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, 262 deletions

diff --git a/tools/closure_linter-2.3.4/closure_linter/requireprovidesorter.py b/tools/closure_linter-2.3.4/closure_linter/requireprovidesorter.py
deleted file mode 100755
index dc0c63f..0000000
--- a/tools/closure_linter-2.3.4/closure_linter/requireprovidesorter.py
+++ /dev/null
@@ -1,262 +0,0 @@
-#!/usr/bin/env python
-#
-# Copyright 2011 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.
-
-"""Contains logic for sorting goog.provide and goog.require statements.
-
-Closurized JavaScript files use goog.provide and goog.require statements at the
-top of the file to manage dependencies. These statements should be sorted
-alphabetically, however, it is common for them to be accompanied by inline
-comments or suppression annotations. In order to sort these statements without
-disrupting their comments and annotations, the association between statements
-and comments/annotations must be maintained while sorting.
-
-  RequireProvideSorter: Handles checking/fixing of provide/require statements.
-"""
-
-
-
-from closure_linter import javascripttokens
-from closure_linter import tokenutil
-
-# Shorthand
-Type = javascripttokens.JavaScriptTokenType
-
-
-class RequireProvideSorter(object):
-  """Checks for and fixes alphabetization of provide and require statements.
-
-  When alphabetizing, comments on the same line or comments directly above a
-  goog.provide or goog.require statement are associated with that statement and
-  stay with the statement as it gets sorted.
-  """
-
-  def CheckProvides(self, token):
-    """Checks alphabetization of goog.provide statements.
-
-    Iterates over tokens in given token stream, identifies goog.provide tokens,
-    and checks that they occur in alphabetical order by the object being
-    provided.
-
-    Args:
-      token: A token in the token stream before any goog.provide tokens.
-
-    Returns:
-      A tuple containing the first provide token in the token stream and a list
-      of provided objects sorted alphabetically. For example:
-
-      (JavaScriptToken, ['object.a', 'object.b', ...])
-
-      None is returned if all goog.provide statements are already sorted.
-    """
-    provide_tokens = self._GetRequireOrProvideTokens(token, 'goog.provide')
-    provide_strings = self._GetRequireOrProvideTokenStrings(provide_tokens)
-    sorted_provide_strings = sorted(provide_strings)
-    if provide_strings != sorted_provide_strings:
-      return [provide_tokens[0], sorted_provide_strings]
-    return None
-
-  def CheckRequires(self, token):
-    """Checks alphabetization of goog.require statements.
-
-    Iterates over tokens in given token stream, identifies goog.require tokens,
-    and checks that they occur in alphabetical order by the dependency being
-    required.
-
-    Args:
-      token: A token in the token stream before any goog.require tokens.
-
-    Returns:
-      A tuple containing the first require token in the token stream and a list
-      of required dependencies sorted alphabetically. For example:
-
-      (JavaScriptToken, ['object.a', 'object.b', ...])
-
-      None is returned if all goog.require statements are already sorted.
-    """
-    require_tokens = self._GetRequireOrProvideTokens(token, 'goog.require')
-    require_strings = self._GetRequireOrProvideTokenStrings(require_tokens)
-    sorted_require_strings = sorted(require_strings)
-    if require_strings != sorted_require_strings:
-      return (require_tokens[0], sorted_require_strings)
-    return None
-
-  def FixProvides(self, token):
-    """Sorts goog.provide statements in the given token stream alphabetically.
-
-    Args:
-      token: The first token in the token stream.
-    """
-    self._FixProvidesOrRequires(
-        self._GetRequireOrProvideTokens(token, 'goog.provide'))
-
-  def FixRequires(self, token):
-    """Sorts goog.require statements in the given token stream alphabetically.
-
-    Args:
-      token: The first token in the token stream.
-    """
-    self._FixProvidesOrRequires(
-        self._GetRequireOrProvideTokens(token, 'goog.require'))
-
-  def _FixProvidesOrRequires(self, tokens):
-    """Sorts goog.provide or goog.require statements.
-
-    Args:
-      tokens: A list of goog.provide or goog.require tokens in the order they
-              appear in the token stream. i.e. the first token in this list must
-              be the first goog.provide or goog.require token.
-    """
-    strings = self._GetRequireOrProvideTokenStrings(tokens)
-    sorted_strings = sorted(strings)
-
-    # A map from required/provided object name to tokens that make up the line
-    # it was on, including any comments immediately before it or after it on the
-    # same line.
