Remove google closure, and start reworking the build system

Squashed commit of the following:

commit 446aae2afd089c28abd1d03a5fd20d4735837e16
Author: Trevor Elliott <trevor@galois.com>
Date:   Thu May 16 11:50:17 2013 -0700

    stage-dir doesn't need to be cleaned

      Since everything goes into a common build tree now, cleaning just
    involves removing the entire build tree.

commit d8f531ddf8ee1406ec915502c28dc0eb3912d0ee
Author: Trevor Elliott <trevor@galois.com>
Date:   Thu May 16 11:47:10 2013 -0700

    Switch to placing build artifacts in a build tree

commit 9eedeec8d6a1012b1b7e466120260276b1e952d4
Author: Trevor Elliott <trevor@galois.com>
Date:   Thu May 16 11:35:01 2013 -0700

    Remove the closure_compiler and closure_linter

commit 5784158cf2cd55f0ffd01147ae014379ecc857fd
Author: Trevor Elliott <trevor@galois.com>
Date:   Thu May 16 11:34:27 2013 -0700

    Move the scripts in build to tools/bin

commit 64a6a53ea0fd5e299e9d17c0e4f8fedf305272dc
Author: Trevor Elliott <trevor@galois.com>
Date:   Thu May 16 11:27:55 2013 -0700

    Build jsdoc

      Also, remove the old Makefiles that were in doc, as they're not necessary
    anymore.

commit 1ef0d9e39cd4a24807ee6ca956fbc627fb851b9d
Author: Trevor Elliott <trevor@galois.com>
Date:   Thu May 16 11:18:59 2013 -0700

    Conditionally build the manual

commit c326c58059e0d5035edecfd6261ee42797c49c2c
Author: Trevor Elliott <trevor@galois.com>
Date:   Thu May 16 11:13:31 2013 -0700

    Get the html manual building again

commit 480fa132ffb0562eb3f61d45d79d3315b1d3cc29
Author: Trevor Elliott <trevor@galois.com>
Date:   Thu May 16 11:13:01 2013 -0700

    Move doc specific .gitignore stuff to doc/.gitignore

commit 8c108d4e0df848839bcd6b4c22d623053f590e95
Author: Trevor Elliott <trevor@galois.com>
Date:   Wed May 15 10:42:41 2013 -0700

    Fix some path inconsistencies in the contexts build.mk

commit ee53404be09cf26983365374da84ade564b92926
Author: Trevor Elliott <trevor@galois.com>
Date:   Wed May 15 10:37:40 2013 -0700

    Preliminary build system changes

     * Chrome extension builds, but there are problems

commit 474c6b88190787aeffd960ffb5855d31770e7141
Author: Trevor Elliott <trevor@galois.com>
Date:   Mon May 13 19:06:31 2013 -0700

