  1/E Term
+
+b
+  1/Sqrt(E) Term
+
+c
+  Constant Term
+
+.. describe:: jetResEtaRanges;
+
+  A list of \|eta\| Ranges.  This list allows for different resolutions in
+  different \|eta\| regions.  Each range is itself a two element list. 
+  ::
+
+    jetResEtaRanges:
+     - [minEta, MaxEta] #first eta range
+     - [minEta, MaxEta] #second eta range
+
+.. describe:: jetResConstTerm:
+
+  A list of jet resolution constant terms.  This must be the same length as 
+  jetResEtaRanges
+
+.. describe:: jetResOneOverETerm:
+
+  A list of jet coefficients to 1/E terms.  This must be the same length as 
+  jetResEtaRanges
+
+.. describe:: jetResOneOverSqrtETerm:
+
+  A list of jet coefficients to 1/Sqrt(E) terms.  
+  This must be the same length as 
+  jetResEtaRanges
+
+.. describe:: jetResPtCut:
+
+  Below this pt, jets are not smeared.  This can be used to keep many low-pt
+  jets from being smeared by resolution parameters that are not applicable
+  to low-pt.

=== added directory 'docs/text'
=== removed file 'external/HepMC/.sconsign.dblite'
Binary files external/HepMC/.sconsign.dblite	2012-02-17 10:56:24 +0000 and external/HepMC/.sconsign.dblite	1970-01-01 00:00:00 +0000 differ
=== modified file 'external/SConscript'
--- external/SConscript	2012-04-25 09:31:26 +0000
+++ external/SConscript	2013-05-01 15:50:43 +0000
@@ -1,11 +1,12 @@
 # SPODS--Simple Physics Object based Detector Simulation
-# Copyright (C) 2011, 2012 Justin Hugon
+# Copyright (C) 2011, 2012, 2013 Justin Hugon
 
 #Versions
 #  scons: 2.1.0
 #  yaml-cpp: 0.2.7
 #  HepMC: 2.06.05
 #  fastjet: 3.0.1
+#  tclap: 1.2.1
 
 SConscript([
 	"yaml-cpp/SConscript",

=== removed file 'external/fastjet/.sconsign.dblite'
Binary files external/fastjet/.sconsign.dblite	2012-02-17 10:56:24 +0000 and external/fastjet/.sconsign.dblite	1970-01-01 00:00:00 +0000 differ
=== added directory 'external/tclap'
=== added file 'external/tclap/AUTHORS'
--- external/tclap/AUTHORS	1970-01-01 00:00:00 +0000
+++ external/tclap/AUTHORS	2013-05-01 15:50:43 +0000
@@ -0,0 +1,6 @@
+
+original author: Michael E. Smoot
+invaluable contributions: Daniel Aarno
+more contributions: Erik Zeek
+more contributions: Fabien Carmagnac (Tinbergen-AM)
+outstanding editing: Carol Smoot

=== added file 'external/tclap/COPYING'
--- external/tclap/COPYING	1970-01-01 00:00:00 +0000
+++ external/tclap/COPYING	2013-05-01 15:50:43 +0000
@@ -0,0 +1,25 @@
+
+
+Copyright (c) 2003 Michael E. Smoot 
+
+Permission is hereby granted, free of charge, to any person 
+obtaining a copy of this software and associated documentation 
+files (the "Software"), to deal in the Software without restriction, 
+including without limitation the rights to use, copy, modify, merge, 
+publish, distribute, sublicense, and/or sell copies of the Software, 
+and to permit persons to whom the Software is furnished to do so, 
+subject to the following conditions:
+
+The above copyright notice and this permission notice shall be 
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, 
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES 
+OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND 
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS 
+BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN 
+AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR 
+IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN 
+THE SOFTWARE.
+
+

=== added file 'external/tclap/ChangeLog'
--- external/tclap/ChangeLog	1970-01-01 00:00:00 +0000
+++ external/tclap/ChangeLog	2013-05-01 15:50:43 +0000
@@ -0,0 +1,1760 @@
[phone]:08  mes5k
+
+	* include/tclap/Arg.h: patch that allows arg start strings to be
+	  pound defined to easily conform to different platforms
+
[phone]:58  mes5k
+
+	* docs/Makefile.am: being slightly more precise about what we clean
+
[phone]:30  mes5k
+
+	* include/tclap/: DocBookOutput.h, StdOutput.h,
+	  ZshCompletionOutput.h: fixed shadow variable name problem
+
[phone]:05  mes5k
+
+	* include/tclap/CmdLine.h: fixed minor memory leak
+
[phone]:26  macbishop
+
+	* configure.in, config/ac_cxx_warn_effective_cxx.m4: Check if
+	  compiler supports Weffec++ and if so use it (fixes compilation
+	  issue with e.g. SunStudio compiler)
+
[phone]:45  macbishop
+
+	* include/tclap/ArgTraits.h: Updated documentation for ArgTraits to
+	  reference StringLike and ValueLike classes.
+
[phone]:32  macbishop
+
+	* examples/test10.cpp: Added explicit cast to supress warning about
+	  deprecated conversion from string constant to char*
+
[phone]:18  mes5k
+
+	* docs/Makefile.am: now using a slightly different variable for doc
+	  install to support out-of-tree builds
+
[phone]:37  mes5k
+
+	* configure.in: bumped version number to 1.2.1
+
[phone]:30  mes5k
+
+	* docs/style.css: tweaked style so it doesn't blink
+
[phone]:21  mes5k
+
+	* tests/: test57.out, test57.sh, test76.out: tweaked tests to
+	  reflect fix for mutually exclusive switches
+
[phone]:20  mes5k
+
+	* include/tclap/: SwitchArg.h, XorHandler.h: finally fixed bug
+	  relating to mutually exclusive combined switched
+
[phone]:12  mes5k
+
+	* include/tclap/Arg.h: minor reformat
+
[phone]:10  mes5k
+
+	* include/tclap/CmdLine.h: minor reformatting
+
[phone]:13  mes5k
+
+	* examples/Makefile.am, examples/test20.cpp, tests/Makefile.am,
+	  tests/test74.out, tests/test74.sh, tests/test75.out,
+	  tests/test75.sh, tests/test76.out, tests/test76.sh,
+	  tests/test77.out, tests/test77.sh: added failing tests for XOR
+	  error message bug
+
[phone]:52  mes5k
+
+	* include/tclap/StandardTraits.h: applied Tom Fogal's win64 patch
+	  for size_t
+
[phone]:38  mes5k
+
+	* docs/Makefile.am: hopefully fixed out-of-tree doc installation
+
[phone]:50  mes5k
+
+	* include/tclap/: Arg.h, ArgTraits.h, CmdLine.h, HelpVisitor.h,
+	  MultiArg.h, ValueArg.h, ValuesConstraint.h, VersionVisitor.h,
+	  XorHandler.h, ZshCompletionOutput.h: fixed all effective c++
+	  warnings based on patch from Andrew Marlow
+
[phone]:41  mes5k
+
+	* configure.in: added more compiler warnings
+
[phone]:49  mes5k
+
+	* include/tclap/SwitchArg.h, include/tclap/ValueArg.h,
+	  tests/test22.out, tests/test24.out: make error message a bit more
+	  meaningful
+
[phone]:42  mes5k
+
+	* include/tclap/StandardTraits.h: added a check for wchar_t to deal
+	  with a potential problem with MS compilers
+
[phone]:28  mes5k
+
+	* docs/index.html: updated for 1.2.0
+
[phone]:41  mes5k
+
+	* docs/Makefile.am: another update to support older automake
+
[phone]:23  mes5k
+
+	* docs/Makefile.am: removed an errant space
+
[phone]:15  mes5k
+
+	* docs/Makefile.am: added a definition for docdir, which doesnt
+	  exist for old versions of automake
+
[phone]:02  mes5k
+
+	* docs/Makefile.am: corrected the doc install directory structure
+
[phone]:55  mes5k
+
+	* NEWS: updated for 1.2.0
+
[phone]:53  mes5k
+
+	* docs/: manual.html, manual.xml: updated for 1.2.0 including text
+	  on ArgTraits
+
[phone]:26  mes5k
+
+	* Makefile.am, configure.in, tclap.pc.in, docs/Makefile.am,
+	  examples/Makefile.am: applying patches to make gnu compiler args
+	  conditional, to install docs, and to add pkgconfig support to the
+	  installation
+
[phone]:49  mes5k
+
+	* configure.in, tests/Makefile.am, tests/test73.out,
+	  tests/test73.sh: added test 73 based on bug reported by user
+
[phone]:09  mes5k
+
+	* include/tclap/UnlabeledValueArg.h: updated incorrect api docs
+	  again
+
[phone]:04  mes5k
+
+	* include/tclap/UnlabeledValueArg.h: updated incorrect api doc
+
[phone]:10  mes5k
+
+	* AUTHORS: added author
+
[phone]:05  mes5k
+
+	* include/tclap/: Arg.h, CmdLine.h, CmdLineInterface.h, MultiArg.h,
+	  MultiSwitchArg.h, SwitchArg.h, ValueArg.h: added support for
+	  resetting a command line
+
[phone]:04  mes5k
+
+	* docs/manual.html, docs/manual.xml, examples/Makefile.am,
+	  examples/test19.cpp, include/tclap/Arg.h, tests/Makefile.am,
+	  tests/test29.out, tests/test29.sh, tests/test71.out,
+	  tests/test71.sh, tests/test72.out, tests/test72.sh: added support
+	  for parsing hex and octal ints as well as small fix to support
+	  gcc 4.4
+
[phone]:29  mes5k
+
+	* docs/manual.xml: updated note on xor
+
[phone]:21  mes5k
+
+	* docs/manual.xml: added note on xor
+
[phone]:18  zeekec
+
+	* examples/test18.cpp, include/tclap/CmdLine.h, tests/Makefile.am,
+	  tests/test70.out, tests/test70.sh: Rethrow ExitExceptions if
+	  we're not handling exceptions.
+
[phone]:52  zeekec
+
+	* include/tclap/Arg.h: Silence some compiler warnings.	The const
+	  on return-by-value is ignored.
+
[phone]:20  zeekec
+
+	* include/tclap/CmdLine.h, examples/Makefile.am,
+	  examples/test18.cpp, tests/Makefile.am, tests/test69.out,
+	  tests/test69.sh: Allow internal handling of parse errors to be
+	  turned off.  This allows exceptions for parse errors to be
+	  propagated to the caller.  Exiting the program in parse is a bad
+	  idea generally, as we have no way of knowing what cleanup needs
+	  to be done in the main program.
+
[phone]:48  mes5k
+
+	* include/tclap/StdOutput.h: bug in while loop
+
[phone]:15  mes5k
+
+	* include/tclap/: CmdLine.h, SwitchArg.h: added length checks to
+	  strings that can otherwise break with Metroworks compilers
+
[phone]:21  macbishop
+
+	* examples/: Makefile.am, test17-a.cpp, test17.cpp: Added test that
+	  tclap does not define any hard symbols (bug 1907017)
+
[phone]:04  mes5k
+
+	* include/tclap/CmdLine.h: added a new include to support exit in
+	  environments where it isnt defined
+
[phone]:02  mes5k
+
+	* examples/test7.cpp, include/tclap/Arg.h, tests/test46.out:
+	  tweaked tests to support dashes in arg names
+
[phone]:28  mes5k
+
+	* include/tclap/Arg.h: allowed dash char in arg names
+
[phone]:05  zeekec
+
+	* include/tclap/Makefile.am: Added Traits files to the list of
+	  files to be installed.
+
[phone]:18  macbishop
+
+	* examples/test14.cpp, examples/test15.cpp, examples/test16.cpp,
+	  include/tclap/Arg.h, include/tclap/ArgTraits.h,
+	  include/tclap/StandardTraits.h, configure.in,
+	  config/ac_cxx_have_long_long.m4, examples/Makefile.am:
+	  Refactoring of the arg-traits functionality. The purpose is to
+	  make it easier to make you own classes, and types defined in the
+	  standard library work well with tclap. I'll try to write up some
+	  documenation of how to achieve this as-well.
+
[phone]:33  mes5k
+
+	* examples/test13.cpp: added attribution
+
[phone]:30  mes5k
+
+	* examples/test13.cpp: fixed a warning message
+
[phone]:27  mes5k
+
+	* examples/Makefile.am, examples/test13.cpp,
+	  include/tclap/SwitchArg.h, tests/Makefile.am, tests/test68.out,
+	  tests/test68.sh: a bug fix for parsing vectors of strings and
+	  making sure that combined switches dont get confused
+
[phone]:49  mes5k
+
+	* include/tclap/OptionalUnlabeledTracker.h: added inline
+
[phone]:09  mes5k
+
+	* include/tclap/Arg.h, tests/test42.out, tests/test54.out: fixed
+	  the delimiter in Arg::longID and Arg::shortID
+
[phone]:17  macbishop
+
+	* examples/Makefile.am, include/tclap/Arg.h,
+	  include/tclap/DocBookOutput.h,
+	  include/tclap/ZshCompletionOutput.h: Suppress some warnings,
+	  compile with -Wextra by default
+
[phone]:02  macbishop
+
+	* include/tclap/Arg.h, include/tclap/MultiArg.h,
+	  include/tclap/ValueArg.h, tests/runtests.sh, tests/test63.out,
+	  tests/test63.sh, tests/test64.out, tests/test64.sh,
+	  tests/test65.out, tests/test65.sh, tests/test66.out,
+	  tests/test66.sh, tests/test67.out, tests/test67.sh,
+	  tests/testCheck.sh, examples/Makefile.am, examples/test11.cpp,
+	  examples/test12.cpp: Use ArgTraits instead of ValueExtractor
+	  specialization Bug 1711487
+
[phone]:11  macbishop
+
+	* examples/Makefile.am, examples/test10.cpp,
+	  include/tclap/CmdLine.h, include/tclap/CmdLineInterface.h: Run
+	  CmdLine::parse with argv as pointer to const pointer to const
+	  char
+
[phone]:28  mes5k
+
+	* include/tclap/Arg.h, tests/test18.out: changed the blankChar to
+	  the bell character instead of *
+
[phone]:28  mes5k
+
+	* examples/test4.cpp, include/tclap/DocBookOutput.h,
+	  include/tclap/Makefile.am, include/tclap/ZshCompletionOutput.h:
+	  added patches for ZSH and DocBook output
+
[phone]:08  mes5k
+
+	* include/tclap/: CmdLine.h, CmdLineInterface.h: added a new parse
+	  method that accepts a vector
+
[phone]:59  macbishop
+
+	* include/tclap/: MultiArg.h, MultiSwitchArg.h,
+	  UnlabeledMultiArg.h, UnlabeledValueArg.h, ValueArg.h: Supressed
+	  some warnings
+
[phone]:59  macbishop
+
+	* include/tclap/CmdLine.h: Catch ExitException and exit. This
+	  allows all resources used during parsing to be released, bug
+	  1662188.
