get build working on Windows

Squashed commit of the following:

commit 78f325fb36011b100eb1fea766eeb3605ab71718
Author: Seth Tisue <seth@tisue.net>
Date:   Tue Mar 13 13:08:14 2012 -0400

    remove debugging output

commit f69260dfbfe05d5ebbe9def0696c9afee75526b4
Author: Seth Tisue <seth@tisue.net>
Date:   Tue Mar 13 13:07:17 2012 -0400

    remove debugging output

commit 8d3b21bdec25c8608c00950a70c3e6d73e3eafc1
Author: TheBizzle <jason.bertsche@gmail.com>
Date:   Tue Mar 13 11:57:39 2012 -0500

    Fixing ancient, accidental flippings of the execute bit

commit ae0f736ede61848bbeb42e8e6a3da5528be38b14
Author: TheBizzle <jason.bertsche@gmail.com>
Date:   Mon Mar 12 18:14:09 2012 -0500

    Getting 'test-fast' working

commit 15f14be64734a1f93453ac48ec58121dfce18c58
Author: TheBizzle <jason.bertsche@gmail.com>
Date:   Mon Mar 12 18:08:58 2012 -0500

    Getting Windows build compiling

commit 8bc3f35d7303fa6b52428868a1ab2120a582a297
Author: TheBizzle <jason.bertsche@gmail.com>
Date:   Mon Mar 12 17:31:53 2012 -0500

    Fixes for bad merge

commit 8ae786d33d10eadf4ac3eeaa1dd544271280d645
Author: TheBizzle <jason.bertsche@gmail.com>
Date:   Mon Mar 12 16:37:07 2012 -0500

    Fixing SBT's 'native-jogl-libs' command to work on Windows

commit c4e2c65954e82840e5a04e5ebd1030bb33cd35d9
Author: TheBizzle <jason.bertsche@gmail.com>
Date:   Mon Mar 12 12:12:36 2012 -0500

    Updating extensions (for Windows/Cygwin)

commit 13a85e0179ffe4008d41f4d885e59ea6931fdff7
Author: TheBizzle <jason.bertsche@gmail.com>
Date:   Fri Mar 9 16:57:26 2012 -0600

    Build should now work on both Windows and non-Windows

commit bcde0b834237fc4de47d9ff25ddb2bf8b1c924a9
Author: TheBizzle <jason.bertsche@gmail.com>
Date:   Wed Mar 7 17:04:25 2012 -0600

    Windows build cleanup

commit 2a4e6bb95bd9776cd6653a9b2e079ee3d70ff30b
Author: TheBizzle <jason.bertsche@gmail.com>
Date:   Wed Mar 7 15:54:26 2012 -0600

    Fixing PMD to not freak out with spam on Windows

commit b756b44fc40dbc8e0de549ac17d6af2117c408e2
Author: TheBizzle <jason.bertsche@gmail.com>
Date:   Tue Mar 6 11:14:14 2012 -0600

    More test fixes for the Windows build on 'core'

commit 26e6e15b7c44802efd15335c95dcb745f915e690
Author: TheBizzle <jason.bertsche@gmail.com>
Date:   Mon Mar 5 14:26:31 2012 -0600

    Fixing potential issue with locating extensions on Windows
    No tests were actually affected by this

commit 73b671f69165f8cbc4fe9e4ea900cbc3095406ff
Author: TheBizzle <jason.bertsche@gmail.com>
Date:   Mon Mar 5 13:38:37 2012 -0600

    ModelsLibrary now plays nice with Windows file separators

commit 32ea362ea498035f3e92ee850af94d0a5088097f
Author: TheBizzle <jason.bertsche@gmail.com>
Date:   Mon Mar 5 12:13:43 2012 -0600

    First wave of test fixes for Windows (mostly line endings)

commit 4be4664354995e08ed146a6fe0ef965790845de5
Author: TheBizzle <jason.bertsche@gmail.com>
Date:   Thu Feb 16 12:23:19 2012 -0600

    Improvements on Windows core build
fix Makefile regression
(cherry picked from commit 10e2de4b53947ab03ba62c06b97f57e973bb5563)
Submodules now clone through 'git' (not 'http')
Windows installer: include NetLogoLite.jar.pack.gz (fixes #103)
Merge branch 'master' into core

Conflicts:
	.gitmodules
	bin/release.sh
	dist/HubNet Client.app/Contents/Info.plist
	dist/NetLogo.app/Contents/Info.plist
	dist/NetLogo.install4j
	dist/announce.txt
	dist/index.html
	docs/applet.html
	docs/dictionary.html
	docs/interface.html
	extensions/bitmap
	extensions/gis
	extensions/gogo
	extensions/network
	extensions/qtj
	project/build/Libraries.scala
	project/build/autogen/TokenLexer.flex
	src/main/org/nlogo/app/AppletSaver.scala
	src/main/org/nlogo/lab/gui/ProtocolEditable.scala
	src/main/org/nlogo/swing/WindowDragger.java
	src/main/org/nlogo/window/GUIWorkspace.java
	src/main/org/nlogo/window/WorldViewSettings3D.java
	src/main/org/nlogo/workspace/AbstractWorkspace.java
	src/test/org/nlogo/app/InfoFormatterTests.scala
	src/test/org/nlogo/app/ProceduresToHtmlTests.scala
	src/test/org/nlogo/compiler/TestAllSyntaxes.scala
	src/test/org/nlogo/headless/TestCompileBenchmarks.scala
	src/test/org/nlogo/lex/TokenizerTests.scala
	src/test/org/nlogo/sdm/LoaderTests.scala
	src/tools/org/nlogo/tools/InfoTabDocGenerator.scala
	test/commands/Timer.txt