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, 116 deletions

diff --git a/tools/closure_linter-2.3.4/closure_linter/javascriptstatetracker.py b/tools/closure_linter-2.3.4/closure_linter/javascriptstatetracker.py
deleted file mode 100755
index 2ce5c02..0000000
--- a/tools/closure_linter-2.3.4/closure_linter/javascriptstatetracker.py
+++ /dev/null
@@ -1,116 +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.
-
-"""Parser for JavaScript files."""
-
-
-
-from closure_linter import javascripttokens
-from closure_linter import statetracker
-from closure_linter import tokenutil
-
-# Shorthand
-Type = javascripttokens.JavaScriptTokenType
-
-
-class JsDocFlag(statetracker.DocFlag):
-  """Javascript doc flag object.
-
-  Attribute:
-    flag_type: param, return, define, type, etc.
-    flag_token: The flag token.
-    type_start_token: The first token specifying the flag JS type,
-      including braces.
-    type_end_token: The last token specifying the flag JS type,
-      including braces.
-    type: The JavaScript type spec.
-    name_token: The token specifying the flag name.
-    name: The flag name
-    description_start_token: The first token in the description.
-    description_end_token: The end token in the description.
-    description: The description.
-  """
-
-  # Please keep these lists alphabetized.
-
-  # Some projects use the following extensions to JsDoc.
-  # TODO(robbyw): determine which of these, if any, should be illegal.
-  EXTENDED_DOC = frozenset([
-      'class', 'code', 'desc', 'final', 'hidden', 'inheritDoc', 'link',
-      'meaning', 'protected', 'notypecheck', 'throws'])
-
-  LEGAL_DOC = EXTENDED_DOC | statetracker.DocFlag.LEGAL_DOC
-
-  def __init__(self, flag_token):
-    """Creates the JsDocFlag object and attaches it to the given start token.
-
-    Args:
-      flag_token: The starting token of the flag.
-    """
-    statetracker.DocFlag.__init__(self, flag_token)
-
-
-class JavaScriptStateTracker(statetracker.StateTracker):
-  """JavaScript state tracker.
-
-  Inherits from the core EcmaScript StateTracker adding extra state tracking
-  functionality needed for JavaScript.
-  """
-
-  def __init__(self):
-    """Initializes a JavaScript token stream state tracker."""
-    statetracker.StateTracker.__init__(self, JsDocFlag)
-
-  def InTopLevel(self):
-    """Compute whether we are at the top level in the class.
-
-    This function call is language specific.  In some languages like
-    JavaScript, a function is top level if it is not inside any parenthesis.
-    In languages such as ActionScript, a function is top level if it is directly
-    within a class.
-
-    Returns:
-      Whether we are at the top level in the class.
-    """
-    return not self.InParentheses()
-
-  def GetBlockType(self, token):
-    """Determine the block type given a START_BLOCK token.
-
-    Code blocks come after parameters, keywords  like else, and closing parens.
-
-    Args:
-      token: The current token. Can be assumed to be type START_BLOCK
-    Returns:
-      Code block type for current token.
-    """
-    last_code = tokenutil.SearchExcept(token, Type.NON_CODE_TYPES, None,
-                                       True)
-    if last_code.type in (Type.END_PARAMETERS, Type.END_PAREN,
-                          Type.KEYWORD) and not last_code.IsKeyword('return'):
-      return self.CODE
-    else:
-      return self.OBJECT_LITERAL
-
-  def HandleToken(self, token, last_non_space_token):
-    """Handles the given token and updates state.
-
-    Args:
-      token: The token to handle.
-      last_non_space_token:
-    """
-    super(JavaScriptStateTracker, self).HandleToken(token,
-                                                    last_non_space_token)