+
[phone]:57  macbishop
+
+	* include/tclap/: DocBookOutput.h, HelpVisitor.h, StdOutput.h,
+	  VersionVisitor.h: raise ExitException instead of calling exit
+
[phone]:54  macbishop
+
+	* include/tclap/ArgException.h: Added exit-exception class
+
[phone]:52  macbishop
+
+	* tests/testCheck.sh: Exit with exit status 1 if a test fails
+	  (required by runtests.sh)
+
[phone]:52  macbishop
+
+	* tests/runtests.sh: Run the correct tests (not 0)
+
[phone]:51  macbishop
+
+	* examples/: test4.cpp, test7.cpp: Supressed warnings
+
[phone]:12  mes5k
+
+	* include/tclap/StdOutput.h: minor change to support a bug in
+	  VisualC++ 2005
+
[phone]:42  mes5k
+
+	* docs/: README, manual.html, manual.xml: updated docs to reflect
+	  that Output must handle the exit rather than the CmdLine object
+
[phone]:32  mes5k
+
+	* include/tclap/: CmdLine.h, DocBookOutput.h, StdOutput.h: moved
+	  exit from CmdLine to StdOutput to provide users more control over
+	  when/how the exit happens
+
[phone]:29  mes5k
+
+	* examples/test4.cpp: added exit() to failure method
+
[phone]:13  mes5k
+
+	* docs/: manual.html, manual.xml: fixed typo in SwitchArg
+	  constructors
+
[phone]:05  mes5k
+
+	* include/tclap/CmdLine.h, tests/Makefile.am, tests/test10.out,
+	  tests/test17.out, tests/test4.out, tests/test51.out,
+	  tests/test62.out, tests/test62.sh: printing more useful message
+	  when missing required args and catching ArgException reference
+
[phone]:49  mes5k
+
+	* include/tclap/SwitchArg.h, tests/Makefile.am, tests/test61.out,
+	  tests/test61.sh: made a fix for a bug where - chars were within
+	  unlabeled value args
+
[phone]:13  mes5k
+
+	* include/tclap/StdOutput.h: minor tweak to a min function
+	  signature
+
[phone]:05  mes5k
+
+	* docs/index.html: updated for 1.1.0
+
[phone]:04  mes5k
+
+	* AUTHORS: new author
+
[phone]:55  mes5k
+
+	* config/Makefile.am: so that m4 macros will be included in release
+	  files to ease incorporation of tclap in other projects
+
[phone]:36  mes5k
+
+	* include/tclap/CmdLine.h: removed a deprecated constructor
+
[phone]:35  mes5k
+
+	* docs/: manual.xml, manual.html: manual update
+
[phone]:11  mes5k
+
+	* Makefile.am, configure.in: added m4 macros to help others
+	  distributing the software and updated the version number
+
[phone]:52  mes5k
+
+	* config/bb_enable_doxygen.m4: for some reason, the AS_HELP_STRING
+	  function was messing up autoconf 2.57 -- maybe that's just an old
+	  version?  We can change it back as necessary
+
[phone]:51  mes5k
+
+	* examples/test8.cpp, include/tclap/SwitchArg.h: SwitchArg
+	  interface change
+
[phone]:59  macbishop
+
+	* docs/: manual.html, manual.xml: Updated the example
+
[phone]:44  mes5k
+
+	* include/tclap/ArgException.h: patch for a mem leak in
+	  ArgException
+
[phone]:16  mes5k
+
+	* include/tclap/: CmdLineOutput.h, Visitor.h: added virtual
+	  destructors
+
[phone]:15  zeekec
+
+	* examples/: test1.cpp, test2.cpp, test3.cpp, test4.cpp, test5.cpp,
+	  test6.cpp, test7.cpp, test8.cpp, test9.cpp: Use local header
+	  files first instead of installed headers.
+
[phone]:12  zeekec
+
+	* Makefile.am: Added ACLOCAL_AMFLAGS for autoreconf.
+
[phone]:10  zeekec
+
+	* config/: ac_cxx_have_sstream.m4, ac_cxx_have_strstream.m4: Moved
+	  the requires, header check, and language save and restore outside
+	  of the cache check.
+
[phone]:00  zeekec
+
+	* config/: stamp-h.in, stamp-h1: Removed timestamp files (generated
+	  by configure).
+
[phone]:05  zeekec
+
+	* include/tclap/Constraint.h: Added virtual destructor to silence
+	  warnings.
+
[phone]:01  zeekec
+
+	* ChangeLog: Generated with cvs2cl.
+
[phone]:25  mes5k
+
+	* config/stamp-h1, examples/test2.cpp, examples/test3.cpp,
+	  examples/test5.cpp, examples/test8.cpp, include/tclap/Arg.h,
+	  include/tclap/CmdLine.h, include/tclap/MultiArg.h,
+	  include/tclap/StdOutput.h, include/tclap/UnlabeledMultiArg.h,
+	  include/tclap/UnlabeledValueArg.h, include/tclap/ValueArg.h,
+	  include/tclap/XorHandler.h: added gcc warning patch
+
[phone]:36  zeekec
+
+	* examples/Makefile.am: Set INCLUDES to top_srcdir for out of
+	  source builds.
+
[phone]:33  zeekec
+
+	* include/tclap/: UnlabeledMultiArg.h, UnlabeledValueArg.h: Add
+	  using toString statements (for gcc >= 3.4).
+
[phone]:31  zeekec
+
+	* config/bb_enable_doxygen.m4: Properly quote BB_ENABLE_DOXYGEN.
+
[phone]:04  mes5k
+
+	* include/tclap/Arg.h: merged some new changes
+
[phone]:28  mes5k
+
+	* docs/index.html: fixed spelling mistake
+
[phone]:35  mes5k
+
+	* include/tclap/: Makefile.am, OptionalUnlabeledTracker.h,
+	  UnlabeledMultiArg.h, UnlabeledValueArg.h: fix to handle optional
+	  unlabeled args
+
[phone]:33  mes5k
+
+	* examples/: test2.cpp, test3.cpp, test7.cpp, test8.cpp, test9.cpp:
+	  Unlabeled changes
+
[phone]:04  mes5k
+
+	* include/tclap/: Arg.h, DocBookOutput.h, MultiArg.h: updated
+	  docbook output
+
[phone]:08  mes5k
+
+	* include/tclap/: ValuesConstraint.h, XorHandler.h: add std::
+	  prefix to some finds
+
[phone]:35  zeekec
+
+	* include/tclap/CmdLine.h: Made deleteOnExit's protected to
+	  facilitate derivation.
+
[phone]:30  zeekec
+
+	* config/config.h.in: Removed autotools generated file.
+
[phone]:26  zeekec
+
+	* configure.in, docs/Doxyfile.in, tests/Makefile.am,
+	  tests/test1.sh, tests/test10.sh, tests/test11.sh,
+	  tests/test12.sh, tests/test13.sh, tests/test14.sh,
+	  tests/test15.sh, tests/test16.sh, tests/test17.sh,
+	  tests/test18.sh, tests/test19.sh, tests/test2.sh,
+	  tests/test20.sh, tests/test21.sh, tests/test22.sh,
+	  tests/test23.sh, tests/test24.sh, tests/test25.sh,
+	  tests/test26.sh, tests/test27.sh, tests/test28.sh,
+	  tests/test29.sh, tests/test3.sh, tests/test30.sh,
+	  tests/test31.sh, tests/test32.sh, tests/test33.sh,
+	  tests/test34.sh, tests/test35.sh, tests/test36.sh,
+	  tests/test37.sh, tests/test38.sh, tests/test39.sh,
+	  tests/test4.sh, tests/test40.sh, tests/test41.sh,
+	  tests/test42.sh, tests/test43.sh, tests/test44.sh,
+	  tests/test45.sh, tests/test46.sh, tests/test47.sh,
+	  tests/test48.sh, tests/test49.sh, tests/test5.sh,
+	  tests/test50.sh, tests/test51.sh, tests/test52.sh,
+	  tests/test53.sh, tests/test54.sh, tests/test55.sh,
+	  tests/test56.sh, tests/test57.sh, tests/test58.sh,
+	  tests/test59.sh, tests/test6.sh, tests/test60.sh, tests/test7.sh,
+	  tests/test8.sh, tests/test9.sh: Made changes to directory
+	  references to allow out of source builds.
+
[phone]:25  mes5k
+
+	* aclocal.m4: doh
+
[phone]:18  mes5k
+
+	* include/tclap/CmdLine.h: removed -v from version switch
+
[phone]:14  mes5k
+
+	* include/tclap/Arg.h: removed value required
+
[phone]:03  mes5k
+
+	* examples/: test2.cpp, test3.cpp, test6.cpp, test8.cpp, test9.cpp:
+	  UnlabeledValueArg change
+
[phone]:02  mes5k
+
+	* tests/: test10.out, test11.out, test12.out, test15.out,
+	  test16.out, test17.out, test22.out, test23.out, test24.out,
+	  test26.out, test27.out, test28.out, test29.out, test30.out,
+	  test31.out, test32.out, test35.out, test36.out, test38.out,
+	  test39.out, test4.out, test40.out, test41.out, test42.out,
+	  test43.out, test44.out, test45.out, test46.out, test49.out,
+	  test50.out, test51.out, test52.out, test53.out, test54.out,
+	  test57.out, test59.out, test60.out, test7.out: new output for
+	  default version and value required
+
[phone]:01  mes5k
+
+	* tests/: test59.sh, test8.sh: new style version and required
+	  UnlabeledValueArgs
+
[phone]:59  mes5k
+
+	* tests/testCheck.sh: a script to compare test output
+
[phone]:54  mes5k
+
+	* include/tclap/UnlabeledValueArg.h: now optionally required
+
[phone]:33  mes5k
+
+	* tests/: test58.out, test59.out, test58.sh, test59.sh, test60.out,
+	  test60.sh, Makefile.am: tests for MultiSwitchArg
+
[phone]:27  mes5k
+
+	* include/tclap/Makefile.am, examples/Makefile.am,
+	  examples/test9.cpp: MultiSwitchArg
+
[phone]:26  mes5k
+
+	* include/tclap/: CmdLine.h, CmdLineInterface.h, StdOutput.h: added
+	  a bool to the constructor that allows automatic -h and -v to be
+	  turned off
+
[phone]:57  mes5k
+
+	* docs/: manual.html, manual.xml: added MultiSwitchArg docs
+
[phone]:33  mes5k
+
+	* include/tclap/MultiSwitchArg.h: fixed typo
+
[phone]:29  mes5k
+
+	* include/tclap/SwitchArg.h: Fixed minor bug involving combined
+	  switch error messages: now they're consistent.
+
[phone]:28  mes5k
+
+	* include/tclap/MultiSwitchArg.h: initial checkin
+
[phone]:41  mes5k
+
+	* include/tclap/UnlabeledMultiArg.h: added alreadySet
+
[phone]:13  mes5k
+
+	* tests/Makefile.am: xor test
+
[phone]:04  mes5k
+
+	* examples/test5.cpp: change for xor bug
+
[phone]:04  mes5k
+
+	* tests/: test20.out, runtests.sh, test20.sh, test21.out,
+	  test21.sh, test22.out, test23.out, test24.out, test25.out,
+	  test25.sh, test33.out, test33.sh, test44.out, test57.out,
+	  test57.sh: changes for xor bug
+
[phone]:03  mes5k
+
+	* include/tclap/: Arg.h, MultiArg.h, UnlabeledMultiArg.h,
+	  XorHandler.h: fixed xor bug
+
[phone]:48  macbishop
+
+	* include/tclap/Arg.h: Removed check on description in
+	  Arg::operator== since multiple args should be able to have the
+	  same description.
