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, 292 deletions

diff --git a/tools/closure_compiler/README b/tools/closure_compiler/README
deleted file mode 100644
index e6d12c4..0000000
--- a/tools/closure_compiler/README
+++ /dev/null
@@ -1,292 +0,0 @@
-/*
- * Copyright 2009 The Closure Compiler Authors.
- *
- * 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.
- */
-
-//
-// Contents
-//
-
-The Closure Compiler performs checking, instrumentation, and
-optimizations on JavaScript code. The purpose of this README is to
-explain how to build and run the Closure Compiler.
-
-The Closure Compiler requires Java 6 or higher.
-http://www.java.com/
-
-
-//
-// Building The Closure Compiler
-//
-
-There are three ways to get a Closure Compiler executable.
-
-1) Use one we built for you.
-
-Pre-built Closure binaries can be found at
-http://code.google.com/p/closure-compiler/downloads/list
-
-
-2) Check out the source and build it with Apache Ant.
-
-First, check out the full source tree of the Closure Compiler. There
-are instructions on how to do this at the project site.
-http://code.google.com/p/closure-compiler/source/checkout
-
-Apache Ant is a cross-platform build tool.
-http://ant.apache.org/
-
-At the root of the source tree, there is an Ant file named
-build.xml. To use it, navigate to the same directory and type the
-command
-
-ant jar
-
-This will produce a jar file called "build/compiler.jar".
-
-
-3) Check out the source and build it with Eclipse.
-
-Eclipse is a cross-platform IDE.
-http://www.eclipse.org/
-
-Under Eclipse's File menu, click "New > Project ..." and create a
-"Java Project."  You will see an options screen. Give the project a
-name, select "Create project from existing source," and choose the
-root of the checked-out source tree as the existing directory. Verify
-that you are using JRE version 6 or higher.
-
-Eclipse can use the build.xml file to discover rules. When you
-navigate to the build.xml file, you will see all the build rules in
-the "Outline" pane. Run the "jar" rule to build the compiler in
-build/compiler.jar.
-
-
-//
-// Running The Closure Compiler
-//
-
-Once you have the jar binary, running the Closure Compiler is straightforward.
-
-On the command line, type
-
-java -jar compiler.jar
-
-This starts the compiler in interactive mode. Type
-
-var x = 17 + 25;
-
-then hit "Enter", then hit "Ctrl-Z" (on Windows) or "Ctrl-D" (on Mac or Linux)
-and "Enter" again. The Compiler will respond:
-
-var x=42;
-
-The Closure Compiler has many options for reading input from a file,
-writing output to a file, checking your code, and running
-optimizations. To learn more, type
-
-java -jar compiler.jar --help
-
-You can read more detailed documentation about the many flags at
-http://code.google.com/closure/compiler/docs/gettingstarted_app.html
-
-
-//
-// Compiling Multiple Scripts
-//
-
-If you have multiple scripts, you should compile them all together with
-one compile command.
-
-java -jar compiler.jar --js=in1.js --js=in2.js ... --js_output_file=out.js
-
-The Closure Compiler will concatenate the files in the order they're
-passed at the command line.
-
-If you need to compile many, many scripts together, you may start to
-run into problems with managing dependencies between scripts. You
-should check out the Closure Library. It contains functions for
-enforcing dependencies between scripts, and a tool called calcdeps.py
-that knows how to give scripts to the Closure Compiler in the right
-order.
-
-http://code.google.com/p/closure-library/
-
-//
-// Licensing
-//
-
-Unless otherwise stated, all source files are licensed under
-the Apache License, Version 2.0.
-
-
------
-Code under:
-src/com/google/javascript/rhino
-test/com/google/javascript/rhino
-
-URL: http://www.mozilla.org/rhino
-Version:  1.5R3, with heavy modifications
-License:  Netscape Public License and MPL / GPL dual license
-
-Description: A partial copy of Mozilla Rhino. Mozilla Rhino is an
-implementation of JavaScript for the JVM.  The JavaScript parser and
-the parse tree data structures were extracted and modified
-significantly for use by Google's JavaScript compiler.
-
-Local Modifications: The packages have been renamespaced. All code not
-relavant to parsing has been removed. A JSDoc parser and static typing
-system have been added.
-
-
------
-Code in:
-lib/rhino
-
-Rhino
-URL: http://www.mozilla.org/rhino
-Version:  Trunk
-License:  Netscape Public License and MPL / GPL dual license
-
-Description: Mozilla Rhino is an implementation of JavaScript for the JVM.
-
-Local Modifications: Minor changes to parsing JSDoc that usually get pushed
-up-stream to Rhino trunk.
-
-
------
-Code in:
-lib/args4j.jar
-
-Args4j
-URL: https://args4j.dev.java.net/
-Version: 2.0.12
-License: MIT
-
-Description:
-args4j is a small Java class library that makes it easy to parse command line
-options/arguments in your CUI application.
-
-Local Modifications: None.
-
-
------
-Code in:
-lib/guava.jar
-
-Guava Libraries
-URL: http://code.google.com/p/guava-libraries/
-Version:  r08
-License: Apache License 2.0
-
-Description: Google's core Java libraries.
-
-Local Modifications: None.
-
-
------
-Code in:
-lib/jsr305.jar
-
-Annotations for software defect detection
-URL: http://code.google.com/p/jsr-305/
-Version: svn revision 47
-License: BSD License
-
-Description: Annotations for software defect detection.
-
-Local Modifications: None.
-
-
------
-Code in:
-lib/jarjar.jar
-
-Jar Jar Links
-URL: http://jarjar.googlecode.com/
-Version: 1.1
-License: Apache License 2.0
-
-Description:
-A utility for repackaging Java libraries.
-
-Local Modifications: None.
-
-
-----
-Code in:
-lib/junit.jar
-
-JUnit
-URL:  http://sourceforge.net/projects/junit/
-Version:  4.8.2
-License:  Common Public License 1.0
-
-Description: A framework for writing and running automated tests in Java.
-
-Local Modifications: None.
-
-
----
-Code in:
-lib/protobuf-java.jar
-
-Protocol Buffers
-URL: http://code.google.com/p/protobuf/
-Version: 2.3.0
-License: New BSD License
-
-Description: Supporting libraries for protocol buffers,
-an encoding of structured data.
-
-Local Modifications: None
-
-
----
-Code in:
-lib/ant.jar
-lib/ant-launcher.jar
-
-URL: http://ant.apache.org/bindownload.cgi
-Version: 1.8.1
-License: Apache License 2.0
-Description:
-  Ant is a Java based build tool. In theory it is kind of like "make"
-  without make's wrinkles and with the full portability of pure java code.
-
-Local Modifications: None
-
-
----
-Code in:
-lib/json.jar
-URL: http://json.org/java/index.html
-Version: JSON version 20090211
-License: MIT license
-Description:
-JSON is a set of java files for use in transmitting data in JSON format.
-
-Local Modifications: None
-
----
-Code in:
-tools/maven-ant-tasks-2.1.1.jar
-URL: http://maven.apache.org
-Version 2.1.1
-License: Apache License 2.0
-Description:
-  Maven Ant tasks are used to manage dependencies and to install/deploy to
-  maven repositories.
-
-Local Modifications: None