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, 133 deletions

diff --git a/tools/closure_linter-2.3.4/closure_linter/errors.py b/tools/closure_linter-2.3.4/closure_linter/errors.py
deleted file mode 100755
index 9e9a8f0..0000000
--- a/tools/closure_linter-2.3.4/closure_linter/errors.py
+++ /dev/null
@@ -1,133 +0,0 @@
-#!/usr/bin/env python
-#
-# Copyright 2007 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.
-
-"""Error codes for JavaScript style checker."""
-
-__author__ = ('robbyw@google.com (Robert Walker)',
-              'ajp@google.com (Andy Perelson)')
-
-
-def ByName(name):
-  """Get the error code for the given error name.
-
-  Args:
-    name: The name of the error
-
-  Returns:
-    The error code
-  """
-  return globals()[name]
-
-
-# "File-fatal" errors - these errors stop further parsing of a single file
-FILE_NOT_FOUND = -1
-FILE_DOES_NOT_PARSE = -2
-
-# Spacing
-EXTRA_SPACE = 1
-MISSING_SPACE = 2
-EXTRA_LINE = 3
-MISSING_LINE = 4
-ILLEGAL_TAB = 5
-WRONG_INDENTATION = 6
-WRONG_BLANK_LINE_COUNT = 7
-
-# Semicolons
-MISSING_SEMICOLON = 10
-MISSING_SEMICOLON_AFTER_FUNCTION = 11
-ILLEGAL_SEMICOLON_AFTER_FUNCTION = 12
-REDUNDANT_SEMICOLON = 13
-
-# Miscellaneous
-ILLEGAL_PROTOTYPE_MEMBER_VALUE = 100
-LINE_TOO_LONG = 110
-LINE_STARTS_WITH_OPERATOR = 120
-COMMA_AT_END_OF_LITERAL = 121
-MULTI_LINE_STRING = 130
-UNNECESSARY_DOUBLE_QUOTED_STRING = 131
-
-# Requires, provides
-GOOG_REQUIRES_NOT_ALPHABETIZED = 140
-GOOG_PROVIDES_NOT_ALPHABETIZED = 141
-MISSING_GOOG_REQUIRE = 142
-MISSING_GOOG_PROVIDE = 143
-EXTRA_GOOG_REQUIRE = 144
-EXTRA_GOOG_PROVIDE = 145
-
-# JsDoc
-INVALID_JSDOC_TAG = 200
-INVALID_USE_OF_DESC_TAG = 201
-NO_BUG_NUMBER_AFTER_BUG_TAG = 202
-MISSING_PARAMETER_DOCUMENTATION = 210
-EXTRA_PARAMETER_DOCUMENTATION = 211
-WRONG_PARAMETER_DOCUMENTATION = 212
-MISSING_JSDOC_TAG_TYPE = 213
-MISSING_JSDOC_TAG_DESCRIPTION = 214
-MISSING_JSDOC_PARAM_NAME = 215
-OUT_OF_ORDER_JSDOC_TAG_TYPE = 216
-MISSING_RETURN_DOCUMENTATION = 217
-UNNECESSARY_RETURN_DOCUMENTATION = 218
-MISSING_BRACES_AROUND_TYPE = 219
-MISSING_MEMBER_DOCUMENTATION = 220
-MISSING_PRIVATE = 221
-EXTRA_PRIVATE = 222
-INVALID_OVERRIDE_PRIVATE = 223
-INVALID_INHERIT_DOC_PRIVATE = 224
-MISSING_JSDOC_TAG_THIS = 225
-UNNECESSARY_BRACES_AROUND_INHERIT_DOC = 226
-INVALID_AUTHOR_TAG_DESCRIPTION = 227
-JSDOC_PREFER_QUESTION_TO_PIPE_NULL = 230
-JSDOC_ILLEGAL_QUESTION_WITH_PIPE = 231
-JSDOC_MISSING_OPTIONAL_TYPE = 232
-JSDOC_MISSING_OPTIONAL_PREFIX = 233
-JSDOC_TAG_DESCRIPTION_ENDS_WITH_INVALID_CHARACTER = 240
-# TODO(robbyw): Split this in to more specific syntax problems.
-INCORRECT_SUPPRESS_SYNTAX = 250
-INVALID_SUPPRESS_TYPE = 251
-UNNECESSARY_SUPPRESS = 252
-
-# File ending
-FILE_MISSING_NEWLINE = 300
-FILE_IN_BLOCK = 301
-
-# Interfaces
-INTERFACE_CONSTRUCTOR_CANNOT_HAVE_PARAMS = 400
-INTERFACE_METHOD_CANNOT_HAVE_CODE = 401
-
-# ActionScript specific errors:
-# TODO(user): move these errors to their own file and move all JavaScript
-# specific errors to their own file as well.
-# All ActionScript specific errors should have error number at least 1000.
-FUNCTION_MISSING_RETURN_TYPE = 1132
-PARAMETER_MISSING_TYPE = 1133
-VAR_MISSING_TYPE = 1134
-PARAMETER_MISSING_DEFAULT_VALUE = 1135
-IMPORTS_NOT_ALPHABETIZED = 1140
-IMPORT_CONTAINS_WILDCARD = 1141
-UNUSED_IMPORT = 1142
-INVALID_TRACE_SEVERITY_LEVEL = 1250
-MISSING_TRACE_SEVERITY_LEVEL = 1251
-MISSING_TRACE_MESSAGE = 1252
-REMOVE_TRACE_BEFORE_SUBMIT = 1253
-REMOVE_COMMENT_BEFORE_SUBMIT = 1254
-# End of list of ActionScript specific errors.
-
-NEW_ERRORS = frozenset([
-    # Errors added after 2.0.2:
-    WRONG_INDENTATION,
-    MISSING_SEMICOLON,
-    # Errors added after 2.3.4:
-    ])