+
[phone]:41  mes5k
+
+	* NEWS: updated for constraints
+
[phone]:37  mes5k
+
+	* docs/: manual.html, manual.xml: updated for constraints
+
[phone]:05  mes5k
+
+	* examples/test7.cpp: changed for constraint
+
[phone]:00  mes5k
+
+	* include/tclap/: MultiArg.h, ValueArg.h: fixed exceptions and
+	  typeDesc for constraints
+
[phone]:59  mes5k
+
+	* tests/: test35.out, test36.out, test38.out, test39.out: changed
+	  for constraints
+
[phone]:07  mes5k
+
+	* examples/test6.cpp: changed to constraint
+
[phone]:06  mes5k
+
+	* include/tclap/Makefile.am: added constraints
+
[phone]:05  mes5k
+
+	* include/tclap/: Constraint.h, ValuesConstraint.h: initial checkin
+
[phone]:05  mes5k
+
+	* include/tclap/StdOutput.h: comment change
+
[phone]:01  mes5k
+
+	* include/tclap/CmdLine.h: added Constraint includes
+
[phone]:55  mes5k
+
+	* include/tclap/: MultiArg.h, UnlabeledMultiArg.h,
+	  UnlabeledValueArg.h, ValueArg.h: Changed allowedList to
+	  Constraint
+
[phone]:08  mes5k
+
+	* configure.in: next vers
+
[phone]:13  mes5k
+
+	* NEWS: update
+
[phone]:51  mes5k
+
+	* docs/: manual.html, manual.xml: fixed output override bug
+
[phone]:45  mes5k
+
+	* tests/: test18.out, test43.out: change for output override bug
+
[phone]:28  mes5k
+
+	* examples/test4.cpp: fixed output override bug
+
[phone]:22  mes5k
+
+	* include/tclap/: CmdLine.h, HelpVisitor.h, VersionVisitor.h: fixed
+	  output bug
+
[phone]:01  mes5k
+
+	* configure.in: 1.0.4
+
[phone]:16  mes5k
+
+	* examples/test7.cpp: changed for long prog names bug
+
[phone]:15  mes5k
+
+	* tests/: test38.out, test39.out, test46.out: changed test7 for
+	  long prog names
+
[phone]:31  mes5k
+
+	* NEWS: updates for 1.0.3a
+
[phone]:21  mes5k
+
+	* docs/manual.html, docs/manual.xml, include/tclap/CmdLine.h: fixed
+	  output memory leak
+
[phone]:10  mes5k
+
+	* include/tclap/StdOutput.h: hacky fix to long prog name bug
+
[phone]:57  mes5k
+
+	* configure.in: 1.0.3a
+
[phone]:53  mes5k
+
+	* tests/: Makefile.am, test15.out, test16.out, test17.out,
+	  test31.out, test32.out, test13.sh, test14.sh, test15.sh,
+	  test16.sh, test17.sh, test42.out, test55.out, test55.sh,
+	  test56.out, test56.sh: updated for - arg bug
+
[phone]:51  mes5k
+
+	* examples/test3.cpp: tweaked to support tests for '-' arg bug
+
[phone]:16  mes5k
+
+	* include/tclap/Arg.h: fixed a bug involving blank _flags and - as
+	  an UnlabeledValueArg
+
[phone]:19  mes5k
+
+	* docs/style.css: minor tweak for h1
+
[phone]:10  mes5k
+
+	* NEWS: update
+
[phone]:39  mes5k
+
+	* include/tclap/CmdLine.h: removed ostream include
+
[phone]:11  mes5k
+
+	* include/tclap/: Arg.h, CmdLine.h, CmdLineOutput.h, StdOutput.h:
+	  cleaned up iterator names
+
[phone]:10  mes5k
+
+	* include/tclap/DocBookOutput.h: removed ostream
+
[phone]:35  mes5k
+
+	* configure.in, docs/Doxyfile.in: added dot check
+
[phone]:58  mes5k
+
+	* configure.in: 1.0.3
+
[phone]:57  mes5k
+
+	* include/tclap/: UnlabeledMultiArg.h, UnlabeledValueArg.h: removed
+	  two stage lookup ifdefs
+
[phone]:56  mes5k
+
+	* docs/index.html: updated
+
[phone]:45  mes5k
+
+	* docs/: manual.html, manual.xml: updates for using stuff and new
+	  output
+
[phone]:05  mes5k
+
+	* include/tclap/: DocBookOutput.h, Makefile.am: adding docbook
+	  stuff
+
[phone]:07  mes5k
+
+	* examples/test4.cpp: reflects new output handling
+
[phone]:07  mes5k
+
+	* include/tclap/: Arg.h, CmdLine.h, CmdLineInterface.h,
+	  CmdLineOutput.h, HelpVisitor.h, Makefile.am, StdOutput.h,
+	  VersionVisitor.h, XorHandler.h: changed output around
+
[phone]:06  mes5k
+
+	* include/tclap/PrintSensibly.h: subsumed by StdOutput
+
[phone]:13  mes5k
+
+	* docs/manual.html: tweak
+
[phone]:58  mes5k
+
+	* NEWS, README: updates
+
[phone]:51  mes5k
+
+	* docs/Makefile.am: added manual.xml
+
[phone]:47  mes5k
+
+	* docs/: manual.html, manual.xml, style.css: minor tweaks
+
[phone]:34  mes5k
+
+	* configure.in: 1.0.2
+
[phone]:30  mes5k
+
+	* docs/README: init
+
[phone]:30  mes5k
+
+	* docs/style.css: new style
+
[phone]:30  mes5k
+
+	* docs/: manual.html, manual.xml: manual.html is now generated from
+	  manual.xml
+
[phone]:26  mes5k
+
+	* include/tclap/: MultiArg.h, ValueArg.h: yet another fix for
+	  HAVE_SSTREAM stuff
+
[phone]:42  mes5k
+
+	* NEWS: 1.0.1
+
[phone]:03  mes5k
+
+	* configure.in: new release
+
[phone]:41  mes5k
+
+	* include/tclap/: ValueArg.h, MultiArg.h: fixed config.h problems
+
[phone]:44  mes5k
+
+	* docs/manual.xml: manual as docbook
+
[phone]:56  mes5k
+
+	* docs/style.css: added visited color to links
+
[phone]:38  mes5k
+
+	* docs/index.html: fixed mailto
+
[phone]:58  mes5k
+
+	* docs/: manual.html: minor tweaks
+
[phone]:13  mes5k
+
+	* docs/manual.html: updated for new test1
+
[phone]:02  mes5k
+
+	* include/tclap/CmdLine.h: catch by ref
+
[phone]:01  mes5k
+
+	* examples/: test1.cpp, test2.cpp, test3.cpp, test4.cpp, test5.cpp,
+	  test6.cpp, test7.cpp, test8.cpp: changed test1 and now catching
+	  exceptions by ref
+
[phone]:38  mes5k
+
+	* tests/: test1.out, test1.sh, test2.out, test3.out, test3.sh,
+	  test4.out, test40.out: changes for new test1
+
[phone]:50  mes5k
+
+	* examples/test1.cpp: fixed includes
+
[phone]:03  mes5k
+
+	* docs/index.html: changed link
+
[phone]:02  mes5k
+
+	* include/tclap/: ValueArg.h, MultiArg.h: changed enum names
+	  because of alpha conflicts
+
[phone]:04  mes5k
+
+	* include/tclap/: CmdLine.h, CmdLineInterface.h, MultiArg.h,
+	  PrintSensibly.h, SwitchArg.h, UnlabeledMultiArg.h,
+	  UnlabeledValueArg.h, ValueArg.h, XorHandler.h: cleaned up some
+	  includes and added ifdefs for sstream
+
[phone]:00  mes5k
+
+	* examples/test5.cpp: fixed a bizarre bug
+
[phone]:59  mes5k
+
+	* tests/: test20.out, test21.out, test25.out, test33.out: fixed a
+	  test5 bug
+
[phone]:17  mes5k
+
+	* Makefile.am: added msc
+
[phone]:06  mes5k
+
+	* configure.in: added msc stuff
+
[phone]:05  mes5k
+
+	* msc/: examples/Makefile.am, Makefile.am: init
+
[phone]:00  mes5k
+
+	* NEWS: update
+
[phone]:58  mes5k
+
+	* msc/README: init
+
[phone]:47  mes5k
+
+	* msc/: tclap-beta.ncb, tclap-beta.sln, tclap-beta.suo,
+	  tclap-beta.vcproj, examples/test1.vcproj, examples/test2.vcproj,
+	  examples/test3.vcproj, examples/test4.vcproj,
+	  examples/test5.vcproj, examples/test6.vcproj,
+	  examples/test7.vcproj, examples/test8.vcproj: init
+
[phone]:18  mes5k
+
+	* docs/Makefile.am: added stylesheet
+
[phone]:51  mes5k
+
+	* AUTHORS: more
+
[phone]:39  mes5k
+
+	* NEWS, AUTHORS: added 1.0 notes
+
[phone]:04  mes5k
+
+	* examples/test4.cpp: shows how to alter output
+
[phone]:03  mes5k
+
+	* tests/test18.out: updated output
+
[phone]:03  mes5k
+
+	* include/tclap/CmdLineInterface.h: added failure to the interface
+
[phone]:07  mes5k
+
+	* include/tclap/ArgException.h: doh. now what() is proper
+
[phone]:44  mes5k
+
+	* include/tclap/CmdLine.h: made destructor virtual
+
[phone]:20  mes5k
+
+	* include/tclap/CmdLine.h: moved all output handling into separate
+	  methods
+
[phone]:19  mes5k
+
+	* include/tclap/Arg.h: made processArg pure virtual
+
[phone]:19  mes5k
+
+	* include/tclap/ArgException.h: fixed documentation omission
+
[phone]:09  mes5k
+
+	* docs/style.css: tweak
+
[phone]:22  mes5k
+
+	* docs/style.css: color change
+
[phone]:54  mes5k
+
+	* include/tclap/ArgException.h: added type description
+
[phone]:16  mes5k
+
+	* docs/: index.html, manual.html, style.css: added CSS style
+
[phone]:17  mes5k
+
+	* docs/manual.html: more updates
+
[phone]:24  mes5k
+
+	* docs/: index.html, manual.html: proofing updates
+
[phone]:37  mes5k
+
+	* docs/: index.html, manual.html: xhtml and tidied
+
[phone]:36  mes5k
+
+	* docs/Doxyfile.in: added dot  handling
+
[phone]:30  mes5k
+
+	* include/tclap/: Arg.h, ArgException.h, CmdLine.h, MultiArg.h,
+	  SwitchArg.h, ValueArg.h: added new Exception classes
+
[phone]:53  mes5k
+
+	* include/tclap/ArgException.h: minor tweaks
+
[phone]:32  mes5k
+
+	* docs/manual.html: updates yet again
+
[phone]:00  mes5k
+
+	* docs/manual.html: updates
+
[phone]:50  mes5k
+
+	* docs/manual.html: substantial updates
+
[phone]:54  mes5k
+
+	* include/tclap/: Arg.h, CmdLine.h, CmdLineInterface.h, MultiArg.h,
+	  PrintSensibly.h, ValueArg.h: minor formatting
+
[phone]:50  mes5k
+
+	* docs/manual.html: updates
+
[phone]:17  mes5k
+
+	* tests/runtests.sh: minor fix so that we run all tests
+
[phone]:51  macbishop
+
+	* docs/Doxyfile.in: Removed src subdir
+
[phone]:49  macbishop
+
+	* examples/Makefile.am: Removed libtclap.a deps
+
[phone]:46  macbishop
+
+	* configure.in: Removed creation of src/Makefile
+
[phone]:34  macbishop
+
+	* Makefile.am: Removed src subdir
+
[phone]:31  macbishop
+
+	* src/: Arg.cpp, CmdLine.cpp, Makefile.am, PrintSensibly.cpp,
+	  SwitchArg.cpp, XorHandler.cpp: Implementation now in header files
+
[phone]:27  macbishop
+
+	* include/tclap/: Arg.h, ArgException.h, CmdLine.h, HelpVisitor.h,
+	  Makefile.am, MultiArg.h, PrintSensibly.h, SwitchArg.h,
+	  UnlabeledMultiArg.h, UnlabeledValueArg.h, ValueArg.h,
+	  VersionVisitor.h, XorHandler.h, CmdLineInterface.h,
+	  CommandLine.h: Moving the implementation of tclap to the header
+	  files presented me with two major problems. 1) There where static
+	  functions and variables that could cause link errors if tclap
+	  where used in different files (e.g. file1.cc and file2.cc
+	  included tclap then compiling both files would give hard symbols
+	  for some variables which would produce multiple definition when
+	  linking) 2) The dependencies of tclap was a bit strange (CmdLine
+	  depends on Args and Args depends on CmdLine for instance)
+
+	  The first problem I solved by removing all static variables
+	  putting them in static member functions (which are weak-symbols).
+	  So for instance every where there previously was something like x
+	  = _delimiter there now is x = delimiter() or in case of write
+	  acces delimiterRef() = x instead of _delimiter = x (I had to
+	  append the Ref because there where already functions with the
+	  same name as the variables). To solve the problem with static
+	  functions I simply inlined them. This causes the compiler to
+	  produce a weak symbol or inline if appropriate. We can put the
+	  functions inside the class declaration later to make the code
+	  look better. This worked fine in all but two cases. In the
+	  ValueArg and MultiArg classes I had to do a "hack" to work around
+	  the specialization template for extractValue<std::string>. The
+	  code for this is very simple but it might look strange an stupid
+	  at first but it is only to resolve the specialisation to a weak
+	  symbol. What I did was I put the implementations of extractValue
+	  in a helper class and I could then create a specialized class
+	  instead of function and everything worked out. I think now in
+	  retrospect there might be better solutions to this but I'll think
+	  a bit more on it (maybe some type of inlining on the specialized
+	  version would suffice but I'm not sure).
+
+	  To handle the dependencies I had to do some rewriting. The first
+	  step was to introduce a new class CmdLineInterface that is a
+	  purely abstract base of CmdLine that specifies the functions
+	  needed by Arg and friends. Thus Arg classes now takes an
+	  CmdLineInterface object as input instead (however only CmdLine
+	  can ever be instantiated of-course). With this extra class
+	  cleaning up the dependencies was quite simple, I've attached a
+	  dependency graph to the mail (depgraph.png). I also cleaned up
+	  the #includes so now only what actually needs inclusion is
+	  included. A nice side effect of this is that the impl. of CmdLine
+	  is now put back into CmdLine.h (where I guess you wanted it)
+	  which (recursivly) includes everything else needed.
+
+	  Just to make things clear for myself regarding the class
+	  dependencies I made a class TCLAP::Exception that inherits from
+	  std::exception and is a base of ArgException (Exception does
+	  nothing currently). If we don't want the Exception class it can
+	  be removed, however I think it could be a nice logic to have a
+	  base Exception class that every exception inherits from, but we
+	  can discuss that when we decide how to handle exceptions.
+
[phone]:07  macbishop
+
+	* tests/runtests.sh: Now return 0 if all tests fail and 1 if any
+	  test fail
+
[phone]:58  macbishop
+
+	* tests/runtests.sh: Runs all tests and sumarizes the result
+
[phone]:09  mes5k
+
+	* include/tclap/CommandLine.h: added some comments
+
[phone]:08  mes5k
+
+	* src/CmdLine.cpp: formatting only
+
[phone]:05  macbishop
+
+	* include/tclap/CommandLine.h: Recommit because something is
+	  strange. The changes are that memory allocated in _construct is
+	  deallocated when the CmdLine obj is destroyed
+
[phone]:32  macbishop
+
+	* src/CmdLine.cpp: Memory allocated in _constructor is now deleted
+	  when the object is destroyed
+
[phone]:54  mes5k
+
+	* include/tclap/: Arg.h, ArgException.h, CmdLine.h, CommandLine.h,
+	  HelpVisitor.h, IgnoreRestVisitor.h, MultiArg.h, PrintSensibly.h,
+	  SwitchArg.h, UnlabeledMultiArg.h, UnlabeledValueArg.h,
+	  ValueArg.h, VersionVisitor.h, Visitor.h, XorHandler.h: changed
+	  ifndef labels
+
[phone]:53  macbishop
+
+	* include/tclap/Arg.h: Had to make ~Arg() public because it won't
+	  be possible to delete Arg*s if it is not, and we want that (I
+	  think).
+
[phone]:24  mes5k
+
+	* configure.in: version 1.0.0
+
[phone]:54  mes5k
+
+	* include/tclap/Arg.h, include/tclap/ArgException.h,
+	  include/tclap/HelpVisitor.h, include/tclap/IgnoreRestVisitor.h,
+	  include/tclap/MultiArg.h, include/tclap/SwitchArg.h,
+	  include/tclap/UnlabeledMultiArg.h, include/tclap/ValueArg.h,
+	  include/tclap/VersionVisitor.h, include/tclap/Visitor.h,
+	  src/Arg.cpp, src/SwitchArg.cpp: cleaned up a bunch of things
+
[phone]:35  mes5k
+
+	* tests/: Makefile.am, test47.out, test47.sh, test48.out,
+	  test48.sh, test49.out, test49.sh, test50.out, test50.sh,
+	  test51.out, test51.sh, test52.out, test52.sh, test53.out,
+	  test53.sh, test54.out, test54.sh: added tests for CmdLine arg
+
[phone]:33  mes5k
+
+	* examples/: Makefile.am, test8.cpp: added new test for CmdLine arg
+
[phone]:32  mes5k
+
+	* src/Arg.cpp, src/SwitchArg.cpp, include/tclap/Arg.h,
+	  include/tclap/MultiArg.h, include/tclap/SwitchArg.h,
+	  include/tclap/UnlabeledMultiArg.h,
+	  include/tclap/UnlabeledValueArg.h, include/tclap/ValueArg.h: got
+	  CmdLine arg working
+
[phone]:08  mes5k
+
+	* configure: shouldn't be in cvs
+
[phone]:56  macbishop
+
+	* src/: Arg.cpp, SwitchArg.cpp: Added support for automatic
+	  addition to a CmdLine parser
+
[phone]:55  macbishop
+
+	* include/tclap/: Arg.h, MultiArg.h, SwitchArg.h,
+	  UnlabeledMultiArg.h, UnlabeledValueArg.h, ValueArg.h: Support for
+	  automatic addition to a CmdLine parser
+
[phone]:09  mes5k
+
+	* src/CmdLine.cpp: fixed a warning in MSVC++
+
[phone]:11  mes5k
+
+	* include/tclap/Makefile.in, docs/Makefile.in,
+	  examples/Makefile.in, tests/Makefile.in: not needed
+
[phone]:08  mes5k
+
+	* Makefile.in, src/Makefile.in, include/Makefile.in: not needed
+
[phone]:14  mes5k
+
+	* src/CmdLine.cpp: now throws exception on matching
+	  names/flags/desc
+
[phone]:12  mes5k
+
+	* examples/test4.cpp, examples/test7.cpp, tests/test38.out,
+	  tests/test39.out, tests/test43.out, tests/test46.out: fixed to
+	  handle new exception on matching names/flags/desc
+
[phone]:25  mes5k
+
+	* docs/Doxyfile.in: updated Doxyfile for newer doxygen
+
[phone]:27  mes5k
+
+	* examples/: test1.cpp, test2.cpp, test3.cpp, test4.cpp, test5.cpp,
+	  test6.cpp: changed namespace std handling
+
[phone]:25  mes5k
+
+	* examples/test7.cpp: added more args to better test output
+	  printing
+
[phone]:24  mes5k
+
+	* src/Arg.cpp, src/CmdLine.cpp, src/PrintSensibly.cpp,
+	  src/SwitchArg.cpp, src/XorHandler.cpp, include/tclap/Arg.h,
+	  include/tclap/ArgException.h, include/tclap/CommandLine.h,
+	  include/tclap/MultiArg.h, include/tclap/PrintSensibly.h,
+	  include/tclap/SwitchArg.h, include/tclap/UnlabeledMultiArg.h,
+	  include/tclap/UnlabeledValueArg.h, include/tclap/ValueArg.h,
+	  include/tclap/XorHandler.h: changed namespace std handling
+
[phone]:24  mes5k
+
+	* tests/: test15.out, test16.out, test17.out, test22.out,
+	  test23.out, test24.out, test31.out, test32.out, test38.out,
+	  test39.out, test42.out, test44.out, test46.out: fixed test output
+	  for new formatting
+
[phone]:09  macbishop
+
+	* include/tclap/: UnlabeledMultiArg.h, UnlabeledValueArg.h:
+	  Compilation was broken due to undef. symbols in compilers with 2
+	  stage name-lookup (such as gcc >= 3.4). The fix for this is to
+	  tell the compiler what symbols to use withlines like: using
+	  MultiArg<T>::_name;
+
+	  This is now done and everything compiles fine. Since I'm not sure
+	  about the support for things like using MultiArg<T>::_name; on
+	  all compilers it is ifdef:ed away by default. To get 2 stage
+	  name-lookup to work you have to add -DTWO_STAGE_NAME_LOOKUP to
+	  your CXXFLAGS before running configure.
