build system overhaul

* Added support for a protected directory whose contents are only made public in binary form

* Simplified and reorganized build.xml to improve readability and maintainability

* build.xml now autodetects most build properties:
    -Includes private/protected if they exist
    -No more STING_BUILD_TYPE or specialized targets for public-only, etc.

* Build targets have changed! There are now two main build options:

"ant"       build everything (GATK and Queue)
"ant gatk"  build just the GATK

It was too hard to build everything before -- now it is the default.

* To run tests with debugging, use -Dtest.debug=true -Dtest.debug.port=XXXX on the command line.
  Much better than the old comment/uncomment method!

ivy.xml

@@ -83,10 +83,6 @@
 
     <!-- testing and evaluation dependencies -->
     <dependency org="org.testng" name="testng" rev="5.14.1" conf="test" />
-    <dependency org="net.sourceforge.findbugs" name="findbugs" rev="1.3.2" conf="test"/>
-    <dependency org="net.sourceforge.findbugs" name="findbugs-ant" rev="1.3.2" conf="test"/>
-    <dependency org="net.sourceforge.findbugs" name="annotations" rev="1.3.2" conf="test"/>
-    <dependency org="net.sourceforge.findbugs" name="jsr305" rev="1.3.2" conf="test"/>
     <dependency org="com.google.code.caliper" name="caliper" rev="1.0-SNAPSHOT" conf="test" />
 
     <!-- Contracts for Java and dependencies -->

protected/java/src/org/broadinstitute/sting/package-info.java

@@ -0,0 +1,5 @@
+/**
+ * Provides map/reduce application framework highly optimized for analysis of sequencing data.
+ * @version 1.0
+ */
+package org.broadinstitute.sting;

public/packages/CreatePackager.xsl

@@ -100,6 +100,21 @@
 	</xsl:if>
       </xsl:for-each>
     </target>
+
+    <target name="protectedrelease">
+        <xsl:for-each select="protectedrelease/executable">
+	        <copy todir="{@directory}/{$package.basename}"><fileset dir="{$package.dir}" /></copy>
+	        <xsl:if test="@symlink">
+	             <symlink link="{@directory}/{@symlink}" resource="{$package.basename}" overwrite="true" />
+	        </xsl:if>
+        </xsl:for-each>
+        <xsl:for-each select="protectedrelease/archive">
+	        <copy file="{$dist.dir}/packages/{$package.filename}" todir="{@directory}" />
+	        <xsl:if test="@symlink">
+	            <symlink link="{@directory}/{@symlink}" resource="{$package.filename}" overwrite="true" />
+	        </xsl:if>
+        </xsl:for-each>
+    </target>
   </project>
 </xsl:template>
 

public/packages/GenomeAnalysisTK.xml

@@ -24,4 +24,9 @@
     <executable directory="/humgen/gsa-hpprojects/GATK/bin" symlink="current" />
     <archive directory="/web/ftp/pub/gsa/GenomeAnalysisTK" symlink="GenomeAnalysisTK-latest.tar.bz2" />
   </release>
+  <protectedrelease>
+    <!-- TODO: Determine where the protected releases should be stored -->
+    <executable directory="" symlink="current" />
+    <archive directory="" symlink="GenomeAnalysisTK-latest.tar.bz2" />
+  </protectedrelease>
 </package>