    Remove the closure toolkit

1 files changed, 0 insertions, 190 deletions

diff --git a/tools/closure_linter-2.3.4/closure_linter/common/simplefileflags.py b/tools/closure_linter-2.3.4/closure_linter/common/simplefileflags.py
deleted file mode 100755
index 3402bef..0000000
--- a/tools/closure_linter-2.3.4/closure_linter/common/simplefileflags.py
+++ /dev/null
@@ -1,190 +0,0 @@
-#!/usr/bin/env python
-#
-# Copyright 2008 The Closure Linter Authors. All Rights Reserved.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#      http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS-IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-"""Determines the list of files to be checked from command line arguments."""
-
-__author__ = ('robbyw@google.com (Robert Walker)',
-              'ajp@google.com (Andy Perelson)')
-
-import glob
-import os
-import re
-
-import gflags as flags
-
-
-FLAGS = flags.FLAGS
-
-flags.DEFINE_multistring(
-    'recurse',
-    None,
-    'Recurse in to the subdirectories of the given path',
-    short_name='r')
-flags.DEFINE_list(
-    'exclude_directories',
-    ('_demos'),
-    'Exclude the specified directories (only applicable along with -r or '
-    '--presubmit)',
-    short_name='e')
-flags.DEFINE_list(
-    'exclude_files',
-    ('deps.js'),
-    'Exclude the specified files',
-    short_name='x')
-
-
-def MatchesSuffixes(filename, suffixes):
-  """Returns whether the given filename matches one of the given suffixes.
-
-  Args:
-    filename: Filename to check.
-    suffixes: Sequence of suffixes to check.
-
-  Returns:
-    Whether the given filename matches one of the given suffixes.
-  """
-  suffix = filename[filename.rfind('.'):]
-  return suffix in suffixes
-
-
-def _GetUserSpecifiedFiles(argv, suffixes):
-  """Returns files to be linted, specified directly on the command line.
-
-  Can handle the '*' wildcard in filenames, but no other wildcards.
-
-  Args:
-    argv: Sequence of command line arguments. The second and following arguments
-      are assumed to be files that should be linted.
-    suffixes: Expected suffixes for the file type being checked.
-
-  Returns:
-    A sequence of files to be linted.
-  """
-  files = argv[1:] or []
-  all_files = []
-  lint_files = []
-
-   # Perform any necessary globs.
-  for f in files:
-    if f.find('*') != -1:
-      for result in glob.glob(f):
-        all_files.append(result)
-    else:
-      all_files.append(f)
-
-  for f in all_files:
-    if MatchesSuffixes(f, suffixes):
-      lint_files.append(f)
-  return lint_files
-
-
-def _GetRecursiveFiles(suffixes):
-  """Returns files to be checked specified by the --recurse flag.
-
-  Args:
-    suffixes: Expected suffixes for the file type being checked.
-
-  Returns:
-    A list of files to be checked.
-  """
-  lint_files = []
-  # Perform any request recursion
-  if FLAGS.recurse:
-    for start in FLAGS.recurse:
-      for root, subdirs, files in os.walk(start):
-        for f in files:
-          if MatchesSuffixes(f, suffixes):
-            lint_files.append(os.path.join(root, f))
-  return lint_files
-
-
-def GetAllSpecifiedFiles(argv, suffixes):
-  """Returns all files specified by the user on the commandline.
-
-  Args:
-    argv: Sequence of command line arguments. The second and following arguments
-      are assumed to be files that should be linted.
-    suffixes: Expected suffixes for the file type
-
-  Returns:
-    A list of all files specified directly or indirectly (via flags) on the
-    command line by the user.
-  """
-  files = _GetUserSpecifiedFiles(argv, suffixes)
-
-  if FLAGS.recurse:
-    files += _GetRecursiveFiles(suffixes)
-
-  return FilterFiles(files)
-
-
-def FilterFiles(files):
-  """Filters the list of files to be linted be removing any excluded files.
-
-  Filters out files excluded using --exclude_files and  --exclude_directories.
-
-  Args:
-    files: Sequence of files that needs filtering.
-
-  Returns:
-    Filtered list of files to be linted.
-  """
-  num_files = len(files)
-
-  ignore_dirs_regexs = []
-  for ignore in FLAGS.exclude_directories:
-    ignore_dirs_regexs.append(re.compile(r'(^|[\\/])%s[\\/]' % ignore))
-
-  result_files = []
-  for f in files:
-    add_file = True
-    for exclude in FLAGS.exclude_files:
-      if f.endswith('/' + exclude) or f == exclude:
-        add_file = False
-        break
-    for ignore in ignore_dirs_regexs:
-      if ignore.search(f):
-        # Break out of ignore loop so we don't add to
-        # filtered files.
-        add_file = False
-        break
-    if add_file:
-      # Convert everything to absolute paths so we can easily remove duplicates
-      # using a set.
-      result_files.append(os.path.abspath(f))
-
-  skipped = num_files - len(result_files)
-  if skipped:
-    print 'Skipping %d file(s).' % skipped
-
-  return set(result_files)
-
-
-def GetFileList(argv, file_type, suffixes):
-  """Parse the flags and return the list of files to check.
-
-  Args:
-    argv: Sequence of command line arguments.
-    suffixes: Sequence of acceptable suffixes for the file type.
-
-  Returns:
-    The list of files to check.
-  """
-  return sorted(GetAllSpecifiedFiles(argv, suffixes))
-
-
-def IsEmptyArgumentList(argv):
-  return not (len(argv[1:]) or FLAGS.recurse)