+
[phone]:34  mes5k
+
+	* src/PrintSensibly.cpp: smartened printing even further
+
[phone]:35  mes5k
+
+	* src/PrintSensibly.cpp: fixed int messiness
+
[phone]:32  mes5k
+
+	* autotools.sh: made path explicit
+
[phone]:05  mes5k
+
+	* include/tclap/: MultiArg.h, ValueArg.h: changed allowed separator
+
[phone]:53  mes5k
+
+	* tests/: Makefile.am, test10.out, test11.out, test12.out,
+	  test15.out, test16.out, test17.out, test18.out, test22.out,
+	  test23.out, test24.out, test26.out, test27.out, test28.out,
+	  test29.out, test30.out, test31.out, test32.out, test35.out,
+	  test36.out, test38.out, test39.out, test4.out, test40.out,
+	  test40.sh, test41.out, test41.sh, test42.out, test42.sh,
+	  test43.out, test43.sh, test44.out, test44.sh, test45.out,
+	  test45.sh, test46.out, test46.sh, test7.out, test7.sh: changed
+	  error output and added usage stuff
+
[phone]:52  mes5k
+
+	* NEWS, README: updated
+
[phone]:47  mes5k
+
+	* configure.in: changed to 0.9.9
+
[phone]:46  mes5k
+
+	* examples/test7.cpp: tweaked for usage
+
[phone]:45  mes5k
+
+	* include/tclap/: CmdLine.h, CommandLine.h, Makefile.am,
+	  PrintSensibly.h, XorHandler.h: added usage stuff
+
[phone]:43  mes5k
+
+	* src/: CmdLine.cpp, Makefile.am, PrintSensibly.cpp,
+	  XorHandler.cpp: tweaked usage
+
[phone]:02  mes5k
+
+	* docs/manual.html: updated for allowed
+
[phone]:01  mes5k
+
+	* tests/: test34.out, test34.sh, test35.out, test35.sh, test36.out,
+	  test36.sh, test37.out, test37.sh, test38.out, test38.sh,
+	  test39.out, test39.sh, Makefile.am: allow tests
+
[phone]:56  mes5k
+
+	* include/tclap/ValueArg.h: doh
+
[phone]:34  mes5k
+
+	* NEWS: allow
+
[phone]:31  mes5k
+
+	* include/tclap/Arg.h: made isReq virtual
+
[phone]:30  mes5k
+
+	* include/tclap/: MultiArg.h, UnlabeledMultiArg.h,
+	  UnlabeledValueArg.h, ValueArg.h: added allow
+
[phone]:29  mes5k
+
+	* examples/: Makefile.am, test6.cpp, test7.cpp: added tests for
+	  allowed
+
[phone]:28  mes5k
+
+	* docs/: index.html, manual.html: minor typos
+
[phone]:18  mes5k
+
+	* Makefile.am, autotools.sh, examples/Makefile.am, src/Makefile.am:
+	  fixed for autotools for mandrake
+
[phone]:09  mes5k
+
+	* configure.in: 0.9.8a
+
[phone]:23  mes5k
+
+	* tests/: test22.out, test23.out, test24.out: output updates
+
[phone]:21  mes5k
+
+	* include/tclap/: Arg.h, UnlabeledMultiArg.h, UnlabeledValueArg.h:
+	  now the Arg adds itself to the CmdLine arglist
+
[phone]:20  mes5k
+
+	* src/: Arg.cpp, CmdLine.cpp: reworked how we add args to list
+
[phone]:52  mes5k
+
+	* NEWS: update
+
[phone]:04  mes5k
+
+	* examples/test5.cpp: change
+
[phone]:03  mes5k
+
+	* src/SwitchArg.cpp: allowing blank flags
+
[phone]:54  mes5k
+
+	* configure.in: 0.9.8
+
[phone]:52  mes5k
+
+	* tests/: Makefile.am, test20.out, test21.out, test22.out,
+	  test23.out, test24.out, test25.out, test33.out, test33.sh:
+	  updates
+
[phone]:39  mes5k
+
+	* docs/manual.html: blank args
+
[phone]:16  mes5k
+
+	* tests/: test15.out, test16.out, test17.out, test20.out,
+	  test20.sh, test21.out, test21.sh, test22.out, test23.out,
+	  test24.out, test25.out, test25.sh, test31.out, test32.out:
+	  updates
+
[phone]:05  mes5k
+
+	* examples/: test5.cpp, test3.cpp: minor fixes and new args
+
[phone]:56  mes5k
+
+	* include/tclap/Arg.h: added new var
+
[phone]:54  mes5k
+
+	* src/: Arg.cpp, CmdLine.cpp, SwitchArg.cpp: allowing blank flags
+
[phone]:37  mes5k
+
+	* src/XorHandler.cpp: fix for the output
+
[phone]:41  mes5k
+
+	* NEWS: added info
+
[phone]:24  mes5k
+
+	* tests/: test12.out, test15.out, test16.out, test17.out: fixed
+	  test3 stuff
+
[phone]:20  mes5k
+
+	* tests/: test26.out, test26.sh, test27.out, test27.sh, test28.out,
+	  test28.sh, test29.out, test29.sh, test30.out, test30.sh,
+	  test31.out, test31.sh, test32.out, test32.sh, Makefile.am: added
+	  tests for reading extra incorrect values from arg
+
[phone]:18  mes5k
+
+	* examples/test3.cpp: add multi float
+
[phone]:18  mes5k
+
+	* include/tclap/: MultiArg.h, ValueArg.h: fixed error reading
+	  incorrect extra values in an arg
+
[phone]:56  mes5k
+
+	* include/tclap/XorHandler.h: added include
+
[phone]:21  mes5k
+
+	* include/tclap/XorHandler.h: added doxyen
+
[phone]:00  mes5k
+
+	* docs/manual.html: xor stuff
+
[phone]:56  mes5k
+
+	* examples/test5.cpp: prettified
+
[phone]:27  mes5k
+
+	* examples/: Makefile.am, test5.cpp: xor stuff
+
[phone]:24  mes5k
+
+	* configure.in: 0.9.7
+
[phone]:22  mes5k
+
+	* src/: Arg.cpp, CmdLine.cpp, Makefile.am, XorHandler.cpp: added
+	  xor
+
[phone]:20  mes5k
+
+	* include/tclap/: Arg.h, CmdLine.h, CommandLine.h,
+	  UnlabeledValueArg.h, XorHandler.h, Makefile.am: xor stuff
+
[phone]:14  mes5k
+
+	* tests/: test1.sh, test10.sh, test11.sh, test12.sh, test13.sh,
+	  test14.sh, test15.sh, test16.sh, test17.sh, test18.sh, test19.sh,
+	  test2.sh, test20.sh, test21.sh, test22.sh, test23.sh, test24.sh,
+	  test25.sh, test3.sh, test4.sh, test5.sh, test6.sh, test7.sh,
+	  test8.sh, test9.sh, Makefile.am, test20.out, test21.out,
+	  test22.out, test23.out, test24.out, test25.out: added new tests
+	  and comments
+
[phone]:36  mes5k
+
+	* include/tclap/: CmdLine.h, CommandLine.h, MultiArg.h, ValueArg.h:
+	  fix for strings with spaces
+
[phone]:39  mes5k
+
+	* docs/index.html: spelling
+
[phone]:18  mes5k
+
+	* docs/: index.html, manual.html: updates
+
[phone]:51  mes5k
+
+	* NEWS: update
+
[phone]:30  mes5k
+
+	* include/tclap/CmdLine.h, src/CmdLine.cpp: added backward
+	  compatibility
+
[phone]:11  mes5k
+
+	* src/Arg.cpp: fixed warning
+
[phone]:04  mes5k
+
+	* examples/: Makefile.am, test4.cpp: added new test
+
[phone]:00  mes5k
+
+	* tests/Makefile.am: added two new tests
+
[phone]:59  mes5k
+
+	* include/tclap/: Arg.h, ArgException.h, CmdLine.h, HelpVisitor.h,
+	  IgnoreRestVisitor.h, MultiArg.h, SwitchArg.h,
+	  UnlabeledMultiArg.h, UnlabeledValueArg.h, ValueArg.h,
+	  VersionVisitor.h, Visitor.h: fixed combined switch stuff and
+	  added doxygen comments
+
[phone]:58  mes5k
+
+	* src/: Arg.cpp, CmdLine.cpp, SwitchArg.cpp: fixed some combined
+	  switch stuff
+
[phone]:50  mes5k
+
+	* tests/: test18.out, test18.sh, test19.out, test19.sh: new tests
+
[phone]:32  mes5k
+
+	* autotools.sh: init
+
[phone]:31  mes5k
+
+	* include/tclap/UnlabeledMultiArg.h: delim stuff
+
[phone]:14  mes5k
+
+	* examples/test1.cpp: new fangled
+
[phone]:11  mes5k
+
+	* configure.in: 0.9.6
+
[phone]:10  mes5k
+
+	* tests/: test13.sh, test14.sh: updated
+
[phone]:09  mes5k
+
+	* tests/: test10.out, test11.out, test12.out, test13.out,
+	  test14.out, test15.out, test16.out, test4.out: updates
+
[phone]:07  mes5k
+
+	* tests/Makefile.am: added test
+
[phone]:06  mes5k
+
+	* tests/: test17.out, test17.sh: first checkin
+
[phone]:01  mes5k
+
+	* src/Arg.cpp: removed message
+
[phone]:59  mes5k
+
+	* examples/Makefile.am: added warnings
+
[phone]:58  mes5k
+
+	* examples/: test2.cpp, test3.cpp: fixed warnings
+
[phone]:53  mes5k
+
+	* Makefile.am: added warnings
+
[phone]:52  mes5k
+
+	* src/Arg.cpp, src/CmdLine.cpp, src/SwitchArg.cpp,
+	  examples/test3.cpp: added delimiter
+
[phone]:50  mes5k
+
+	* src/Makefile.am: added warnings
+
[phone]:48  mes5k
+
+	* include/tclap/: Arg.h, ArgException.h, CmdLine.h, MultiArg.h,
+	  UnlabeledValueArg.h, ValueArg.h: delimiter changes
+
[phone]:26  mes5k
+
+	* include/tclap/Makefile.am: added new visitor
+
[phone]:20  mes5k
+
+	* include/tclap/Makefile.am: updates
+
[phone]:13  mes5k
+
+	* config/: mkinstalldirs, install-sh, missing, depcomp: init
+	  checkin
+
[phone]:11  mes5k
+
+	* NEWS: update
+
[phone]:06  mes5k
+
+	* examples/Makefile.am, examples/test1.cpp, examples/test2.cpp,
+	  examples/test3.cpp, INSTALL, Makefile.in: updates
+
[phone]:01  mes5k
+
+	* Makefile.am, configure.in: added tests
+
[phone]:00  mes5k
+
+	* docs/: index.html, manual.html: updated docs
+
[phone]:59  mes5k
+
+	* include/tclap/: Arg.h, CmdLine.h, IgnoreRestVisitor.h,
+	  MultiArg.h, SwitchArg.h, UnlabeledMultiArg.h,
+	  UnlabeledValueArg.h, ValueArg.h: big update
+
[phone]:57  mes5k
+
+	* src/: CmdLine.cpp, SwitchArg.cpp, Arg.cpp: new update
+
[phone]:56  mes5k
+
+	* tests/: test10.sh, test11.sh, test12.sh, test1.sh, test13.sh,
+	  test14.sh, test15.sh, test16.sh, test2.sh, test3.sh, test4.sh,
+	  test5.sh, test6.sh, test7.sh, test8.sh, test9.sh, test10.out,
+	  test11.out, test12.out, test13.out, test14.out, test15.out,
+	  test16.out, test1.out, test2.out, test3.out, test4.out,
+	  test5.out, test6.out, test7.out, Makefile.am, test8.out,
+	  test9.out, Makefile.in, genOut.pl: initial checkin
+
[phone]:39  mes5k
+
+	* NEWS, configure.in, AUTHORS, COPYING, ChangeLog, Makefile.am,
+	  Makefile.in, README, aclocal.m4, configure,
+	  config/ac_cxx_have_sstream.m4, config/ac_cxx_have_strstream.m4,
+	  config/ac_cxx_namespaces.m4, config/bb_enable_doxygen.m4,
+	  config/config.h.in, config/stamp-h.in, config/stamp-h1,
+	  examples/Makefile.am, examples/Makefile.in, examples/test1.cpp,
+	  examples/test2.cpp, include/Makefile.am, include/Makefile.in,
+	  include/tclap/Arg.h, include/tclap/ArgException.h,
+	  include/tclap/CmdLine.h, include/tclap/HelpVisitor.h,
+	  include/tclap/MultiArg.h, docs/Doxyfile.in, docs/Makefile.am,
+	  docs/Makefile.in, docs/index.html, docs/manual.html,
+	  include/tclap/Makefile.am, include/tclap/Makefile.in,
+	  include/tclap/SwitchArg.h, include/tclap/ValueArg.h,
+	  include/tclap/VersionVisitor.h, include/tclap/Visitor.h,
+	  src/Arg.cpp, src/CmdLine.cpp, src/Makefile.am, src/Makefile.in,
+	  src/SwitchArg.cpp: Initial revision
+
[phone]:39  mes5k
+
+	* NEWS, configure.in, AUTHORS, COPYING, ChangeLog, Makefile.am,
+	  Makefile.in, README, aclocal.m4, configure,
+	  config/ac_cxx_have_sstream.m4, config/ac_cxx_have_strstream.m4,
+	  config/ac_cxx_namespaces.m4, config/bb_enable_doxygen.m4,
+	  config/config.h.in, config/stamp-h.in, config/stamp-h1,
+	  examples/Makefile.am, examples/Makefile.in, examples/test1.cpp,
+	  examples/test2.cpp, include/Makefile.am, include/Makefile.in,
+	  include/tclap/Arg.h, include/tclap/ArgException.h,
+	  include/tclap/CmdLine.h, include/tclap/HelpVisitor.h,
+	  include/tclap/MultiArg.h, docs/Doxyfile.in, docs/Makefile.am,
+	  docs/Makefile.in, docs/index.html, docs/manual.html,
+	  include/tclap/Makefile.am, include/tclap/Makefile.in,
+	  include/tclap/SwitchArg.h, include/tclap/ValueArg.h,
+	  include/tclap/VersionVisitor.h, include/tclap/Visitor.h,
+	  src/Arg.cpp, src/CmdLine.cpp, src/Makefile.am, src/Makefile.in,
+	  src/SwitchArg.cpp: initial release
+

=== added file 'external/tclap/INSTALL'
--- external/tclap/INSTALL	1970-01-01 00:00:00 +0000
+++ external/tclap/INSTALL	2013-05-01 15:50:43 +0000
@@ -0,0 +1,182 @@
+Basic Installation
+==================
+
+   These are generic installation instructions.