-    tokens_map = self._GetTokensMap(tokens)
-
-    # Iterate over the map removing all tokens.
-    for name in tokens_map:
-      tokens_to_delete = tokens_map[name]
-      for i in tokens_to_delete:
-        tokenutil.DeleteToken(i)
-
-    # Re-add all tokens in the map in alphabetical order.
-    insert_after = tokens[0].previous
-    for string in sorted_strings:
-      for i in tokens_map[string]:
-        tokenutil.InsertTokenAfter(i, insert_after)
-        insert_after = i
-
-  def _GetRequireOrProvideTokens(self, token, token_string):
-    """Gets all goog.provide or goog.require tokens in the given token stream.
-
-    Args:
-      token: The first token in the token stream.
-      token_string: One of 'goog.provide' or 'goog.require' to indicate which
-                    tokens to find.
-
-    Returns:
-      A list of goog.provide or goog.require tokens in the order they appear in
-      the token stream.
-    """
-    tokens = []
-    while token:
-      if token.type == Type.IDENTIFIER:
-        if token.string == token_string:
-          tokens.append(token)
-        elif token.string not in ['goog.require', 'goog.provide']:
-          # The goog.provide and goog.require identifiers are at the top of the
-          # file. So if any other identifier is encountered, return.
-          break
-      token = token.next
-
-    return tokens
-
-  def _GetRequireOrProvideTokenStrings(self, tokens):
-    """Gets a list of strings corresponding to the given list of tokens.
-
-    The string will be the next string in the token stream after each token in
-    tokens. This is used to find the object being provided/required by a given
-    goog.provide or goog.require token.
-
-    Args:
-      tokens: A list of goog.provide or goog.require tokens.
-
-    Returns:
-      A list of object names that are being provided or required by the given
-      list of tokens. For example:
-
-      ['object.a', 'object.c', 'object.b']
-    """
-    token_strings = []
-    for token in tokens:
-      name = tokenutil.Search(token, Type.STRING_TEXT).string
-      token_strings.append(name)
-    return token_strings
-
-  def _GetTokensMap(self, tokens):
-    """Gets a map from object name to tokens associated with that object.
-
-    Starting from the goog.provide/goog.require token, searches backwards in the
-    token stream for any lines that start with a comment. These lines are
-    associated with the goog.provide/goog.require token. Also associates any
-    tokens on the same line as the goog.provide/goog.require token with that
-    token.
-
-    Args:
-      tokens: A list of goog.provide or goog.require tokens.
-
-    Returns:
-      A dictionary that maps object names to the tokens associated with the
-      goog.provide or goog.require of that object name. For example:
-
-      {
-        'object.a': [JavaScriptToken, JavaScriptToken, ...],
-        'object.b': [...]
-      }
-
-      The list of tokens includes any comment lines above the goog.provide or
-      goog.require statement and everything after the statement on the same
-      line. For example, all of the following would be associated with
-      'object.a':
-
-      /** @suppress {extraRequire} */
-      goog.require('object.a'); // Some comment.
-    """
-    tokens_map = {}
-    for token in tokens:
-      object_name = tokenutil.Search(token, Type.STRING_TEXT).string
-      # If the previous line starts with a comment, presume that the comment
-      # relates to the goog.require or goog.provide and keep them together when
-      # sorting.
-      first_token = token
-      previous_first_token = tokenutil.GetFirstTokenInPreviousLine(first_token)
-      while previous_first_token.IsAnyType(Type.COMMENT_TYPES):
-        first_token = previous_first_token
-        previous_first_token = tokenutil.GetFirstTokenInPreviousLine(
-            first_token)
-
-      # Find the last token on the line.
-      last_token = tokenutil.GetLastTokenInSameLine(token)
-
-      all_tokens = self._GetTokenList(first_token, last_token)
-      tokens_map[object_name] = all_tokens
-    return tokens_map
-
-  def _GetTokenList(self, first_token, last_token):
-    """Gets a list of all tokens from first_token to last_token, inclusive.
-
-    Args:
-      first_token: The first token to get.
-      last_token: The last token to get.
-
-    Returns:
-      A list of all tokens between first_token and last_token, including both
-      first_token and last_token.
-
-    Raises:
-      Exception: If the token stream ends before last_token is reached.
-    """
-    token_list = []
-    token = first_token
-    while token != last_token:
-      if not token:
-        raise Exception('ran out of tokens')
-      token_list.append(token)
-      token = token.next
-    token_list.append(last_token)
-
-    return token_list