+
+   The `configure' shell script attempts to guess correct values for
+various system-dependent variables used during compilation.  It uses
+those values to create a `Makefile' in each directory of the package.
+It may also create one or more `.h' files containing system-dependent
+definitions.  Finally, it creates a shell script `config.status' that
+you can run in the future to recreate the current configuration, a file
+`config.cache' that saves the results of its tests to speed up
+reconfiguring, and a file `config.log' containing compiler output
+(useful mainly for debugging `configure').
+
+   If you need to do unusual things to compile the package, please try
+to figure out how `configure' could check whether to do them, and mail
+diffs or instructions to the address given in the `README' so they can
+be considered for the next release.  If at some point `config.cache'
+contains results you don't want to keep, you may remove or edit it.
+
+   The file `configure.in' is used to create `configure' by a program
+called `autoconf'.  You only need `configure.in' if you want to change
+it or regenerate `configure' using a newer version of `autoconf'.
+
+The simplest way to compile this package is:
+
+  1. `cd' to the directory containing the package's source code and type
+     `./configure' to configure the package for your system.  If you're
+     using `csh' on an old version of System V, you might need to type
+     `sh ./configure' instead to prevent `csh' from trying to execute
+     `configure' itself.
+
+     Running `configure' takes awhile.  While running, it prints some
+     messages telling which features it is checking for.
+
+  2. Type `make' to compile the package.
+
+  3. Optionally, type `make check' to run any self-tests that come with
+     the package.
+
+  4. Type `make install' to install the programs and any data files and
+     documentation.
+
+  5. You can remove the program binaries and object files from the
+     source code directory by typing `make clean'.  To also remove the
+     files that `configure' created (so you can compile the package for
+     a different kind of computer), type `make distclean'.  There is
+     also a `make maintainer-clean' target, but that is intended mainly
+     for the package's developers.  If you use it, you may have to get
+     all sorts of other programs in order to regenerate files that came
+     with the distribution.
+
+Compilers and Options
+=====================
+
+   Some systems require unusual options for compilation or linking that
+the `configure' script does not know about.  You can give `configure'
+initial values for variables by setting them in the environment.  Using
+a Bourne-compatible shell, you can do that on the command line like
+this:
+     CC=c89 CFLAGS=-O2 LIBS=-lposix ./configure
+
+Or on systems that have the `env' program, you can do it like this:
+     env CPPFLAGS=-I/usr/local/include LDFLAGS=-s ./configure
+
+Compiling For Multiple Architectures
+====================================
+
+   You can compile the package for more than one kind of computer at the
+same time, by placing the object files for each architecture in their
+own directory.  To do this, you must use a version of `make' that
+supports the `VPATH' variable, such as GNU `make'.  `cd' to the
+directory where you want the object files and executables to go and run
+the `configure' script.  `configure' automatically checks for the
+source code in the directory that `configure' is in and in `..'.
+
+   If you have to use a `make' that does not supports the `VPATH'
+variable, you have to compile the package for one architecture at a time
+in the source code directory.  After you have installed the package for
+one architecture, use `make distclean' before reconfiguring for another
+architecture.
+
+Installation Names
+==================
+
+   By default, `make install' will install the package's files in
+`/usr/local/bin', `/usr/local/man', etc.  You can specify an
+installation prefix other than `/usr/local' by giving `configure' the
+option `--prefix=PATH'.
+
+   You can specify separate installation prefixes for
+architecture-specific files and architecture-independent files.  If you
+give `configure' the option `--exec-prefix=PATH', the package will use
+PATH as the prefix for installing programs and libraries.
+Documentation and other data files will still use the regular prefix.
+
+   In addition, if you use an unusual directory layout you can give
+options like `--bindir=PATH' to specify different values for particular
+kinds of files.  Run `configure --help' for a list of the directories
+you can set and what kinds of files go in them.
+
+   If the package supports it, you can cause programs to be installed
+with an extra prefix or suffix on their names by giving `configure' the
+option `--program-prefix=PREFIX' or `--program-suffix=SUFFIX'.
+
+Optional Features
+=================
+
+   Some packages pay attention to `--enable-FEATURE' options to
+`configure', where FEATURE indicates an optional part of the package.
+They may also pay attention to `--with-PACKAGE' options, where PACKAGE
+is something like `gnu-as' or `x' (for the X Window System).  The
+`README' should mention any `--enable-' and `--with-' options that the
+package recognizes.
+
+   For packages that use the X Window System, `configure' can usually
+find the X include and library files automatically, but if it doesn't,
+you can use the `configure' options `--x-includes=DIR' and
+`--x-libraries=DIR' to specify their locations.
+
+Specifying the System Type
+==========================
+
+   There may be some features `configure' can not figure out
+automatically, but needs to determine by the type of host the package
+will run on.  Usually `configure' can figure that out, but if it prints
+a message saying it can not guess the host type, give it the
+`--host=TYPE' option.  TYPE can either be a short name for the system
+type, such as `sun4', or a canonical name with three fields:
+     CPU-COMPANY-SYSTEM
+
+See the file `config.sub' for the possible values of each field.  If
+`config.sub' isn't included in this package, then this package doesn't
+need to know the host type.
+
+   If you are building compiler tools for cross-compiling, you can also
+use the `--target=TYPE' option to select the type of system they will
+produce code for and the `--build=TYPE' option to select the type of
+system on which you are compiling the package.
+
+Sharing Defaults
+================
+
+   If you want to set default values for `configure' scripts to share,
+you can create a site shell script called `config.site' that gives
+default values for variables like `CC', `cache_file', and `prefix'.
+`configure' looks for `PREFIX/share/config.site' if it exists, then
+`PREFIX/etc/config.site' if it exists.  Or, you can set the
+`CONFIG_SITE' environment variable to the location of the site script.
+A warning: not all `configure' scripts look for a site script.
+
+Operation Controls
+==================
+
+   `configure' recognizes the following options to control how it
+operates.
+
+`--cache-file=FILE'
+     Use and save the results of the tests in FILE instead of
+     `./config.cache'.  Set FILE to `/dev/null' to disable caching, for
+     debugging `configure'.
+
+`--help'
+     Print a summary of the options to `configure', and exit.
+
+`--quiet'
+`--silent'
+`-q'
+     Do not print messages saying which checks are being made.  To
+     suppress all normal output, redirect it to `/dev/null' (any error
+     messages will still be shown).
+
+`--srcdir=DIR'
+     Look for the package's source code in directory DIR.  Usually
+     `configure' can determine that directory automatically.
+
+`--version'
+     Print the version of Autoconf used to generate the `configure'
+     script, and exit.
+
+`configure' also accepts some other, not widely useful, options.

=== added file 'external/tclap/NEWS'
--- external/tclap/NEWS	1970-01-01 00:00:00 +0000
+++ external/tclap/NEWS	2013-05-01 15:50:43 +0000
@@ -0,0 +1,95 @@
+
+4/3/03 -  Checked in a good sized update that move support of the library
+closer to that of the POSIX/GNU standards.  Switches can now be combined into
+single arguments, -- is supported and MultiArgs now allow for multiple labeled
+args.  I've also changed things a bit by subclassing MultiArg and ValueArg
+to get unlabeled versions of these classes.  I think this is a bit cleaner
+design, despite two new classes.
+
+1/7/04 - ... and with great trepidation, I release 0.9.6.  Loads of changes.  
+The big change is that you can now define the delimiter used to separate 
+argument flags and argument values. So if you prefer arguments of the style 
+"-s=asdf"  instead of "-s asdf", you can do so.  I've also fixed a number of 
+warnings generated and fixed a few pathologic bugs related to combined
+switches.  That said, I suspect that there may be a few significant bugs
+in this release that I haven't uncovered yet.  Please let me know ASAP if
+you find any.
+
+2/6/04 - Another big release: 0.9.7.  First is a bugfix submitted by 
+Matthias Stiller that specializes the _extractValue method in a couple of
+places that allows strings with spaces to be correctly read by tclap.  A
+second bug found by John Ling has been fixed so that exceptions are thrown 
+if more than one value is parsed from a single arg or if the second value 
+parsed is invalid.   A big new feature has been added that allows args to
+be xor'd.  This means that two (or more) args can be specified such that
+one and only one of the args is required.  If a second arg is found an
+exception is thrown.  See the manual for details.  As always, let me know
+if you run into any problems.
+
+2/10/04 - A minor release: 0.9.8.  A couple of bug fixes for 0.9.7 are
+included and a feature has been added that allows Args to be specified 
+without short options, meaning the user is forced to use only long options.
+This is useful for programs with more options than map sensibly to single
+chars.
+
+7/3/04 - Added a new constructor and handling to the various value args
+that allows the user to provide a list of values that the input arg values 
+should be restricted to.  
+
+8/9/04 - Created a function to print the output nicely, meaning line wraps
+are handled somewhat sensibly now.  Also changed error handling slightly. 
+Instead of printing the entire usage, I just print a short usage.  If
+someone really hates this, its easy to change back.  Let me know if this 
+causes problems.  I think this equals release 0.9.9!
+
+10/19/04 - A number of changes that should substantially improve the library.
+The most important being that we've moved the implementation of the library
+entirely into the header files.  This means there is no longer a library to
+complile against, you simply have to #include <tclap/CmdLine.h>.  New
+constructors have been added to the various Arg classes that allow them to 
+be constructed with a CmdLine reference so that you no longer need to call
+the add method if you prefer it that way.  The output generated by the library
+has been confined to a few methods in the CmdLine class.  This means to 
+generate different output you can extend CmdLine and override the offending
+methods.  A number of style changes have been made in the code base to 
+conform better to C++ best practices.   A thoughtful user has contributed
+project files for the building the examples Microsoft Visual Studio.  See
+the README file in the msc directory for more details
+
+And so we have release 1.0!
+
+10/30/04 - A few bugfixes.  Now checking for include.h before including it. 
+This will help Windows users who don't have it.  Also changed test1 so that 
+it doesn't use toupper, which apparently causes problem for non-ASCII 
+character sets.
+
+10/31/04 - A few more tweaks, none of which should be noticeable to people
+who are already using the lib without trouble. Maybe I shouldn't release 
+things early in the morning!  Also note that manual.html is now generated 
+from manual.xml.  If you have your own docbook xsl style that you prefer, 
+then have at it.
+
+12/3/04 - Some minor bug fixes including the removal of the two stage name
+lookup ifdefs which means that the software should work out of the box 
+for gcc 3.4+.  Isolated output in a separate class that should make
+customization of output easier.  I also included a rudimentary output class
+that generated a (bad) Docbook command summary when used. 
+
+1/4/05 - Several bug fixes, but no new features. Fixed a bug when mandatory 
+long args and unlabeled args were used together and weren't working properly.
+Now they can be used together. Fixed another bug in spacePrint where long 
+program names caused an infinite loop.  Finally, fixed a small memory leak.
+
+1/6/05 - Fixed a bug where setting the output object for a CmdLine didn't
+register for version or usage generation. Doh!  Created a Constraint interface
+that should facilitate the creation of different constraints on Args.
+This has involved changing the constructor interface, so if you've been using
+allowed lists, you'll need to make a small modification to your existing code.
+See examples/test6.cpp for details.
+
+9/26/09 - Whoa, long break.  Primarily a bug-fix release, but we did switch 
+to using traits, which necessitates the minor version bump. Take a look 
+at test11.cpp and test12.cpp for examples on using ArgTraits for extending 
+tclap for different types.
+
+4/16/11 - Another long break!  Several minor bug and memory leak fixes.

=== added file 'external/tclap/README'
--- external/tclap/README	1970-01-01 00:00:00 +0000
+++ external/tclap/README	2013-05-01 15:50:43 +0000
@@ -0,0 +1,16 @@
+
+TCLAP - Templatized Command Line Argument Parser
+
+This is a simple C++ library that facilitates parsing command line
+arguments in a type independent manner.  It doesn't conform exactly
+to either the GNU or POSIX standards, although it is close.  See
+docs/manual.html for descriptions of how things work or look at the
+simple examples in the examples dir.
+
+To find out what the latest changes are read the NEWS file in this directory.
+
+
+Any and all feedback is welcome to:  Mike Smoot <[e-mail]>
+
+
+

=== added directory 'external/tclap/include'
=== added directory 'external/tclap/include/tclap'
=== added file 'external/tclap/include/tclap/Arg.h'
--- external/tclap/include/tclap/Arg.h	1970-01-01 00:00:00 +0000
+++ external/tclap/include/tclap/Arg.h	2013-05-01 15:50:43 +0000
@@ -0,0 +1,692 @@
+// -*- Mode: c++; c-basic-offset: 4; tab-width: 4; -*-
+
+/******************************************************************************
+ *
+ *  file:  Arg.h
+ *
+ *  Copyright (c) 2003, Michael E. Smoot .
+ *  Copyright (c) 2004, Michael E. Smoot, Daniel Aarno .
+ *  All rights reverved.
+ *
+ *  See the file COPYING in the top directory of this distribution for
+ *  more information.
+ *
+ *  THE SOFTWARE IS PROVIDED _AS IS_, WITHOUT WARRANTY OF ANY KIND, EXPRESS
+ *  OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ *  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+ *  THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ *  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ *  FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ *  DEALINGS IN THE SOFTWARE.
+ *
+ *****************************************************************************/
+
+
+#ifndef TCLAP_ARGUMENT_H
+#define TCLAP_ARGUMENT_H
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#else
+#define HAVE_SSTREAM
+#endif
+
+#include <string>
+#include <vector>
+#include <list>
+#include <iostream>
+#include <iomanip>
+#include <cstdio>
+
+#if defined(HAVE_SSTREAM)
+#include <sstream>
+typedef std::istringstream istringstream;
+#elif defined(HAVE_STRSTREAM)
+#include <strstream>
+typedef std::istrstream istringstream;
+#else
+#error "Need a stringstream (sstream or strstream) to compile!"
+#endif
+
+#include <tclap/ArgException.h>
+#include <tclap/Visitor.h>
+#include <tclap/CmdLineInterface.h>
+#include <tclap/ArgTraits.h>
+#include <tclap/StandardTraits.h>
+
+namespace TCLAP {
+
+/**
+ * A virtual base class that defines the essential data for all arguments.
+ * This class, or one of its existing children, must be subclassed to do
+ * anything.
+ */
+class Arg
+{
+	private:
+		/**
+		 * Prevent accidental copying.
+		 */
+		Arg(const Arg& rhs);
+
+		/**
+		 * Prevent accidental copying.
+		 */
+		Arg& operator=(const Arg& rhs);
+
+		/**
+		 * Indicates whether the rest of the arguments should be ignored.
+		 */
+		static bool& ignoreRestRef() { static bool ign = false; return ign; }
+
+		/**
+		 * The delimiter that separates an argument flag/name from the
+		 * value.
+		 */
+		static char& delimiterRef() { static char delim = ' '; return delim; }
+
+	protected:
+
+		/**
+		 * The single char flag used to identify the argument.
+		 * This value (preceded by a dash {-}), can be used to identify
+		 * an argument on the command line.  The _flag can be blank,
+		 * in fact this is how unlabeled args work.  Unlabeled args must
+		 * override appropriate functions to get correct handling. Note
+		 * that the _flag does NOT include the dash as part of the flag.
+		 */
+		std::string _flag;
+
+		/**
+		 * A single work namd indentifying the argument.
+		 * This value (preceded by two dashed {--}) can also be used
+		 * to identify an argument on the command line.  Note that the
+		 * _name does NOT include the two dashes as part of the _name. The
+		 * _name cannot be blank.
+		 */
+		std::string _name;
+
+		/**
+		 * Description of the argument.
+		 */
+		std::string _description;
+
+		/**
+		 * Indicating whether the argument is required.
+		 */
+		bool _required;
+
+		/**
+		 * Label to be used in usage description.  Normally set to
+		 * "required", but can be changed when necessary.
+		 */
+		std::string _requireLabel;
+
+		/**
+		 * Indicates whether a value is required for the argument.
+		 * Note that the value may be required but the argument/value
+		 * combination may not be, as specified by _required.
+		 */
+		bool _valueRequired;
+
+		/**
+		 * Indicates whether the argument has been set.
+		 * Indicates that a value on the command line has matched the
+		 * name/flag of this argument and the values have been set accordingly.
+		 */
+		bool _alreadySet;
+
+		/**
+		 * A pointer to a vistitor object.
+		 * The visitor allows special handling to occur as soon as the
+		 * argument is matched.  This defaults to NULL and should not
+		 * be used unless absolutely necessary.
+		 */
+		Visitor* _visitor;
+
+		/**
+		 * Whether this argument can be ignored, if desired.
+		 */
+		bool _ignoreable;
+
+		/**
+		 * Indicates that the arg was set as part of an XOR and not on the
+		 * command line.
+		 */
+		bool _xorSet;
+
+		bool _acceptsMultipleValues;
+
+		/**
+		 * Performs the special handling described by the Vistitor.
+		 */
+		void _checkWithVisitor() const;
+
+		/**
+		 * Primary constructor. YOU (yes you) should NEVER construct an Arg
+		 * directly, this is a base class that is extended by various children
+		 * that are meant to be used.  Use SwitchArg, ValueArg, MultiArg,
+		 * UnlabeledValueArg, or UnlabeledMultiArg instead.
+		 *
+		 * \param flag - The flag identifying the argument.
+		 * \param name - The name identifying the argument.
+		 * \param desc - The description of the argument, used in the usage.
+		 * \param req - Whether the argument is required.
+		 * \param valreq - Whether the a value is required for the argument.
+		 * \param v - The visitor checked by the argument. Defaults to NULL.
+		 */
+ 		Arg( const std::string& flag,
+			 const std::string& name,
+			 const std::string& desc,
+			 bool req,
+			 bool valreq,
+			 Visitor* v = NULL );
+
+	public:
+		/**
+		 * Destructor.
+		 */
+		virtual ~Arg();
+
+		/**
+		 * Adds this to the specified list of Args.
+		 * \param argList - The list to add this to.
+		 */
+		virtual void addToList( std::list<Arg*>& argList ) const;
+
+		/**
+		 * Begin ignoring arguments since the "--" argument was specified.
+		 */
+		static void beginIgnoring() { ignoreRestRef() = true; }
+
+		/**
+		 * Whether to ignore the rest.
+		 */
+		static bool ignoreRest() { return ignoreRestRef(); }
+
+		/**
+		 * The delimiter that separates an argument flag/name from the
+		 * value.
+		 */
+		static char delimiter() { return delimiterRef(); }
+
+		/**
+		 * The char used as a place holder when SwitchArgs are combined.
+		 * Currently set to the bell char (ASCII 7).
+		 */
+		static char blankChar() { return (char)7; }
+
+		/**
+		 * The char that indicates the beginning of a flag.  Defaults to '-', but
+		 * clients can define TCLAP_FLAGSTARTCHAR to override.
+		 */
+#ifndef TCLAP_FLAGSTARTCHAR
+#define TCLAP_FLAGSTARTCHAR '-'
+#endif
+		static char flagStartChar() { return TCLAP_FLAGSTARTCHAR; }
+
+		/**
+		 * The sting that indicates the beginning of a flag.  Defaults to "-", but
+		 * clients can define TCLAP_FLAGSTARTSTRING to override. Should be the same
+		 * as TCLAP_FLAGSTARTCHAR.
+		 */
+#ifndef TCLAP_FLAGSTARTSTRING
+#define TCLAP_FLAGSTARTSTRING "-"
+#endif
+		static const std::string flagStartString() { return TCLAP_FLAGSTARTSTRING; }
+
+		/**
+		 * The sting that indicates the beginning of a name.  Defaults to "--", but
+		 *  clients can define TCLAP_NAMESTARTSTRING to override.
+		 */
+#ifndef TCLAP_NAMESTARTSTRING
+#define TCLAP_NAMESTARTSTRING "--"
+#endif
+		static const std::string nameStartString() { return TCLAP_NAMESTARTSTRING; }
+
+		/**
+		 * The name used to identify the ignore rest argument.
+		 */
+		static const std::string ignoreNameString() { return "ignore_rest"; }
+
+		/**
+		 * Sets the delimiter for all arguments.
+		 * \param c - The character that delimits flags/names from values.
+		 */
+		static void setDelimiter( char c ) { delimiterRef() = c; }
+
+		/**
+		 * Pure virtual method meant to handle the parsing and value assignment
+		 * of the string on the command line.
+		 * \param i - Pointer the the current argument in the list.
+		 * \param args - Mutable list of strings. What is
+		 * passed in from main.
+		 */
+		virtual bool processArg(int *i, std::vector<std::string>& args) = 0;
+
+		/**
+		 * Operator ==.
+		 * Equality operator. Must be virtual to handle unlabeled args.
+		 * \param a - The Arg to be compared to this.
+		 */
+		virtual bool operator==(const Arg& a) const;
+
+		/**
+		 * Returns the argument flag.
+		 */
+		const std::string& getFlag() const;
+
+		/**
+		 * Returns the argument name.
+		 */
+		const std::string& getName() const;
+
+		/**
+		 * Returns the argument description.
+		 */
+		std::string getDescription() const;
+
+		/**
+		 * Indicates whether the argument is required.
+		 */
+		virtual bool isRequired() const;
+
+		/**
+		 * Sets _required to true. This is used by the XorHandler.
+		 * You really have no reason to ever use it.
+		 */
+		void forceRequired();
+
+		/**
+		 * Sets the _alreadySet value to true.  This is used by the XorHandler.
+		 * You really have no reason to ever use it.
+		 */
+		void xorSet();
+
+		/**
+		 * Indicates whether a value must be specified for argument.
+		 */
+		bool isValueRequired() const;
+
+		/**
+		 * Indicates whether the argument has already been set.  Only true
+		 * if the arg has been matched on the command line.
+		 */
+		bool isSet() const;
+
+		/**
+		 * Indicates whether the argument can be ignored, if desired.
+		 */
+		bool isIgnoreable() const;
+
+		/**
+		 * A method that tests whether a string matches this argument.
+		 * This is generally called by the processArg() method.  This
+		 * method could be re-implemented by a child to change how
+		 * arguments are specified on the command line.
+		 * \param s - The string to be compared to the flag/name to determine
+		 * whether the arg matches.
+		 */
+		virtual bool argMatches( const std::string& s ) const;
+
+		/**
+		 * Returns a simple string representation of the argument.
+		 * Primarily for debugging.
+		 */
+		virtual std::string toString() const;
+
+		/**
+		 * Returns a short ID for the usage.
+		 * \param valueId - The value used in the id.
+		 */
+		virtual std::string shortID( const std::string& valueId = "val" ) const;
+
+		/**
+		 * Returns a long ID for the usage.
+		 * \param valueId - The value used in the id.
+		 */
+		virtual std::string longID( const std::string& valueId = "val" ) const;
+
+		/**
+		 * Trims a value off of the flag.
+		 * \param flag - The string from which the flag and value will be
+		 * trimmed. Contains the flag once the value has been trimmed.
+		 * \param value - Where the value trimmed from the string will
+		 * be stored.
+		 */
+		virtual void trimFlag( std::string& flag, std::string& value ) const;
+
+		/**
+		 * Checks whether a given string has blank chars, indicating that
+		 * it is a combined SwitchArg.  If so, return true, otherwise return
+		 * false.
+		 * \param s - string to be checked.
+		 */
+		bool _hasBlanks( const std::string& s ) const;
+
+		/**
+		 * Sets the requireLabel. Used by XorHandler.  You shouldn't ever
+		 * use this.
+		 * \param s - Set the requireLabel to this value.
+		 */
+		void setRequireLabel( const std::string& s );
+
+		/**
+		 * Used for MultiArgs and XorHandler to determine whether args
+		 * can still be set.
+		 */
+		virtual bool allowMore();
+
+		/**
+		 * Use by output classes to determine whether an Arg accepts
+		 * multiple values.
+		 */
+		virtual bool acceptsMultipleValues();
+
+		/**
+		 * Clears the Arg object and allows it to be reused by new
+		 * command lines.
+		 */
+		 virtual void reset();
+};
+
+/**
+ * Typedef of an Arg list iterator.
+ */
+typedef std::list<Arg*>::iterator ArgListIterator;
+
+/**
+ * Typedef of an Arg vector iterator.
+ */
+typedef std::vector<Arg*>::iterator ArgVectorIterator;
+
+/**
+ * Typedef of a Visitor list iterator.
+ */
+typedef std::list<Visitor*>::iterator VisitorListIterator;
+
+/*
+ * Extract a value of type T from it's string representation contained
+ * in strVal. The ValueLike parameter used to select the correct
+ * specialization of ExtractValue depending on the value traits of T.
+ * ValueLike traits use operator>> to assign the value from strVal.
+ */
+template<typename T> void
+ExtractValue(T &destVal, const std::string& strVal, ValueLike vl)
+{
+    static_cast<void>(vl); // Avoid warning about unused vl
+    std::istringstream is(strVal);
+
+    int valuesRead = 0;
+    while ( is.good() ) {
+	if ( is.peek() != EOF )
+#ifdef TCLAP_SETBASE_ZERO
+	    is >> std::setbase(0) >> destVal;
+#else
+	    is >> destVal;
+#endif
+	else
+	    break;
+
+	valuesRead++;
+    }
+
+    if ( is.fail() )
+	throw( ArgParseException("Couldn't read argument value "
+				 "from string '" + strVal + "'"));
+
+
+    if ( valuesRead > 1 )
+	throw( ArgParseException("More than one valid value parsed from "
+				 "string '" + strVal + "'"));
+
+}
+
+/*
+ * Extract a value of type T from it's string representation contained
+ * in strVal. The ValueLike parameter used to select the correct
+ * specialization of ExtractValue depending on the value traits of T.
+ * StringLike uses assignment (operator=) to assign from strVal.
+ */
+template<typename T> void
+ExtractValue(T &destVal, const std::string& strVal, StringLike sl)
+{
+    static_cast<void>(sl); // Avoid warning about unused sl
+    SetString(destVal, strVal);
+}
+
+//////////////////////////////////////////////////////////////////////
+//BEGIN Arg.cpp
+//////////////////////////////////////////////////////////////////////
+
+inline Arg::Arg(const std::string& flag,
+         const std::string& name,
+         const std::string& desc,
+         bool req,
+         bool valreq,
+         Visitor* v) :
+  _flag(flag),
+  _name(name),
+  _description(desc),
+  _required(req),
+  _requireLabel("required"),
+  _valueRequired(valreq),
+  _alreadySet(false),
+  _visitor( v ),
+  _ignoreable(true),
+  _xorSet(false),
+  _acceptsMultipleValues(false)
+{
+	if ( _flag.length() > 1 )
+		throw(SpecificationException(
+				"Argument flag can only be one character long", toString() ) );
+
+	if ( _name != ignoreNameString() &&
+		 ( _flag == Arg::flagStartString() ||
+		   _flag == Arg::nameStartString() ||
+		   _flag == " " ) )
+		throw(SpecificationException("Argument flag cannot be either '" +
+							Arg::flagStartString() + "' or '" +
+							Arg::nameStartString() + "' or a space.",
+							toString() ) );
+
+	if ( ( _name.substr( 0, Arg::flagStartString().length() ) == Arg::flagStartString() ) ||
+		 ( _name.substr( 0, Arg::nameStartString().length() ) == Arg::nameStartString() ) ||
+		 ( _name.find( " ", 0 ) != std::string::npos ) )
+		throw(SpecificationException("Argument name begin with either '" +
+							Arg::flagStartString() + "' or '" +
+							Arg::nameStartString() + "' or space.",
+							toString() ) );
+
+}
+
+inline Arg::~Arg() { }
+
+inline std::string Arg::shortID( const std::string& valueId ) const
+{
+	std::string id = "";
+
+	if ( _flag != "" )
+		id = Arg::flagStartString() + _flag;
+	else
+		id = Arg::nameStartString() + _name;
+
+	if ( _valueRequired )
+		id += std::string( 1, Arg::delimiter() ) + "<" + valueId  + ">";
+
+	if ( !_required )
+		id = "[" + id + "]";
+
+	return id;
+}
+
+inline std::string Arg::longID( const std::string& valueId ) const
+{
+	std::string id = "";
+
+	if ( _flag != "" )
+	{
+		id += Arg::flagStartString() + _flag;
+
+		if ( _valueRequired )
+			id += std::string( 1, Arg::delimiter() ) + "<" + valueId + ">";
+
+		id += ",  ";
+	}
+
+	id += Arg::nameStartString() + _name;
+
+	if ( _valueRequired )
+		id += std::string( 1, Arg::delimiter() ) + "<" + valueId + ">";
+
+	return id;
+
+}
+
+inline bool Arg::operator==(const Arg& a) const
+{
+	if ( ( _flag != "" && _flag == a._flag ) || _name == a._name)
+		return true;
+	else
+		return false;
+}
+
+inline std::string Arg::getDescription() const
+{
+	std::string desc = "";
+	if ( _required )
+		desc = "(" + _requireLabel + ")  ";
+
+//	if ( _valueRequired )
+//		desc += "(value required)  ";
+
+	desc += _description;
+	return desc;
+}
+
+inline const std::string& Arg::getFlag() const { return _flag; }
+
+inline const std::string& Arg::getName() const { return _name; }
+
+inline bool Arg::isRequired() const { return _required; }
+
+inline bool Arg::isValueRequired() const { return _valueRequired; }
+
+inline bool Arg::isSet() const
+{
+	if ( _alreadySet && !_xorSet )
+		return true;
+	else
+		return false;
+}
+
+inline bool Arg::isIgnoreable() const { return _ignoreable; }
+
+inline void Arg::setRequireLabel( const std::string& s)
+{
+	_requireLabel = s;
+}
+
+inline bool Arg::argMatches( const std::string& argFlag ) const
+{
+	if ( ( argFlag == Arg::flagStartString() + _flag && _flag != "" ) ||
+	       argFlag == Arg::nameStartString() + _name )
+		return true;
+	else
+		return false;
+}
+
+inline std::string Arg::toString() const
+{
+	std::string s = "";
+
+	if ( _flag != "" )
+		s += Arg::flagStartString() + _flag + " ";
+
+	s += "(" + Arg::nameStartString() + _name + ")";
+
+	return s;
+}
+
+inline void Arg::_checkWithVisitor() const
+{
+	if ( _visitor != NULL )
+		_visitor->visit();
+}
+
+/**
+ * Implementation of trimFlag.
+ */
+inline void Arg::trimFlag(std::string& flag, std::string& value) const
+{
+	int stop = 0;
+	for ( int i = 0; static_cast<unsigned int>(i) < flag.length(); i++ )
+		if ( flag[i] == Arg::delimiter() )
+		{
+			stop = i;
+			break;
+		}
+
+	if ( stop > 1 )
+	{
+		value = flag.substr(stop+1);
+		flag = flag.substr(0,stop);
+	}
+
+}
+
+/**
+ * Implementation of _hasBlanks.
+ */
+inline bool Arg::_hasBlanks( const std::string& s ) const
+{
+	for ( int i = 1; static_cast<unsigned int>(i) < s.length(); i++ )
+		if ( s[i] == Arg::blankChar() )
+			return true;
+
+	return false;
+}
+
+inline void Arg::forceRequired()
+{
+	_required = true;
+}
+
+inline void Arg::xorSet()
+{
+	_alreadySet = true;
+	_xorSet = true;
+}
+
+/**
+ * Overridden by Args that need to added to the end of the list.
+ */
+inline void Arg::addToList( std::list<Arg*>& argList ) const
+{
+	argList.push_front( const_cast<Arg*>(this) );
+}
+
+inline bool Arg::allowMore()
+{
+	return false;
+}
+
+inline bool Arg::acceptsMultipleValues()
+{
+	return _acceptsMultipleValues;
+}
+
+inline void Arg::reset()
+{
+	_xorSet = false;
+	_alreadySet = false;
+}
+
+//////////////////////////////////////////////////////////////////////
+//END Arg.cpp
+//////////////////////////////////////////////////////////////////////
+
+} //namespace TCLAP
+
+#endif
+

=== added file 'external/tclap/include/tclap/ArgException.h'
--- external/tclap/include/tclap/ArgException.h	1970-01-01 00:00:00 +0000
+++ external/tclap/include/tclap/ArgException.h	2013-05-01 15:50:43 +0000
@@ -0,0 +1,200 @@
+// -*- Mode: c++; c-basic-offset: 4; tab-width: 4; -*-
+
+/****************************************************************************** 
+ * 
+ *  file:  ArgException.h
+ * 
+ *  Copyright (c) 2003, Michael E. Smoot .
+ *  All rights reverved.
+ * 
+ *  See the file COPYING in the top directory of this distribution for
+ *  more information.
+ *  
+ *  THE SOFTWARE IS PROVIDED _AS IS_, WITHOUT WARRANTY OF ANY KIND, EXPRESS 
+ *  OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 
+ *  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL 
+ *  THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 
+ *  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING 
+ *  FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER 
+ *  DEALINGS IN THE SOFTWARE.  
+ *  
+ *****************************************************************************/ 
+
+
+#ifndef TCLAP_ARG_EXCEPTION_H
+#define TCLAP_ARG_EXCEPTION_H
+
+#include <string>
+#include <exception>
+
+namespace TCLAP {
+
+/**
+ * A simple class that defines and argument exception.  Should be caught
+ * whenever a CmdLine is created and parsed.
+ */
+class ArgException : public std::exception
+{
+	public:
+	
+		/**
+		 * Constructor.
+		 * \param text - The text of the exception.
+		 * \param id - The text identifying the argument source.
+		 * \param td - Text describing the type of ArgException it is.
+		 * of the exception.
+		 */
+		ArgException( const std::string& text = "undefined exception", 
+					  const std::string& id = "undefined",
+					  const std::string& td = "Generic ArgException")
+			: std::exception(), 
+			  _errorText(text), 
+			  _argId( id ), 
+			  _typeDescription(td)
+		{ } 
+		
+		/**
+		 * Destructor.
+		 */
+		virtual ~ArgException() throw() { }
+
+		/**
+		 * Returns the error text.
+		 */
+		std::string error() const { return ( _errorText ); }
+
+		/**
+		 * Returns the argument id.
+		 */
+		std::string argId() const  
+		{ 
+			if ( _argId == "undefined" )
+				return " ";
+			else
+				return ( "Argument: " + _argId ); 
+		}
+
+		/**
+		 * Returns the arg id and error text. 
+		 */
+		const char* what() const throw() 
+		{
+			static std::string ex; 
+			ex = _argId + " -- " + _errorText;
+			return ex.c_str();
+		}
+
+		/**
+		 * Returns the type of the exception.  Used to explain and distinguish
+		 * between different child exceptions.
+		 */
+		std::string typeDescription() const
+		{
+			return _typeDescription; 
+		}
+
+
+	private:
+
+		/**
+		 * The text of the exception message.
+		 */
+		std::string _errorText;
+
+		/**
+		 * The argument related to this exception.
+		 */
+		std::string _argId;
+
+		/**
+		 * Describes the type of the exception.  Used to distinguish
+		 * between different child exceptions.
+		 */
+		std::string _typeDescription;
+
+};
+
+/**
+ * Thrown from within the child Arg classes when it fails to properly
+ * parse the argument it has been passed.
+ */
+class ArgParseException : public ArgException
+{ 
+	public:
+		/**
+		 * Constructor.
+		 * \param text - The text of the exception.
+		 * \param id - The text identifying the argument source 
+		 * of the exception.
+		 */
+		ArgParseException( const std::string& text = "undefined exception", 
+					       const std::string& id = "undefined" )
+			: ArgException( text, 
+			                id, 
+							std::string( "Exception found while parsing " ) + 
+							std::string( "the value the Arg has been passed." ))
+			{ }
+};
+
+/**
+ * Thrown from CmdLine when the arguments on the command line are not
+ * properly specified, e.g. too many arguments, required argument missing, etc.
+ */
+class CmdLineParseException : public ArgException
+{
+	public:
+		/**
+		 * Constructor.
+		 * \param text - The text of the exception.
+		 * \param id - The text identifying the argument source 
+		 * of the exception.
+		 */
+		CmdLineParseException( const std::string& text = "undefined exception", 
+					           const std::string& id = "undefined" )
+			: ArgException( text, 
+			                id,
+							std::string( "Exception found when the values ") +
+							std::string( "on the command line do not meet ") +
+							std::string( "the requirements of the defined ") +
+							std::string( "Args." ))
+		{ }
+};
+
+/**
+ * Thrown from Arg and CmdLine when an Arg is improperly specified, e.g. 
+ * same flag as another Arg, same name, etc.
+ */
+class SpecificationException : public ArgException
+{
+	public:
+		/**
+		 * Constructor.
+		 * \param text - The text of the exception.
+		 * \param id - The text identifying the argument source 
+		 * of the exception.
+		 */
+		SpecificationException( const std::string& text = "undefined exception",
+					            const std::string& id = "undefined" )
+			: ArgException( text, 
+			                id,
+							std::string("Exception found when an Arg object ")+
+							std::string("is improperly defined by the ") +
+							std::string("developer." )) 
+		{ }
+
+};
+
+class ExitException {
+public:
+	ExitException(int estat) : _estat(estat) {}
+
+	int getExitStatus() const { return _estat; }
+
+private:
+	int _estat;
+};
+
+} // namespace TCLAP
+
+#endif
+

=== added file 'external/tclap/include/tclap/ArgTraits.h'
--- external/tclap/include/tclap/ArgTraits.h	1970-01-01 00:00:00 +0000
+++ external/tclap/include/tclap/ArgTraits.h	2013-05-01 15:50:43 +0000
@@ -0,0 +1,87 @@
+// -*- Mode: c++; c-basic-offset: 4; tab-width: 4; -*-
+
+/******************************************************************************
+ *
+ *  file:  ArgTraits.h
+ *
+ *  Copyright (c) 2007, Daniel Aarno, Michael E. Smoot .
+ *  All rights reverved.
+ *
+ *  See the file COPYING in the top directory of this distribution for
+ *  more information.
+ *
+ *  THE SOFTWARE IS PROVIDED _AS IS_, WITHOUT WARRANTY OF ANY KIND, EXPRESS
+ *  OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ *  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+ *  THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ *  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ *  FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ *  DEALINGS IN THE SOFTWARE.
+ *
+ *****************************************************************************/
+
+// This is an internal tclap file, you should probably not have to
+// include this directly
+
+#ifndef TCLAP_ARGTRAITS_H
+#define TCLAP_ARGTRAITS_H
+
+namespace TCLAP {
+
+// We use two empty structs to get compile type specialization
+// function to work
+
+/**
+ * A value like argument value type is a value that can be set using
+ * operator>>. This is the default value type.
+ */
+struct ValueLike {
+    typedef ValueLike ValueCategory;
+	virtual ~ValueLike() {}
+};
+
+/**
+ * A string like argument value type is a value that can be set using
+ * operator=(string). Usefull if the value type contains spaces which
+ * will be broken up into individual tokens by operator>>.
+ */
+struct StringLike {
+	virtual ~StringLike() {}
+};
+
+/**
+ * A class can inherit from this object to make it have string like
+ * traits. This is a compile time thing and does not add any overhead
+ * to the inherenting class.
+ */
+struct StringLikeTrait {
+    typedef StringLike ValueCategory;
+	virtual ~StringLikeTrait() {}
+};
+
+/**
+ * A class can inherit from this object to make it have value like
+ * traits. This is a compile time thing and does not add any overhead
+ * to the inherenting class.
+ */
+struct ValueLikeTrait {
+    typedef ValueLike ValueCategory;
+	virtual ~ValueLikeTrait() {}
+};
+
+/**
+ * Arg traits are used to get compile type specialization when parsing
+ * argument values. Using an ArgTraits you can specify the way that
+ * values gets assigned to any particular type during parsing. The two
+ * supported types are StringLike and ValueLike.
+ */
+template<typename T>
+struct ArgTraits {
+    typedef typename T::ValueCategory ValueCategory;
+	virtual ~ArgTraits() {}
+    //typedef ValueLike ValueCategory;
+};
+
+#endif
+
+} // namespace

=== added file 'external/tclap/include/tclap/CmdLine.h'
--- external/tclap/include/tclap/CmdLine.h	1970-01-01 00:00:00 +0000
+++ external/tclap/include/tclap/CmdLine.h	2013-05-01 15:50:43 +0000
@@ -0,0 +1,633 @@
+// -*- Mode: c++; c-basic-offset: 4; tab-width: 4; -*-
+
+/******************************************************************************
+ *
+ *  file:  CmdLine.h
+ *
+ *  Copyright (c) 2003, Michael E. Smoot .
+ *  Copyright (c) 2004, Michael E. Smoot, Daniel Aarno.
+ *  All rights reverved.
+ *
+ *  See the file COPYING in the top directory of this distribution for
+ *  more information.
+ *
+ *  THE SOFTWARE IS PROVIDED _AS IS_, WITHOUT WARRANTY OF ANY KIND, EXPRESS
+ *  OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ *  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+ *  THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ *  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ *  FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ *  DEALINGS IN THE SOFTWARE.
+ *
+ *****************************************************************************/
+
+#ifndef TCLAP_CMDLINE_H
+#define TCLAP_CMDLINE_H
+
+#include <tclap/SwitchArg.h>
+#include <tclap/MultiSwitchArg.h>
+#include <tclap/UnlabeledValueArg.h>
+#include <tclap/UnlabeledMultiArg.h>
+
+#include <tclap/XorHandler.h>
+#include <tclap/HelpVisitor.h>
+#include <tclap/VersionVisitor.h>
+#include <tclap/IgnoreRestVisitor.h>
+
+#include <tclap/CmdLineOutput.h>
+#include <tclap/StdOutput.h>
+
+#include <tclap/Constraint.h>
+#include <tclap/ValuesConstraint.h>
+
+#include <string>
+#include <vector>
+#include <list>
+#include <iostream>
+#include <iomanip>
+#include <algorithm>
+#include <stdlib.h> // Needed for exit(), which isn't defined in some envs.
+
+namespace TCLAP {
+
+template<typename T> void DelPtr(T ptr)
+{
+	delete ptr;
+}
+
+template<typename C> void ClearContainer(C &c)
+{
+	typedef typename C::value_type value_type;
+	std::for_each(c.begin(), c.end(), DelPtr<value_type>);
+	c.clear();
+}
+
+
+/**
+ * The base class that manages the command line definition and passes
+ * along the parsing to the appropriate Arg classes.
+ */
+class CmdLine : public CmdLineInterface
+{
+	protected:
+
+		/**
+		 * The list of arguments that will be tested against the
+		 * command line.
+		 */
+		std::list<Arg*> _argList;
+
+		/**
+		 * The name of the program.  Set to argv[0].
+		 */
+		std::string _progName;
+
+		/**
+		 * A message used to describe the program.  Used in the usage output.
+		 */
+		std::string _message;
+
+		/**
+		 * The version to be displayed with the --version switch.
+		 */
+		std::string _version;
+
+		/**
+		 * The number of arguments that are required to be present on
+		 * the command line. This is set dynamically, based on the
+		 * Args added to the CmdLine object.
+		 */
+		int _numRequired;
+
+		/**
+		 * The character that is used to separate the argument flag/name
+		 * from the value.  Defaults to ' ' (space).
+		 */
+		char _delimiter;
+
+		/**
+		 * The handler that manages xoring lists of args.
+		 */
+		XorHandler _xorHandler;
+
+		/**
+		 * A list of Args to be explicitly deleted when the destructor
+		 * is called.  At the moment, this only includes the three default
+		 * Args.
+		 */
+		std::list<Arg*> _argDeleteOnExitList;
+
+		/**
+		 * A list of Visitors to be explicitly deleted when the destructor
+		 * is called.  At the moment, these are the Vistors created for the
+		 * default Args.
+		 */
+		std::list<Visitor*> _visitorDeleteOnExitList;
+
+		/**
+		 * Object that handles all output for the CmdLine.
+		 */
+		CmdLineOutput* _output;
+
+		/**
+		 * Should CmdLine handle parsing exceptions internally?
+		 */
+		bool _handleExceptions;
+
+		/**
+		 * Throws an exception listing the missing args.
+		 */
+		void missingArgsException();
+
+		/**
+		 * Checks whether a name/flag string matches entirely matches
+		 * the Arg::blankChar.  Used when multiple switches are combined
+		 * into a single argument.
+		 * \param s - The message to be used in the usage.
+		 */
+		bool _emptyCombined(const std::string& s);
+
+		/**
+		 * Perform a delete ptr; operation on ptr when this object is deleted.
+		 */
+		void deleteOnExit(Arg* ptr);
+
+		/**
+		 * Perform a delete ptr; operation on ptr when this object is deleted.
+		 */
+		void deleteOnExit(Visitor* ptr);
+
+private:
+
+		/**
+		 * Prevent accidental copying.
+		 */
+		CmdLine(const CmdLine& rhs);
+		CmdLine& operator=(const CmdLine& rhs);
+
+		/**
+		 * Encapsulates the code common to the constructors
+		 * (which is all of it).
+		 */
+		void _constructor();
+
+
+		/**
+		 * Is set to true when a user sets the output object. We use this so
+		 * that we don't delete objects that are created outside of this lib.
+		 */
+		bool _userSetOutput;
+
+		/**
+		 * Whether or not to automatically create help and version switches.
+		 */
+		bool _helpAndVersion;
+
+	public:
+
+		/**
+		 * Command line constructor. Defines how the arguments will be
+		 * parsed.
+		 * \param message - The message to be used in the usage
+		 * output.
+		 * \param delimiter - The character that is used to separate
+		 * the argument flag/name from the value.  Defaults to ' ' (space).
+		 * \param version - The version number to be used in the
+		 * --version switch.
+		 * \param helpAndVersion - Whether or not to create the Help and
+		 * Version switches. Defaults to true.
+		 */
+		CmdLine(const std::string& message,
+				const char delimiter = ' ',
+				const std::string& version = "none",
+				bool helpAndVersion = true);
+
+		/**
+		 * Deletes any resources allocated by a CmdLine object.
+		 */
+		virtual ~CmdLine();
+
+		/**
+		 * Adds an argument to the list of arguments to be parsed.
+		 * \param a - Argument to be added.
+		 */
+		void add( Arg& a );
+
+		/**
+		 * An alternative add.  Functionally identical.
+		 * \param a - Argument to be added.
+		 */
+		void add( Arg* a );
+
+		/**
+		 * Add two Args that will be xor'd.  If this method is used, add does
+		 * not need to be called.
+		 * \param a - Argument to be added and xor'd.
+		 * \param b - Argument to be added and xor'd.
+		 */
+		void xorAdd( Arg& a, Arg& b );
+
+		/**
+		 * Add a list of Args that will be xor'd.  If this method is used,
+		 * add does not need to be called.
+		 * \param xors - List of Args to be added and xor'd.
+		 */
+		void xorAdd( std::vector<Arg*>& xors );
+
+		/**
+		 * Parses the command line.
+		 * \param argc - Number of arguments.
+		 * \param argv - Array of arguments.
+		 */
+		void parse(int argc, const char * const * argv);
+
+		/**
+		 * Parses the command line.
+		 * \param args - A vector of strings representing the args.
+		 * args[0] is still the program name.
+		 */
+		void parse(std::vector<std::string>& args);
+
+		/**
+		 *
+		 */
+		CmdLineOutput* getOutput();
+
+		/**
+		 *
+		 */
+		void setOutput(CmdLineOutput* co);
+
+		/**
+		 *
+		 */
+		std::string& getVersion();
+
+		/**
+		 *
+		 */
+		std::string& getProgramName();
+
+		/**
+		 *
+		 */
+		std::list<Arg*>& getArgList();
+
+		/**
+		 *
+		 */
+		XorHandler& getXorHandler();
+
+		/**
+		 *
+		 */
+		char getDelimiter();
+
+		/**
+		 *
+		 */
+		std::string& getMessage();
+
+		/**
+		 *
+		 */
+		bool hasHelpAndVersion();
+
+		/**
+		 * Disables or enables CmdLine's internal parsing exception handling.
+		 *
+		 * @param state Should CmdLine handle parsing exceptions internally?
+		 */
+		void setExceptionHandling(const bool state);
+
+		/**
+		 * Returns the current state of the internal exception handling.
+		 *
+		 * @retval true Parsing exceptions are handled internally.
+		 * @retval false Parsing exceptions are propagated to the caller.
+		 */
+		bool getExceptionHandling() const;
+
+		/**
+		 * Allows the CmdLine object to be reused.
+		 */
+		void reset();
+
+};
+
+
+///////////////////////////////////////////////////////////////////////////////
+//Begin CmdLine.cpp
+///////////////////////////////////////////////////////////////////////////////
+
+inline CmdLine::CmdLine(const std::string& m,
+                        char delim,
+                        const std::string& v,
+                        bool help )
+    :
+  _argList(std::list<Arg*>()),
+  _progName("not_set_yet"),
+  _message(m),
+  _version(v),
+  _numRequired(0),
+  _delimiter(delim),
+  _xorHandler(XorHandler()),
+  _argDeleteOnExitList(std::list<Arg*>()),
+  _visitorDeleteOnExitList(std::list<Visitor*>()),
+  _output(0),
+  _handleExceptions(true),
+  _userSetOutput(false),
+  _helpAndVersion(help)
+{
+	_constructor();
+}
+
+inline CmdLine::~CmdLine()
+{
+	ClearContainer(_argDeleteOnExitList);
+	ClearContainer(_visitorDeleteOnExitList);
+
+	if ( !_userSetOutput ) {
+		delete _output;
+		_output = 0;
+	}
+}
+
+inline void CmdLine::_constructor()
+{
+	_output = new StdOutput;
+
+	Arg::setDelimiter( _delimiter );
+
+	Visitor* v;
+
+	if ( _helpAndVersion )
+	{
+		v = new HelpVisitor( this, &_output );
+		SwitchArg* help = new SwitchArg("h","help",
+		                      "Displays usage information and exits.",
+		                      false, v);
+		add( help );
+		deleteOnExit(help);
+		deleteOnExit(v);
+
+		v = new VersionVisitor( this, &_output );
+		SwitchArg* vers = new SwitchArg("","version",
+		                      "Displays version information and exits.",
+		                      false, v);
+		add( vers );
+		deleteOnExit(vers);
+		deleteOnExit(v);
+	}
+
+	v = new IgnoreRestVisitor();
+	SwitchArg* ignore  = new SwitchArg(Arg::flagStartString(),
+	          Arg::ignoreNameString(),
+	          "Ignores the rest of the labeled arguments following this flag.",
+	          false, v);
+	add( ignore );
+	deleteOnExit(ignore);
+	deleteOnExit(v);
+}
+
+inline void CmdLine::xorAdd( std::vector<Arg*>& ors )
+{
+	_xorHandler.add( ors );
+
+	for (ArgVectorIterator it = ors.begin(); it != ors.end(); it++)
+	{
+		(*it)->forceRequired();
+		(*it)->setRequireLabel( "OR required" );
+		add( *it );
+	}
+}
+
+inline void CmdLine::xorAdd( Arg& a, Arg& b )
+{
+	std::vector<Arg*> ors;
+	ors.push_back( &a );
+	ors.push_back( &b );
+	xorAdd( ors );
+}
+
+inline void CmdLine::add( Arg& a )
+{
+	add( &a );
+}
+
+inline void CmdLine::add( Arg* a )
+{
+	for( ArgListIterator it = _argList.begin(); it != _argList.end(); it++ )
+		if ( *a == *(*it) )
+			throw( SpecificationException(
+			        "Argument with same flag/name already exists!",
+			        a->longID() ) );
+
+	a->addToList( _argList );
+
+	if ( a->isRequired() )
+		_numRequired++;
+}
+
+
+inline void CmdLine::parse(int argc, const char * const * argv)
+{
+		// this step is necessary so that we have easy access to
+		// mutable strings.
+		std::vector<std::string> args;
+		for (int i = 0; i < argc; i++)
+			args.push_back(argv[i]);
+
+		parse(args);
+}
+
+inline void CmdLine::parse(std::vector<std::string>& args)
+{
+	bool shouldExit = false;
+	int estat = 0;
+
+	try {
+		_progName = args.front();
+		args.erase(args.begin());
+
+		int requiredCount = 0;
+
+		for (int i = 0; static_cast<unsigned int>(i) < args.size(); i++) 
+		{
+			bool matched = false;
+			for (ArgListIterator it = _argList.begin();
+			     it != _argList.end(); it++) {
+				if ( (*it)->processArg( &i, args ) )
+				{
+					requiredCount += _xorHandler.check( *it );
+					matched = true;
+					break;
+				}
+			}
+
+			// checks to see if the argument is an empty combined
+			// switch and if so, then we've actually matched it
+			if ( !matched && _emptyCombined( args[i] ) )
+				matched = true;
+
+			if ( !matched && !Arg::ignoreRest() )
+				throw(CmdLineParseException("Couldn't find match "
+				                            "for argument",
+				                            args[i]));
+		}
+
+		if ( requiredCount < _numRequired )
+			missingArgsException();
+
+		if ( requiredCount > _numRequired )
+			throw(CmdLineParseException("Too many arguments!"));
+
+	} catch ( ArgException& e ) {
+		// If we're not handling the exceptions, rethrow.
+		if ( !_handleExceptions) {
+			throw;
+		}
+
+		try {
+			_output->failure(*this,e);
+		} catch ( ExitException &ee ) {
+			estat = ee.getExitStatus();
+			shouldExit = true;
+		}
+	} catch (ExitException &ee) {
+		// If we're not handling the exceptions, rethrow.
+		if ( !_handleExceptions) {
+			throw;
+		}
+
+		estat = ee.getExitStatus();
+		shouldExit = true;
+	}
+
+	if (shouldExit)
+		exit(estat);
+}
+
+inline bool CmdLine::_emptyCombined(const std::string& s)
+{
+	if ( s.length() > 0 && s[0] != Arg::flagStartChar() )
+		return false;
+
+	for ( int i = 1; static_cast<unsigned int>(i) < s.length(); i++ )
+		if ( s[i] != Arg::blankChar() )
+			return false;
+
+	return true;
+}
+
+inline void CmdLine::missingArgsException()
+{
+		int count = 0;
+
+		std::string missingArgList;
+		for (ArgListIterator it = _argList.begin(); it != _argList.end(); it++)
+		{
+			if ( (*it)->isRequired() && !(*it)->isSet() )
+			{
+				missingArgList += (*it)->getName();
+				missingArgList += ", ";
+				count++;
+			}
+		}
+		missingArgList = missingArgList.substr(0,missingArgList.length()-2);
+
+		std::string msg;
+		if ( count > 1 )
+			msg = "Required arguments missing: ";
+		else
+			msg = "Required argument missing: ";
+
+		msg += missingArgList;
+
+		throw(CmdLineParseException(msg));
+}
+
+inline void CmdLine::deleteOnExit(Arg* ptr)
+{
+	_argDeleteOnExitList.push_back(ptr);
+}
+
+inline void CmdLine::deleteOnExit(Visitor* ptr)
+{
+	_visitorDeleteOnExitList.push_back(ptr);
+}
+
+inline CmdLineOutput* CmdLine::getOutput()
+{
+	return _output;
+}
+
+inline void CmdLine::setOutput(CmdLineOutput* co)
+{
+	if ( !_userSetOutput )
+		delete _output;
+	_userSetOutput = true;
+	_output = co;
+}
+
+inline std::string& CmdLine::getVersion()
+{
+	return _version;
+}
+
+inline std::string& CmdLine::getProgramName()
+{
+	return _progName;
+}
+
+inline std::list<Arg*>& CmdLine::getArgList()
+{
+	return _argList;
+}
+
+inline XorHandler& CmdLine::getXorHandler()
+{
+	return _xorHandler;
+}
+
+inline char CmdLine::getDelimiter()
+{
+	return _delimiter;
+}
+
+inline std::string& CmdLine::getMessage()
+{
+	return _message;
+}
+
+inline bool CmdLine::hasHelpAndVersion()
+{
+	return _helpAndVersion;
+}
+
+inline void CmdLine::setExceptionHandling(const bool state)
+{
+	_handleExceptions = state;
+}
+
+inline bool CmdLine::getExceptionHandling() const
+{
+	return _handleExceptions;
+}
+
+inline void CmdLine::reset()
+{
+	for( ArgListIterator it = _argList.begin(); it != _argList.end(); it++ )
+		(*it)->reset();
+	
+	_progName.clear();
+}
+
+///////////////////////////////////////////////////////////////////////////////
+//End CmdLine.cpp
+///////////////////////////////////////////////////////////////////////////////
+
+
+
+} //namespace TCLAP
+#endif

=== added file 'external/tclap/include/tclap/CmdLineInterface.h'
--- external/tclap/include/tclap/CmdLineInterface.h	1970-01-01 00:00:00 +0000
+++ external/tclap/include/tclap/CmdLineInterface.h	2013-05-01 15:50:43 +0000
@@ -0,0 +1,150 @@
+
+/****************************************************************************** 
+ * 
+ *  file:  CmdLineInterface.h
+ * 
+ *  Copyright (c) 2003, Michael E. Smoot .
+ *  Copyright (c) 2004, Michael E. Smoot, Daniel Aarno.
+ *  All rights reverved.
+ *
+ *  See the file COPYING in the top directory of this distribution for
+ *  more information.
+ *  
+ *  THE SOFTWARE IS PROVIDED _AS IS_, WITHOUT WARRANTY OF ANY KIND, EXPRESS 
+ *  OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 
+ *  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL 
+ *  THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 
+ *  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING 
+ *  FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER 
+ *  DEALINGS IN THE SOFTWARE.  
+ *  
+ *****************************************************************************/ 
+
+#ifndef TCLAP_COMMANDLINE_INTERFACE_H
+#define TCLAP_COMMANDLINE_INTERFACE_H
+
+#include <string>
+#include <vector>
+#include <list>
+#include <iostream>
+#include <algorithm>
+
+
+namespace TCLAP {
+     
+class Arg;
+class CmdLineOutput;
+class XorHandler;
+
+/**
+ * The base class that manages the command line definition and passes
+ * along the parsing to the appropriate Arg classes.
+ */
+class CmdLineInterface
+{
+	public:
+
+		/**
+		 * Destructor
+		 */
+		virtual ~CmdLineInterface() {}
+
+		/**
+		 * Adds an argument to the list of arguments to be parsed.
+		 * \param a - Argument to be added. 
+		 */
+		virtual void add( Arg& a )=0;
+
+		/**
+		 * An alternative add.  Functionally identical.
+		 * \param a - Argument to be added. 
+		 */
+		virtual void add( Arg* a )=0;
+
+		/**
+		 * Add two Args that will be xor'd.  
+		 * If this method is used, add does
+		 * not need to be called.
+		 * \param a - Argument to be added and xor'd. 
+		 * \param b - Argument to be added and xor'd. 
+		 */
+		virtual void xorAdd( Arg& a, Arg& b )=0;
+
+		/**
+		 * Add a list of Args that will be xor'd.  If this method is used, 
+		 * add does not need to be called.
+		 * \param xors - List of Args to be added and xor'd. 
+		 */
+		virtual void xorAdd( std::vector<Arg*>& xors )=0;
+
+		/**
+		 * Parses the command line.
+		 * \param argc - Number of arguments.